Studies of Peroxisome

STRUCTURE-FUNCTION
STUDIES OF THE MAMMALIAN

PEROXISOMAL
MULTIFUNCTIONAL ENZYME
TYPE 2 (MFE-2)
ANTTI
HAAPALAINEN
Biocenter Oulu and
Department of Biochemistry,
University of Oulu
OULU 2002
ANTTI HAAPALAINEN
STRUCTURE-FUNCTION STUDIES
OF THE MAMMALIAN
PEROXISOMAL MULTIFUNCTIONAL
ENZYME TYPE 2 (MFE-2)
Academic Dissertation to be presented with the assent of

the Faculty of Science, University of Oulu, for public
discussion in Raahensali (Auditorium L10), Linnanmaa, on
November 8th, 2002, at 2 p.m.
O U L U N Y L I O P I S TO, O U L U 2 0 0 2
Copyright 2002
University of Oulu, 2002
Supervised by
Doctor Tuomo Glumoff
Professor Kalervo Hiltunen
Reviewed by
Docent Sarah Butcher
Docent Matti Poutanen
ISBN 951-42-6838-5
(URL: http://herkules.oulu.fi/isbn9514268385/)
ALSO AVAILABLE IN PRINTED FORMAT

Acta Univ. Oul. A 389, 2002
ISBN 951-42-6837-7
ISSN 0355-3191
(URL: http://herkules.oulu.fi/issn03553191/)
OULU UNIVERSITY PRESS
OULU 2002
Haapalainen, Antti, Structure-function studies of the mammalian peroxisomal

multifunctional enzyme type 2 (MFE-2)
Biocenter Oulu, University of Oulu, P.O.Box 5000, FIN-90014 University of Oulu, Department of
Biochemistry, University of Oulu, P.O.Box 3000, FIN-90014 University of Oulu
Oulu, Finland
2002
Abstract
Mammalian peroxisomes contain two parallel multifunctional enzymes (MFE), MFE type 1 and MFE
type 2 (MFE-2), which are responsible for the degradation of fatty acids. They both catalyze the
second and third reactions of the -oxidation pathway, but through reciprocal stereochemical courses.
MFE-2 possesses (2E)-enoyl-CoA hydratase-2 and (3R)-hydroxyacyl-CoA dehydrogenase activities.
In addition, the carboxy-terminal part is similar to the sterol carrier protein type 2 (SCP-2).
The purpose of this work was to study the structure-function relationship of functional domains
of mammalian MFE-2 by recombinant DNA technology, enzyme kinetics and X-ray crystallography.
The work started with the identification of conserved regions in MFE-2. This information was utilized
when dehydrogenase, hydratase-2 and/or SCP-2-like domain were produced as separate recombinant
proteins. Subsequently, both dehydrogenase and SCP-2-like domains were crystallized and their
crystal structures were solved.
The structure of the dehydrogenase region of rat MFE-2 contains the basic / short-chain alcohol
dehydrogenase/reductase (SDR) fold and the four-helix bundle at the dimer interface, which is typical
of dimeric SDR enzymes. However, the structure has a novel carboxy-terminal domain not seen
among the known structures. This domain lines the active site cavity of the neighbouring monomer,
reflecting cooperative behaviour within a homodimer.
The monomeric SCP-2-like domain of human MFE-2 has the same fold as rabbit SCP-2. The
structure includes a hydrophobic tunnel occupied by an ordered Triton X-100 molecule,
demonstrating the ligand-binding site. Compared to the unliganded rabbit SCP-2 structure, the
position of the carboxy-terminal helix is different. The movement of this helix in the liganded human
SCP-2-like domain resulted in the exposure of a peroxisomal targeting signal, suggesting ligandassisted protein import into peroxisomes.
The roles of conserved protic residues in the hydratase-2 region of human MFE-2 were studied by
mutating them to alanine. In the first step, the ability of mutated variants to utilize oleic acid in vivo
was tested with Saccharomyces cerevisiae fox-2 cells (devoid of endogenous MFE-2). Subsequently,
in vitro characterization of the mutant enzymes revealed two amino acid residues, Glu366 and
Asp510, vital for hydratase-2 activity. The results indicate that the acid-base catalysis is valid for
hydratase-2.
Keywords: -oxidation, dehydrogenase, hydratase, SCP-2, SDR
Acknowledgements
This work was carried out in the Department of Biochemistry and Biocenter Oulu,
University of Oulu, during the years 1997-2002.
I wish to express my deepest gratitude to my supervisors, Dr. Tuomo Glumoff and
Professor Kalervo Hiltunen. Their enormous knowledge, support and advice made it
possible to complete this study. I am especially grateful that I was allowed to express
myself and to make my own decisions whenever possible. I also thank Professor Rik
Wierenga for his valuable comments and interest in my project over the years. I also wish
to thank the Professors Raili Myllyl and Seppo Vainio and all the other group leaders at
the Department of Biochemistry for providing excellent research facilities and a
stimulating working atmosphere.
I am grateful to Docent Sarah Butcher and Docent Matti Poutanen for their valuable
comments on the manuscript of the thesis, and Sirkka-Liisa Leinonen, Lic. Phil., for the
careful revision of the language.
I am deeply indebted to my co-authors, Docent Jorma Jalonen, Dr. Daan van Aalten,
Dr. Yong-Mei Qin, Dr. Pivi Piril, Dr. Dmitry Novikov, Kristian Koski, M.Sc., Mari
Marttila, M.Sc., Gitte Merilinen, M.Sc., and Seppo Kilpelinen, M.Sc., for their
contributions to our joint publications. Dr. Daan van Aalten deserves my warmest thanks
for helping me whenever I was having a hard time with my crystallographic studies and
Dr. Yong-Mei Qin is further acknowledged for her guidance at the beginning of my
doctoral studies.
All the former and present members of the KH team deserve special thanks for their
company over the years. My warmest thanks go to Tiila-Riikka Kiema, Jukka Taskinen,
Kristian Koski, Mari Marttila, Tomi Airenne, Anu Mursula, Juha Torkko, Aare Rokka and
Kalle Savolainen for their fruitful discussions and valuable help in everyday problems.
Especially Jukka, Tomi and Kristian are thanked for their ability to convert the
synchrotron trips into so much fun.
I wish to extend my sincere thanks to the whole staff of our department. Eeva-Liisa
Stefanius, Marika Kamps and Ville Ratas are acknowledged for their excellent technical
assistance and Seppo Kilpelinen, Ari-Pekka Kvist, Jyrki Hnninen and Petri Kursula for
setting up and maintaining the computer systems. Virpi Hannus, Helena Heikura, Anneli
Kaattari, Kysti Kernen, Jaakko Keskitalo, Maila Konttila, Tuula Koret and Pirjo
Mustaniemi are appreciated for their kind help with many practical tasks.
There are so many things I want to thank my mother and father for. Their wisdom,
care and ever-lasting faith in me have helped me in each step of my life. I also want to
thank my sisters and their families for their cheerful company and support. Finally, I owe
my loving thanks to my dear Teija for her loving care and patience.
This work was financially supported by grants from the Sigrid Juslius Foundation,
Academy of Finland and Finnish Cultural Foundation.
Oulu, August 2002
Antti Haapalainen
Abbreviations
ABC
ACBP
AMN
ASP
ATP
CCALD
CD
cDNA
CG
CoA
COOH-terminus
d h SCP-2L
DHA
DHCA
dh SCP-2L
DNA
FABP
FAD
FADH2
17-HSD
HsMFE-2(dh )
IRD
kDa
LCFA
MAD
MFE
MFE-1
MFE-2
NAD+
NADH
NALD
ATP-binding cassette
acyl-CoA-binding protein
adrenomyeloneuropathy
acylation-stimulating protein
adenosine triphosphate
cerebral childhood adrenoleukodystrophy
circular dichroism
complementary DNA
complementation group
coenzyme A
carboxyl terminus
SCP-2-like domain of human MFE-2
docosahexaenoic acid
3,7-dihydroxy-5-cholestanoic acid
dehydrogenase region of rat MFE-2
deoxyribonucleic acid
fatty acid binding protein
flavine adenine dinucleotide
reduced form of flavine adenine dinucleotide
17-hydroxysteroid dehydrogenase
human MFE-2 without dehydrogenase region
infantile Refsum disease
kilodalton(s)
long-chain fatty acid
multiwavelength anomalous dispersion
multifunctional enzyme
multifunctional enzyme type 1
multifunctional enzyme type 2
nicotinamide adenine dinucleotide
reduced form of nicotinamide adenine dinucleotide
neonatal adrenoleukodystrophy
NH2-terminus
nsLTP
PCR
PDB
PMP
PPRE
PTS
PTS1
PTS2
RCDP
RNA
SCP-2
SCP-2L
SCPx
SDR
SDS-PAGE
Se-Met
THCA
VLCAS
VLCFA
X-ALD
ZS
amino terminus
non-specific lipid transfer protein
polymerase chain reaction
Protein Data Bank
peroxisomal membrane protein
peroxisome proliferator response element
peroxisomal targeting signal
peroxisomal targeting signal type 1
peroxisomal targeting signal type 2
rhizomelic chondrodysplasia punctata
ribonucleic acid
sterol carrier protein type 2
sterol carrier protein type 2 like domain
sterol carrier protein x
short-chain alcohol dehydrogenase/reductase
sodium dodecyl sulphate polyacrylamide gel electrophoresis
selenomethionine
3,7,12-trihydroxy-5-cholestanoic acid
very-long-chain acyl-CoA synthetase
very-long-chain fatty acid
X-linked adrenoleukodystrophy
Zellweger syndrome
ngstrm, 10-10 m
List of original articles

This thesis is based on the original articles, which are referred to in the text by their
Roman numerals:
I
Qin YM, Haapalainen AM, Kilpelinen SH, Marttila MS, Koski MK, Glumoff T,
Novikov DK & Hiltunen JK (2000) Human peroxisomal multifunctional enzyme
type 2: site-directed mutagenesis studies show the importance of two protic
residues for 2-enoyl-CoA hydratase 2 activity. J Biol Chem 275: 4965-4972.
II
Haapalainen AM, van Aalten DMF, Merilinen G, Jalonen JE, Piril P, Wierenga
RK, Hiltunen JK & Glumoff T (2001) Crystal structure of the liganded SCP-2like domain of human peroxisomal multifunctional enzyme type 2 at 1.75
resolution. J Mol Biol 313: 1127-1138.
III
Haapalainen AM, Koski MK, Qin YM, Hiltunen JK & Glumoff T (200X) Binary
structure of the two-domain (3R)-hydroxyacyl-CoA dehydrogenase from Rattus
norvegicus peroxisomal multifunctional enzyme type 2 at 2.38 resolution.
(Under revision)
Contents
Acknowledgements
Abbreviations
List of original articles
Contents
1 Introduction ...................................................................................................................13
2 Review of the literature..................................................................................................15
2.1 Fatty acids as an energy store .................................................................................15
2.1.1 Transport of fatty acids ....................................................................................16
2.1.2 Compartmentalization of fatty acid oxidation .................................................16
2.1.3 Activation of fatty acids prior to -oxidation...................................................18
2.2 Peroxisomal -oxidation system.............................................................................19
2.2.1 Peroxisomes.....................................................................................................19
2.2.2 Peroxisomal targeting signals ..........................................................................20
2.2.2.1 Additional targeting signals ......................................................................21
2.2.3 Protein translocation into peroxisomes............................................................22
2.2.4 Transport of fatty acyl-CoAs across peroxisomal membrane ..........................23
2.2.5 Peroxisomal -oxidation cycle ........................................................................24
2.2.5.1 Acyl-CoA oxidases ...................................................................................24
2.2.5.2 Second and third steps are catalyzed by two multifunctional
enzymes....................................................................................................26
2.2.5.3 3-Ketoacyl-CoA thiolases .........................................................................28
2.2.5.4 Auxiliary enzymes ....................................................................................29
2.3 Multifunctionality of MFE-2 ..................................................................................30
2.3.1 Domain structure of various MFE-2s...............................................................30
2.3.2 Catalytic properties of MFE-2 .........................................................................31
2.3.3 Tissue distribution............................................................................................34
2.3.4 (3R)-Hydroxyacyl-CoA dehydrogenase, a member of the
short-chain alcohol dehydrogenase/reductase superfamily.............................35
2.3.5 Sterol carrier protein type 2 .............................................................................38
2.3.5.1 Other fatty acid/fatty acyl-CoA-binding proteins .....................................39
2.4 Peroxisomal -oxidation deficiencies.....................................................................41
3 Outlines of the present study .........................................................................................43

4 Materials and methods...................................................................................................44
4.1 cDNA cloning .........................................................................................................44
4.1.1 Cloning of the (3R)-hydroxyacyl-CoA dehydrogenase region
from rat MFE-2 (III).......................................................................................44
4.1.2 Cloning of human MFE-2 (HsMFE-2) and its variants,
HsMFE-2(dh) and dhSCP-2L (I, II) ........................................................45
4.2 Site-directed mutagenesis (I) ..................................................................................46
4.3 Complementation of Saccharomyces cerevisiae fox-2 with human
MFE-2 and its mutated variants (I) ........................................................................46
4.4 Production of recombinant proteins (I, II) ..............................................................46
4.4.1 Production of selenomethionine-labelled recombinant (3R)hydroxyacyl-CoA dehydrogenase (III) ...........................................................47
4.5 Protein purification (I-III) .......................................................................................47
4.6 Enzyme assays (I, III) .............................................................................................47
4.7 Dynamic light scattering and CD-spectroscopic measurements (I) ........................48
4.8 Surface plasmon resonance measurements (II).......................................................48
4.9 Crystallization, data collection and processing (II, III)...........................................48
4.10 Structural determination, model building and refinement (II, III) ........................49
4.11 Other methods.......................................................................................................49
5 Results ...........................................................................................................................51
5.1 Binary structure of the two-domain (3R)-hydroxyacyl-CoA
dehydrogenase region of rat MFE-2 (III)...............................................................51
5.2 Site-directed mutagenesis studies on (2E)-enoyl-CoA hydratase-2
derived from human MFE-2 (I)..............................................................................55
5.3 Crystal structure of the liganded SCP-2-like domain of human
MFE-2 (II)..............................................................................................................56
6 Discussion......................................................................................................................59
6.1 Structural studies on the (3R)-hydroxyacyl-CoA dehydrogenase
region of rat MFE-2 (III)........................................................................................59
6.2 Importance of two protic residues for (2E)-enoyl-CoA hydratase2 activity (I)............................................................................................................60
6.3 Ligand binding to the SCP-2-like domain of human MFE-2 (II)............................61
7 Conclusions ...................................................................................................................63
8 References .....................................................................................................................65
1 Introduction
Fatty acids, as such, are energy-rich molecules, from which energy is withdrawn during
periods of fasting and starvation. In addition to being structural components of
biomembranes and serving as energy stores, fatty acids and their derivatives act as ligands
for a number of transcription factors and modifiers of enzymatic activity and other
protein functions to sustain vital biochemical processes. During energy conversion, fatty
acids are degraded by the oxidative pathways, such as -oxidation, -oxidation and oxidation, which take place in peroxisomes, mitochondria and/or endoplasmic reticulum.
However, -oxidation is a major process by which fatty acids are oxidized, and this
oxidation occurs in mammals both in mitochondria and in peroxisomes (Lazarow & de
Duve 1976). Prior to oxidation, free fatty acids need to be activated to their CoA esters.
Even though the chemical modifications of fatty acyl-CoAs during peroxisomal and
mitochondrial -oxidations are somewhat similar, the enzymes involved are not. Another
difference is that peroxisomal -oxidation can operate in relative independence of the
cellular energy status. On the contrary, mitochondrial -oxidation is directly linked with
the synthesis of ATP.
Saturated fatty acyl-CoAs are -oxidized by four sequential reactions. This cycle
includes oxidation/dehydrogenation, hydration, dehydrogenation and, finally, thiolytic
cleavage. To overcome double bonds in unsaturated fatty acids, additional auxiliary
enzymes are needed prior to the -oxidation cycle. Each turn of the cycle shortens the
fatty acid chain by two carbons. Unlike the mitochondrial system, the peroxisomal oxidation pathway does not proceed to completion in mammals, and the chain-shortened
acyl-CoA, similarly to acetyl-CoA, is transported to mitochondria to be further oxidized
(for reviews, see Osmundsen et al. 1991, Eaton et al. 1996, Hiltunen & Qin 2000). In
mitochondria, acetyl-CoAs are fed into a citric acid cycle, from which the high electrons
pass via NADH and FADH2 to the respiratory chain, eventually forming ATP and H2O.
Alternatively, in liver, acetyl-CoA may condense with itself to form ketone bodies, which
serve as fuel for other tissues, such as the skeletal and cardiac muscle and brain, during
starvation.
All the characterized -oxidation pathways appear to have a multifunctional enzyme
(MFE). Although all of them catalyze the second and third reaction of the pathway, the
subunit composition and the associated enzymatic activities vary, depending on the
14
species and organelle. The mammalian peroxisome contains two MFEs, MFE type 1
(MFE-1) and MFE type 2 (MFE-2), with different stereochemical specificities (Qin et al.
1997a). MFE-2 acts on 2 carboxylates, resulting in an intermediate with the 3-hydroxyl
group in the R-configuration, which is then dehydrogenated by the same polypeptide
(Hiltunen et al. 1992). This study aimed to reveal the structural basis of mammalian
MFE-2. The NH2-terminal (3R)-hydroxyacyl-CoA dehydrogenase region and the COOHterminal SCP-2-like domain were crystallized and their crystal structures were solved.
Furthermore, the function of the central (2E)-enoyl-CoA hydratase-2 region was
investigated by applying recombinant DNA technology and enzyme kinetics.
2 Review of the literature

2.1 Fatty acids as an energy store
Fatty acids have a central role in a variety of cellular processes, including energy storage
and the synthesis of cellular membranes. In addition, long-chain fatty acids, through their
metabolites (e.g., pheromones, prostaglandins, leukotrienes, thromboxanes, platelet
activating factor), serve as intracellular signalling molecules. Furthermore, fatty acids
have been shown to regulate the expression of genes involved in lipid metabolism and cell
differentiation (Distel et al. 1992a, Grimaldi et al. 1992, for a review, see Grimaldi 2001).
Disturbances in fatty acid metabolism and regulation, especially those involving fatty
acid synthesis and oxidation, may contribute to hyperlipidemia, obesity, insulin resistance
and atherosclerosis (Spiegelman & Flier 1996, Unger et al. 1999).
Higher animals, under fed conditions, preferentially burn carbohydrate to generate
ATP. When the energy (glucose) intake is abundant, fatty acid synthesis is enhanced and
fatty acid oxidation reduced. As a consequence, excess carbohydrate is converted into
fatty acids, which are then stored as a triacylglycerol, in which fatty acids are connected
to glycerol via ester linkage. These hydrophobic triacylglycerols account for most of the
volume of the adipocytes, the large cells specialized for fat storage in adipose tissues (for
a review, see Ramsay 1996). When glucose availability is low during periods of
starvation, the triacylglycerols stored in adipose tissue are hydrolyzed to free fatty acids
and mobilized into plasma. The rate at which triacylglycerides are hydrolysed is
determined by lipoprotein lipase and insulin, which is the principal hormone that
regulates lipoprotein lipase (Seitz et al. 1977, Eaton et al. 1996, Hashimoto et al. 1999a,
Kersten et al. 1999, Leone et al. 1999, Hashimoto et al. 2000). By contrast, the acylationstimulating protein (ASP) pathway modulates the rate at which fatty acids are taken up
and converted to triacylglycerides by adipocytes. Under certain circumstances, however,
reduction of the activity of the ASP pathway may negatively affect the first step of the
process. Consequently, ASP also influences the rate at which fatty acids are released by
adipocytes (for a review, see Sniderman et al. 2000).
16
2.1.1 Transport of fatty acids

Since free fatty acids, above their solubility limit, form insoluble acid soaps (Hicks &
Gebecki 1977, Cistola et al. 1986), the transport of fatty acids in the body must interfere
with other biological molecules. For this reason, in the blood, free fatty acids are
transported mainly in complexes with albumin, and a only very small fraction is bound to
plasma lipoproteins (for a review, see Spector 1984, Hamilton & Kamp 1999).
The mechanisms by which fatty acids cross the plasma membrane of mammalian cells
are a topic of active investigation and debate. According to one model, the movement of
most fatty acids through the plasma membrane is rapid and spontaneous, suggesting that
fatty acids can enter cells by free diffusion rather than by protein-mediated mechanisms
(DeGrella & Light 1980, Kamp & Hamilton 1992, Veerkamp 1995, Ek-Von Mentzer et
al. 2001, Hamilton et al. 2001). Other studies have described the presence of a proteinmediated translocation system, where the transport of fatty acid across the plasma
membrane is facilitated by a fatty acid transport protein, a plasma membrane protein,
possibly requiring energy or the co-transportation of Na+ (Berk et al. 1997, StuhlsatzKrouper et al. 1998). These putative fatty acid transport proteins comprise a large
evolutionarily conserved family of proteins present in organisms ranging from
mycobacterium to man (Hirsch et al. 1998).
Once free fatty acid has reached the inner leaflet of the plasma membrane, it must
move to intracellular sites for utilization. Cytosolic fatty acid-binding proteins (FABP)
(Ockner et al. 1972), which are 14-15 kDa in size, shuttle the intracellular aqueous
insoluble fatty acids to different cellular compartments (Tipping & Ketterer 1981,
Weisiger 1996, Storch & Thumser 2000). To date, 14 members of the FABP gene family
have been identified and divided into two main classes according to their ability to
interact with membranes. The members of one class transfer fatty acids to and from
membranes involving interaction between a positively charged region of the binding
protein and negative charges on the membrane surface (Herr et al. 1996, Hsu & Storch
1996, Gericke et al. 1997, Corsico et al. 1998, Thumser & Storch 2000). The second
class of FABP molecules lack the ability to interact with membranes and are therefore
only able to bind fatty acid monomers already in aqueous solution. So far, eight different
three-dimensional structures of FABPs have been determined from human, bovine, rat
and mouse, revealing highly conserved tertiary structures; ten antiparallel -strands form
a flattened barrel with a hydrophobic pocket in the centre that accommodates
hydrophobic ligands.
2.1.2 Compartmentalization of fatty acid oxidation

Oxidation of fatty acids occurs in three subcellular organelles via -, - and -oxidation,
depending on the species. In mammals, both mitochondria and peroxisomes carry out
fatty acid -oxidation, which is the dominant oxidative pathway (Fig. 1). The -oxidation
of fatty acids in mammals will be discussed in more detail later. Yeast degrades fatty acids
via -oxidation only in peroxisomes (Kunau et al. 1988). Peroxisomal -oxidation
17
Fig. 1. Simplified scheme of the different roles of peroxisomes and mitochondria in cellular
fatty acid -oxidation in mammals. (Modified from Wanders et al. 2001)
is also the primary pathway of fatty acid catabolism in plants. There is also evidence that
-oxidation of short-branched-chain 2-oxo acids takes place in plant mitochondria. In this
pathway, the branched-chain amino acids are broken down and the end products of the
pathway are converted to acyl-CoA esters. The degradation of these esters requires oxidation (for a review, see Graham & Eastmond 2002).
Mammalian peroxisomes degrade fatty carboxylates not only via -oxidation but also
by -oxidation (Fig. 2), since fatty acids with a methyl group at the -position cannot
undergo direct -oxidation. This applies to, for instance, phytanic acid (3,7,11,15tetramethylhexadecanoic acid), which, in the human body, is mainly derived from dairy
products. Phytanic acid is converted from phytol, the side chain of chlorophyll. The oxidation of phytanic acid includes activation of phytanic acid to phytanoyl-CoA by verylong-chain acyl-CoA synthetase, which is localized on the peroxisomal membrane
(Watkins et al. 1994, Pahan & Singh 1995, Watkins et al. 1996). Once inside the
peroxisome, phytanoyl-CoA is converted into 2-hydroxyphytanoyl-CoA by phytanoylCoA hydroxylase (Mihalik et al. 1995, Croes et al. 1996, Jansen et al. 1996, 1997,
Mihalik et al. 1997). Subsequent studies resolved a pathway in which 2hydroxyphytanoyl-CoA first undergoes cleavage to pristanal and formyl-CoA (Verhoeven
et al. 1997, Croes et al. 1997, Jansen et al. 1999, Foulon et al. 1999), after which
pristanal is oxidized to pristanic acid via an as yet undefined aldehyde dehydrogenase.
Prior to -oxidation, the 2-methyl-branched fatty acid, pristanic acid, is activated to
pristanoyl-CoA. The -oxidation of phytanic acid is not stereoselective. Consequently,
two isomers are the end products of the pathway. However, peroxisomal oxidases accept
only 2S-isomers, and racemase is therefore needed to convert 2R- into 2S-isomer (see the
chapter titled Auxiliary enzymes).
18
Fig. 2. -Oxidation of phytanic acid. The numbers refer to the following enzymes: 1, verylong-chain acyl-CoA synthetase; 2, phytanoyl-CoA hydroxylase; 3, 2-hydroxyphytanoyl-CoA
lyase; 4, long-chain aldehyde dehydrogenase (not properly characterized); 5, very-long-chain
acyl-CoA synthetase; 6, 2-methylacyl-CoA racemase. 2S-pristanoyl-CoA is further oxidized
via the peroxisomal -oxidation pathway. (Modified from Van Veldhoven et al. 2001)
Long-chain fatty acids are also ligands for -oxidation. The initial step in -oxidation is
-hydroxylation of fatty acid in smooth endoplasmic reticulum catalyzed by lauric acid
(C12:0) -hydroxylase (Hardwick et al. 1987). Rat and human -hydroxylases do not show
preference for longer-chain fatty acids, such as oleic (C18:1) and arachidonic acid (C20:4)
(Dierks et al. 1998). In contrast, rabbit hydroxylases appear to be highly active towards
arachidonic acid (Johnson et al. 1996). In cytosol, the -hydroxy fatty acid produced by
the initial hydroxylation reaction is dehydrogenated to dicarboxylic acid by alcohol
dehydrogenase and aldehyde dehydrogenase. Especially long-chain dicarboxylic acids
formed via the -oxidation pathway regulate peroxisomal -oxidation enzymes (Kaikaus
et al. 1993); it has been shown that long-chain dicarboxyl-CoAs are almost exclusively
further oxidized by the peroxisomal alcohol oxidase of the classical -oxidation pathway
in human and, to some extent, via pristanoyl-CoA oxidase in rat (for reviews, see Reddy
& Mannaerts 1994, Mannaerts et al. 2000). The recent finding on long-chain fatty acid
oxidase genes in Candida species led to the identification of a family of genes involved in
lipid -oxidation in yeast with homologues in plants and bacteria (Vanhanen et al. 2000).
The identified enzymes were membrane-associated with unknown subcellular location.
2.1.3 Activation of fatty acids prior to -oxidation

The enzymes of -oxidation all act on CoA esters, which means that prerequisite for oxidation is the ATP-dependent thioesterification of fatty acids to their fatty acyl-CoAs,
19
catalysed by acyl-CoA synthetases (Aas & Bremer 1968, Aas 1971). There are specific
acyl-CoA synthetase isoenzymes for long-chain and very-long-chain fatty acids
(VLCFA), which are localized in endoplasmic reticulum, peroxisomal membrane and/or
outer mitochondrial membrane (Kornberg & Pricer 1953, Aas 1971, Singh & Poulos
1988, Lazo et al. 1990, Suzuki et al. 1990, Subramani 1998). Short- and medium-chain
fatty acids are activated only intramitochondrially by two different acyl-CoA synthetases.
One synthetase utilizes preferentially octanoate, whereas butyrate is the fatty acid most
preferred by the other (Scaife & Tichivangana 1980, Fujino et al. 2001). In bacteria, the
activation process requires the cooperative action of the outer membrane-bound fatty acid
transport protein FadL and the inner membrane-associated fatty acyl-CoA synthetase (for
a review, see DiRusso & Black 1999).
Peroxisomal membrane contains long-chain acyl-CoA synthetase. The long-chain
acyl-CoA synthetase is also localized in the mitochondrial outer membrane and in the
endoplasmic reticulum, and the catalytic site of these synthetases is exposed to cytosol
(Hesler et al. 1990, Lazo et al. 1990, Suzuki et al. 1990, Subramani 1998). Very-longchain acyl-CoA synthetase (VLCAS), which activates VLCFAs and has sequence
similarity to the fatty acid transport protein (Schaffer & Lodish 1994), is present in
peroxisomes and in the endoplasmic reticulum but is absent from mitochondria
(Uchiyama et al. 1996). VLCAS and long-chain acyl-CoA synthetase differ with respect
to their molecular and catalytic properties, and the absence of the former synthetase in
mitochondria may partly explain why VLCFAs are -oxidized in peroxisomes. Indirect
immunofluorescent and electron microscopic studies showed that peroxisomal VLCAS is
localized on the matrix side rather than the cytosolic face of peroxisomal membrane
(Smith et al. 2000). Furthermore, the human variant of VLCAS was described to activate
not only VLCFAs but also long- and branched-chain fatty acids (Steinberg et al. 1999). In
rat, bile acid intermediates, which also have a branched methyl group, were shown to be
activated by a separate enzyme, trihydroxycoprostanoyl-CoA synthetase (Van Veldhoven
et al. 1996).
2.2 Peroxisomal -oxidation system

2.2.1 Peroxisomes
Peroxisomes, which are single-membrane organelles, are found in yeast, plants and
mammals, and they are present within almost all cell types. Most commonly, peroxisomes
appear spherical in shape in electron micrographs and have a mean diameter of 0.2 to 1.0
m with a crystalloid core largely composed of urate oxidase (Volkl et al. 1988). The size
and shape depend on the tissue studied and the metabolic circumstances of the species.
For instance, in fibroblasts and glucose-grown yeast cells, peroxisomes are smaller. In
contrast, larger and spherical peroxisomes frequently interconnected by tubular elements
as well as convoluted cup-shaped structures are found in liver and preputial glands,
20
respectively. Some peroxisomes are interconnected and clustered (Mendis-Handagama et
al. 1990) in a way that supports the concept of a peroxisomal reticulum.
The functions of peroxisomes are often specialized by organism and cell type. In
mammals, two major functions of peroxisomes are part of lipid metabolism. Namely,
peroxisomes catalyse the -oxidation of fatty acids and the initial steps in the
biosynthesis of plasmalogens, which are phospholipids present in myelin. Especially,
peroxisomal -oxidation is essential for the catabolism of a variety of substrates that are
not oxidised by mitochondria, such as VLCFAs, dicarboxylic and branched-chain fatty
acids and cholesterol, whose side chain undergoes obligatory -oxidative cleavage upon
conversion to bile acids (Lazarow & de Duve 1976, for reviews, see Wanders & Tager
1998, Wanders et al. 2001). Although eukaryotic cells can survive without peroxisomes,
defects in peroxisome biogenesis have significant metabolic and developmental
consequences (Subramani 1993). Peroxisomes are essential for normal human
development, since defects in peroxisome assembly cause disorders of peroxisome
biogenesis (Lazarow & Moser 1994). These diseases are characterized by severe
developmental abnormalities, particularly within the nervous system, and usually result in
death in early infancy. In yeast, such defects eliminate growth on fatty acids, an important
carbon and energy source in natural environments (Hettema & Tabak 2000). A third
important peroxisomal function is respiration, which involves the metabolism of
hydrogen peroxide. Hydrogen peroxide, which is formed in reactions catalyzed by
various oxidases, is efficiently decomposed by catalase. The energy released in this
reaction is dissipated as heat (de Duve & Baudhuin 1966).
2.2.2 Peroxisomal targeting signals

Since peroxisomes have no genome, the proteins destined for peroxisomes are
synthesized on free ribosomes in cytosol and contain a peroxisomal targeting signal
(PTS), which directs them to peroxisomes; this applies to both membrane and internal
matrix proteins (Fujiki et al. 1984, Miura et al. 1984, Rachubinski et al. 1984, Lazarow &
Fujiki 1985, Borst 1989, Subramani 1993). Targeting to the peroxisomal matrix is
mediated by two cis-acting sequences, PTS1 (Gould et al. 1987, 1988, 1989, 1990a,
1990b, Aitchison et al. 1991, Keller et al. 1991, Aitchison et al. 1992, Blattner et al.
1992, Didion & Roggenkamp 1992, Distel et al. 1992b, Hansen et al. 1992, Miura et al.
1992, Swinkels et al. 1992) and PTS2 (Tsukamoto et al. 1994). At first, the existence of a
tripeptide in the COOH-terminus with the consensus (S/A/C)-(K/R/H)-L was
characterized and named PTS1 (Gould et al. 1989). Subsequent studies revealed a range
of additional functional sequences of PTS1 much larger than expected as well as
significant differences between species (Kragler et al. 1998). For example, in rat
trihydroxycoprostanoyl-CoA and pristanoyl-CoA oxidases the COOH-terminal HKM
and SQL sequences are used as PTS1s, respectively (Baumgart et al. 1996a, Vanhooren
et al. 1996). The first example of tetrapeptide PTS1 was that of human catalase (-KANL)
(Purdue et al. 1996), where lysine has the greatest functional importance. Subsequently,
21
mouse and human 2-methylacyl-CoA racemases were found to contain a critical basic
residue at position -4 as well (Amery et al. 2000, Kotti et al. 2000).
The nonapeptides of the PTS2 signal have a broad consensus sequence of (R/K)(L/V/I)-(XXXXX)-(H/Q)-(L/A/F) in the NH2-terminal part of some peroxisomal matrix
proteins. Despite interspecific variations, the five-amino-acid linker between the
conserved dipeptides seems to be critical (Tsukamoto et al. 1994, Glover et al. 1994,
Flynn et al. 1998). Several studies have pointed out the special importance of Arg1, His8
and Leu9 for targeting into peroxisomes (Flynn et al. 1998). In the crystal structures of
peroxisomal fructose-1,6-bisphosphate aldolases from Leishmania mexicana [Protein
Data Bank (PDB) accession number 1EPX] and Trypanosoma brucei (PDB accession
number 1F27), the PTS2 signal sequences from two monomers interact with each other,
so that there are two PTS2 dimers per aldolase tetramer (Chudzik et al. 2000). The
structures indicated that the exposed Arg1 may play an important role in interacting with
Pex7p, which is the cytosolic receptor for peroxisomal proteins targeted by PTS2s (see
the chapter Protein translocation into peroxisomes), and Leu9 is needed for the
dimerization of the signalling peptide. Since several other proteins with the PTS2 signal
are dimers or higher multimers, the dimeric PTS2 suggests functional importance.
2.2.2.1 Additional targeting signals

There is also evidence of additional PTS signals for membrane and matrix proteins.
Similarly to matrix proteins, integral peroxisomal membrane proteins (PMP) are
synthesized on free polyribosomes and imported posttranslationally from the cytosol
(Fujiki et al. 1984, Diestelktter & Just 1993, Imanaka et al. 1996), though their import
does not require the hydrolysis of ATP (Diestelktter & Just 1993). It has also been
speculated that some of the peroxisomal membrane proteins are transported via the
endoplasmic reticulum (Bodnar & Rachubinski 1991, Titorenko & Rachubinski 1998). In
any case, integral PMPs lack functional PTS1 or PTS2, and their import is hence
independent of the PTS1 and PTS2 receptors (Chang et al. 1999, Hettema et al. 2000).
Integral PMPs are therefore thought to be imported into peroxisomes by a targeting
mechanism different from that used by peroxisomal matrix proteins.
The studies done with Candida boidinii (C. boidinii) PMP47 (Dyer et al. 1996)
revealed that the targeting information lies between the transmembrane domains four and
five in a positively charged intraperoxisomal loop. The loop is necessary and sufficient for
targeting to peroxisomes. The human homologue of C. boidinii PMP47, PMP34, was
shown to contain two additional transmembrane regions, either of which was sufficient
for targeting to the peroxisome membrane (Honsho & Fujiki 2001, Jones et al. 2001).
The hydrophilic peptide, XX(K/R)(K/R)3-7X(T/S)XX(D/E)X (Dyer et al. 1996),
adjacent to at least one transmembrane domain, was observed with other proteins, such as
PMP70, Pex3p and PMP22 (Kammerer et al. 1998, Ghaedi et al. 2000, Pause et al. 2000,
Brosius et al. 2002).
Acyl-CoA oxidases from Saccharomyces cerevisiae (S. cerevisiae) and Candida
tropicalis (C. tropicalis) possess another uncharacterized targeting phenomenon. Both of
22
these oxidases lack PTS1 and PTS2, but are still located in the peroxisomal matrix (Small
et al. 1988, Skoneczny & Lazarow 1998). This might indicate a third branch, PTS3, for
peroxisomal matrix proteins. Nevertheless, the peroxisomal import of S. cerevisiae acylCoA oxidase was shown to be dependent on binding to Pex5p, the PTS1 import receptor
(Klein et al. 2002).
2.2.3 Protein translocation into peroxisomes

Several studies have shown the importance of peroxins, which are responsible for
peroxisome biogenesis. Currently, more than twenty complementation groups of yeast
mutants (pex mutants) have been produced, and twelve complementation groups of
human peroxisome biogenesis disease patients have been identified (for a review, see
Sacksteder & Gould 2000). Because empty peroxisomes, called peroxisomal ghosts, exist
in the cells of almost all of these groups, most of the identified peroxins are probably
involved in the import of soluble peroxisomal enzymes from cytosol into the peroxisomal
matrix (Shimozawa et al. 1998, South & Gould 1999, Hettema et al. 2000). Regarding
the import process itself, it has been shown that ATP hydrolysis (Imanaka et al. 1987,
Wendland & Subramani 1993) and cytosolic factors (Wendland & Subramani 1993),
including heat shock proteins (Walton et al. 1994), are required. In this respect, it has
been suggested that the hydrolysis of ATP is carried out by the ATP-binding proteins,
such as PMP70 (Kamijo et al. 1990), or a newly identified ATPase (Koenig et al. 2002) in
the peroxisomal membranes.
The two targeting signals, PTS1 and PTS2, are recognised by different PTS-specific
receptors. PTS1 interacts directly with its cytosolic receptor, Pex5p. In mammals,
including humans, two isoforms of Pex5p, termed Pex5pS and Pex5pL, with an internal
37 amino acid insertion have been identified (Braverman et al. 1998, Otera et al. 1998).
Pex5pS and Pex5pL form homomeric as well as heteromeric dimers (Otera et al. 2000).
The importance of the interaction between PTS1 and tetratricopeptide repeats in Pex5p
has been characterized by site-directed mutagenesis (Otera et al. 2000, Szilard &
Rachubinski 2000, Klein et al. 2001) and crystallographic (Gatto et al. 2000a,b) studies.
The interaction between Pex5p and S. cerevisiae acyl-CoA oxidase, however, involves
novel contact sites in both proteins. The interaction region in Pex5p is located in a
defined area of the NH2-terminal part of the protein outside the tetratricopeptide repeat
domain involved in PTS1 recognition; the interaction site in S. cerevisiae acyl-CoA
oxidase is located internally and not at the COOH-terminus, where PTS1 is normally
found (Klein et al. 2002). Pex7p, on the other hand, interacts with the PTS2 nonapeptide
and is an important cytosolic receptor for peroxisomal proteins targeted by PTS2s (Zhang
& Lazarow 1996, Rehling et al. 1996, Elgersma et al. 1998).
Both PTS receptors, Pex5p and Pex7p, are recognised by two peroxisomal integral
membrane proteins called Pex13p and Pex14p. Pex13p binds to the PTS1 receptor,
Pex5p, with its cytosolic domain (Gould et al. 1996, Elgersma et al. 1996, Erdmann &
Blobel 1996), and Pex14p binds to the PTS2 receptor, Pex7p (Albertini et al. 1997).
Since Pex5p additionally interacts with other membrane peroxins, such as Pex14p,
23
Pex10p, Pex12p and Pex8p, and Pex7p remains cytosolic in mutants lacking Pex14p
and/or Pex13p, the way in which the translocation machinery acts is not fully understood
(for a review, see Kiel & Veenhuis 2000). Moreover, Pex18p and Pex21p were identified
as key components in the targeting of the Pex7p-cargo complex to peroxisomes (Purdue
et al. 1998). Strong evidence suggests that both cytosolic receptors, Pex5p and Pex7p,
enter the peroxisomal matrix with their cargo protein. In this respect, the interaction with
Pex5pL, but not with Pex5pS, is crucial for the Pex7p-cargo complex to be translocated
inside peroxisomes (Matsumura et al. 2000, Otera et al. 2000). Furthermore, Pex5p and
Pex7p not only bind cargo and deliver it to the peroxisome membrane, but also participate
in multiple rounds of entry into the peroxisome matrix and export to cytosol, indicating
receptor recycling (Braverman et al. 1998, Rehling et al. 2000, Dammai & Subramani
2001).
So far, four peroxins have been implicated in the process of proper PMP import: Pex3p
(Shimozawa et al. 2000), Pex16p (South & Gould 1999), Pex17p and Pex19p
(Matsuzono et al. 1999), although the role of Pex17p is still controversial (Hettema et al.
2000, Harper et al. 2002). Moreover, the NH2-terminal 50 amino acid residues of Pex3p
were associated with the formation of vesicular membrane structures, pre-peroxisomes.
These structures also contained Pex14p, and the membrane of the vesicles was obviously
donated by the nuclear membrane (Faber et al. 2002).
Peroxisomes are capable of importing remarkably large structures, even oligomers of
folded proteins. More interestingly, gold beads 4-9 mm in diameter, coated with PTS1
and then injected into cultured mammalian cells, were taken up by peroxisomes (Walton
et al. 1995). Some multimeric proteins appear to oligomerize after import (Evers et al.
1994, 1996), and other proteins appear to be imported into peroxisomes only when they
first form dimers in the cytosol (Leiper et al. 1996, Titorenko et al. 1998).
2.2.4 Transport of fatty acyl-CoAs across peroxisomal membrane

Continuous -oxidation depends on the availability of acyl-CoA, NAD+, NADPH, free
CoA and export of acetyl groups. This implies the existence of specialized metabolite
transport systems in the peroxisomal membrane. In the mitochondria, the activated longchain fatty acid esters, long-chain acyl-CoAs, are transported by a carnitine-dependent
mechanism through the inner membrane into the matrix, where -oxidation takes place
(for a review, see Kerner & Hoppel 2000). In contrast, the role of the carnitine-associated
pathway in the peroxisomal membrane is not completely known, and it has been
speculated that fatty acyl-CoAs diffuse freely across the membrane. However, two
carnitine acyltransferases, one soluble and the other membrane-associated, were isolated
from rat liver peroxisomes (Singh et al. 1996). Moreover, the carnitine:acylcarnitine
exchange carrier, first characterized in mitochondria, was demonstrated immunologically
in peroxisomal membranes as well (for a review, see Ramsay 2000). Besides this, inside
peroxisomes, human carnitine octanoyltransferase (COT) was found to convert one of the
end products of the peroxisomal -oxidation of pristanic acid, 4,8-dimethylnonanoylCoA, to its corresponding carnitine ester, which is required for its transport into the
24
mitochondrion, where further -oxidation takes place (Ferdinandusse et al. 1999). The
permeability barrier of the peroxisomal membrane is further supported by the
identification of the Pxa1p-Pxa2p dimer, Pex11p, and YPR128cp in S. cerevisiae
responsible for the transport of long-chain acyl-CoAs, medium-chain acyl-CoAs and ATP,
respectively (van Roermund et al. 2000, Nakagawa et al. 2000, van Roermund et al.
2001). In humans, one of the four peroxisomal membrane half ABC transporters was
characterized to be vital for the peroxisomal translocation of VLCFAs because nonfunctionality of this transporter resulted in elevated plasma levels of VLCFAs in the
patients (for a review, see Smith et al. 1999). However, in view of the finding that the
mammalian peroxisomal membrane is highly permeable to H+, it can be concluded that
peroxisomes do not regulate their pH independently (Jankowski et al. 2001).
2.2.5 Peroxisomal -oxidation cycle

2.2.5.1 Acyl-CoA oxidases
Acyl-CoA oxidase (EC 1.3.3.6) is a flavoenzyme that contains one molecule of
noncovalently bound flavine adenine dinucleotide (FAD) per subunit as the prosthetic
group and catalyzes the initial and rate-determining step of the peroxisomal -oxidation
pathway (Fig. 3). In the reductive half-reaction, the substrate acyl-CoA is ,dehydrogenated into the corresponding trans-2-enoyl-CoA and FAD becomes reduced. In
the oxidative half-reaction, FADH2 donates electrons directly to molecular oxygen,
thereby generating H2O2. In mammals, altogether four acyl-CoA oxidases have been
described, which differ in respect to substrate specificity, immunological reactivity and
subunit organization. These oxidases are palmitoyl-CoA oxidase, branched-chain acylCoA oxidase, pristanoyl-CoA oxidase and trihydroxycoprostanoyl-CoA oxidase.
Palmitoyl-CoA oxidase acts on straight-chain fatty acyl-CoAs, and it has been cloned
from rat (Osumi et al. 1984), human (Aoyama et al. 1994a) and mouse (Nhammer et al.
2000). The upstream regions of rat (Osumi et al. 1987) and human (Varanasi et al. 1994,
1996) genes revealed peroxisome proliferator response elements (PPREs) with direct
repeats of the core motif TGACCT, which is required for proliferator-receptor binding.
Two splicing variants of the rat gene were identified, resulting in two oxidases, oxidase I
and oxidase II, slightly differing from the amino acid sequences (Osumi et al. 1980a,
Setoyama et al. 1995). Oxidase I showed optimal activity towards a shorter acyl chain
length with a maximum at C10 compared to oxidase II with a maximum at C14. The
recombinant human palmitoyl-CoA oxidase showed the highest catalytic rate with
25
Fig. 3. Peroxisomal -oxidation cycle of straight-chain fatty acyl-CoA. The numbers refer to
the following enzymes: 1, palmitoyl-CoA oxidase; 2, (2E)-enoyl-CoA hydratase-1 (MFE-1); 3,
(2E)-enoyl-CoA hydratase-2 (MFE-2); 4, (3S)-hydroxyacyl-CoA dehydrogenase (MFE-1); 5,
(3R)-hydroxyacyl-CoA dehydrogenase (MFE-2); 6, 3-ketoacyl-CoA thiolase. The fatty acylCoA shortened by two carbon atoms re-enters the -oxidation cycle. The figure was prepared
with ChemDraw (CambridgeSoft Corporation, MA, USA).
26
saturated fatty acids of 12 to 18 carbon atoms (Chu et al. 1995). Palmitoyl-CoA oxidase
can, however, oxidase longer acyl tails than these, since other studies indicated that the
rat enzyme, for instance, was able to oxidase lignoceroyl-CoA (C24:0) as well (Van
Veldhoven et al. 1992, Wanders et al. 1993). Furthermore, in mice, a knock-out in the
palmitoyl-CoA oxidase-encoding gene resulted in the accumulation of both saturated and
polyunsaturated (5 to 6 double bonds) VLCFAs of 24 to 30 carbon atoms (Fan et al.
1996, Infante et al. 2002). The acceptance of VLCFA-CoAs is further supported by the
recently solved crystal structure of rat palmitoyl-CoA oxidase II. The structure showed a
hydrophobic crevice for binding fatty acyl chains of up to 23 carbon atoms (Nakajima et
al. 2002). All the characterized palmitoyl-CoA oxidases are homodimers composed of
two subunits approximately 70 kDa in size with Ser-Lys-Leu (PTS1) as the three COOHterminal amino acid residues, and they can additionally metabolize mono- and
dicarboxylyl-CoAs and prostaglandin E2-CoA but are inactive towards short-chain
substrates (Van Veldhoven et al. 1992).
In humans, the branched-chain acyl-CoA oxidase functions as the first and ratelimiting step of the -oxidation pathway for 2-methyl-branched-chain fatty acyl-CoAs,
such as pristanoyl-CoA, and bile acid intermediates of di- and trihydroxycoprostanoylCoA (DHCA-CoA and THCA-CoA), which also contain a 2-methyl substitution in their
side chain (Vanhove et al. 1993). Molecular characterization of the human peroxisomal
branched-chain acyl-CoA oxidase revealed a cDNA coding for a protein with Ser-LysLeu peptide in the COOH-terminus (Baumgart et al. 1996b). The purified enzyme
appeared to be a 70 kDa monomeric protein that did not cross-react with antisera raised
against rat palmitoyl-CoA oxidase and pristanoyl-CoA oxidase (see below). Unlike in
humans, the branched-chain -oxidation spiral in rats can be initiated by two different
noninducible oxidases, namely pristanoyl-CoA oxidase, which acts on CoA esters of 2methyl-branched-chain fatty acids, and trihydroxycoprostanoyl-CoA oxidase, which uses
the bile acid intermediate as substrate (Schepers et al. 1990). Both cDNAs for pristanoylCoA oxidase (Vanhooren et al. 1996) and trihydroxycoprostanoyl-CoA oxidase
(Baumgart et al. 1996a) had tripeptides of the conserved PTS1 variants in the
corresponding enzymes. Rat pristanoyl-CoA oxidase is 420 kDa in size and consists of
identical subunits of approximately 70 kDa (Van Veldhoven et al. 1991). In contrast,
trihydroxycoprostanoyl-CoA oxidase is a homodimer of 139 kDa (Baumgart et al.
1996a). More interestingly, the gene coding for the human variant of pristanoyl-CoA
oxidase is present, but its expression is undetectable (Vanhooren et al. 1997).
2.2.5.2 Second and third steps are catalyzed by two multifunctional

enzymes
The second and third reactions of the -oxidation cycle in mammals are catalysed by two
unrelated peroxisomal MFEs. They both catalyse sequential hydratase and dehydrogenase
reactions but through reciprocal stereochemical courses (Fig. 3). In addition to
isomerization of cis-3-enoyl-CoA to trans-2-enoyl-CoA (Palosaari & Hiltunen 1990),
MFE-1 hydrates (2E)-enoyl-CoA to (3S)-hydroxyacyl-CoA and dehydrogenates (3S)-
27
hydroxyacyl-CoA to 3-ketoacyl-CoA (Osumi & Hashimoto 1979). The other
multifunctional enzyme, MFE-2, proceeds via a (3R)-hydroxy intermediate (Fig. 3), and
thus possesses (2E)-enoyl-CoA hydratase-2 and (3R)-hydroxyacyl-CoA dehydrogenase
activities (Dieuaide-Noubhani et al. 1997, Qin et al. 1997a).
MFE-1 has been cloned from various species, including rat (Osumi et al. 1985),
human (Hoefler et al. 1994), guinea pig (Caira et al. 1996) and mouse (Kawai et al.
2001). The rat gene encoding MFE-1 shared similar structural features in the 5'-flanking
region with the 5'-upstream sequence of the gene for acyl-CoA oxidase, which results in
parallel induction of both genes (Ishii et al. 1987). The purified proteins from rat (Osumi
& Hashimoto 1979), mouse (Lalwani et al. 1981) and human (Reddy et al. 1987) showed
a monomeric protein 79 kDa in size. The structures of the NH2-terminal and COOHterminal sides of MFE-1 are similar to those of (2E)-enoyl-CoA hydratase-1 and (3S)hydroxyacyl-CoA dehydrogenase, respectively, of the mitochondrial matrix-bound oxidation enzymes (Ishii et al. 1987, Minami-Ishii et al. 1989). Further alignment of the
homologous proteins indicated that 3-2-enoyl-CoA isomeration occurs in the same
NH2-terminal catalytic domain (Palosaari et al. 1991). The reported kinetic properties
indicate that MFE-1 has catalytic preference for medium straight-chain fatty acyl-CoAs
(Furuta et al. 1980, Osumi & Hashimoto 1980b, Palosaari & Hiltunen 1990). However,
functional MFE-1 is not vital because mutant mice lacking the gene for MFE-1 were
viable and fertile and exhibited no detectable gross phenotypic defects (Qi et al. 1999).
Even though in vitro measurements indicated the capability of rat liver MFE-1 to
dehydrogenate not only straight-chain fatty acyl-CoA but also CoA derivatives of 2methyl-branched-chain fatty acids and bile acid intermediates (Dieuaide-Noubhani et al.
1996), full-length MFE-1 is not sufficient for the formation of a physiological
intermediate in bile acid biosynthesis (Xu & Cuebas 1996).
The second multifunctional enzyme, MFE-2 (EC 1.1.1.62), which degrades (2E)enoyl-CoA via a (3R)-hydroxyl intermediate to 3-ketoacyl-CoA (Fig. 3), has been cloned
from pig (Leenders et al. 1994), human (Adamski et al. 1995), mouse (Normand et al.
1995), rat (Dieuaide-Noubhani et al. 1996, Qin et al. 1997a), chicken (Kobayashi et al.
1997) and guinea pig (Caira et al. 1998). The chromosomal assignment and the gene
structure of MFE-2 have been determined, and it was localized to chromosome 5q2
(Leenders et al. 1996a, Novikov et al. 1997, Mller et al. 1999). A comparison of the
MFE-1 and MFE-2 cDNAs revealed that they have hardly any sequence homology. MFE2, unlike MFE-1, is a homodimer of two approximately 79 kDa subunits (Jiang et al.
1996), but it also has a COOH-terminal PTS1. Moreover, the domain order in MFE-2 is
reversed compared to MFE-1. (3R)-Hydroxyacyl-CoA dehydrogenase, which catalyzes
the third reaction of the -oxidation pathway, is located at the NH2-terminus of MFE-2
and followed by the (2E)-enoyl-CoA hydratase-2 domain, which is responsible for the
second reaction. The hydratase-2 domain in mammalian MFE-2s is followed by a sterol
carrier protein type 2 (SCP-2)-like domain. In vitro characterizations indicated that MFE2 can accept variable substrates, such as medium-chain fatty acyl-CoA (Li et al. 1990,
Jiang et al. 1996, Adamski et al. 1997, Dieuaide-Noubhani et al. 1997, Qin et al. 1997a),
2-methyl-branched-chain fatty acyl-CoA (Dieuaide-Noubhani et al. 1996, Qin et al.
1997a), 24-THCA-CoA intermediate in bile acid synthesis (Dieuaide-Noubhani et al.
1996, 1997, Kurosawa et al. 1997, Qin et al. 1997b), long-chain fatty acyl-CoA
(Dieuaide-Noubhani et al. 1996, Jiang et al. 1997), 17-estradiol (Adamski et al. 1995,
28
Fig. 4. -Oxidation of branched-chain fatty acyl-CoAs. In addition to very-long-chain fatty

acyl-CoAs, mammalian MFE-2 participates in the degradation of (2E)-pristenoyl-CoA and
(24E)-THCA-CoA, the intermediate in bile acid synthesis. The numbers refer to the following
enzymes: 1, very-long-chain acyl-CoA synthetase (human) / trihydroxycoprostanoyl-CoA
synthetase (rat); 2, methylacyl-CoA racemase; 3, branched-chain acyl-CoA oxidase (human) /
pristanoyl-CoA oxidase (rat); 4, branched-chain acyl-CoA oxidase (human) /
trihydroxycoprostanoyl-CoA oxidase (rat); 5, MFE-2; 6, SCPx.
1997) and 5-androstene-3,17-diol (Leenders et al. 1994, Adamski et al. 1995).

However, the inactivation of MFE-2 in mice led to the conclusion that MFE-2 is not only
essential for the degradation of CoA derivatives of 2-methyl-branched-chain fatty acids
and the bile acid intermediates of DHCA and THCA (Fig. 4) but also for the catabolism
of VLCFA-CoAs (Baes et al. 2000).
2.2.5.3 3-Ketoacyl-CoA thiolases

The last step in the peroxisomal -oxidation process, the thiolytical cleavage of 3ketoacyl-CoA into chain-shortened acyl-CoA and acetyl-CoA or propionyl-CoA (Fig. 3
and Fig. 4), is catalyzed by distinct thiolases (EC 2.3.1.16). In rat, two closely related
homodimeric 3-ketoacyl-CoA thiolases, thiolase A and thiolase B, are solely responsible
for the chain shortening of straight-chain fatty acyl-CoAs. The cDNAs for straight-chain
thiolases are 95 % identical, as are the proteins at the amino acid sequence level (Hijikata
et al. 1987, Bodnar & Rachubinski 1990, Hijikata et al. 1990). The major difference lies
in the NH2-terminus. The constitutively expressed thiolase A has an NH2-terminal PTS2
ten amino acid residues longer than thiolase B, whose gene is markedly activated by
peroxisome proliferators (Hijikata et al. 1990, Nicolas-Frances et al. 2000). The specific
activities and substrate specificities of thiolase A and thiolase B isolated from rat livers
29
were virtually identical, and they both carried out thiolytic cleavage of short, medium and
long straight-chain 3-ketoacyl-CoAs with medium chain being the best substrate
(Antonenkov et al. 1997, 1999). Thus far, only one human thiolase has been identified
with similarity to rat straight-chain 3-ketoacyl-CoA thiolases (Bout et al. 1988, Fairbairn
& Tanner 1989, Bout et al. 1991).
In mammalian peroxisomes, the thiolytic function is also performed by the sterol
carrier protein x (SCPx). SCPx is a homodimeric protein composed of 58 kDa subunits
with 3-ketoacyl-CoA thiolase activity in the NH2-terminal domain and SCP-2 function in
the COOH-terminal domain (Mori et al. 1991, Pfeifer et al. 1993, Seedorf et al. 1993,
Ohba et al. 1994). SCPx has broad substrate specificity because, in addition to medium
and long straight-chain 3-ketoacyl-CoAs, it cleaves 2-methyl-branched 3-ketoacyl-CoAs
and the bile acid intermediate 24-keto-THCA-CoA in vitro (Antonenkov et al. 1997).
Mice inactivated for the gene encoding SCPx showed impaired catabolism of 2-methylbranched-chain fatty acyl CoAs. On the other hand, the serum concentrations of
cholesterol, steroids, VLCFA and long-chain fatty acids were not affected. (Seedorf et al.
1998)
In successive cycles of peroxisomal -oxidation, propionyl-CoA, acetyl-CoA and acylCoAs shortened by two carbon atoms are released (Fig. 3). Propionyl-CoA and 4,8dimethyl-nonanoyl-CoA, which are products of the branched-chain acyl-CoA -oxidation
pathway (Fig. 4), are converted into their carnitine esters within the peroxisome and
transported into mitochondria for further oxidation (Jakobs & Wanders 1995, Verhoeven
et al. 1998, Fredinandusse et al. 1999). The peroxisomal palmitoyl-CoA oxidase acts on
very-long and long-chain fatty acyl-CoAs. Therefore, the fatty acyl-CoAs with a chain
length of approximately eight carbons are exported to mitochondria, where their oxidation continues. The fate of acetyl units produced by peroxisomal -oxidation is not
clear (Chu et al. 1995, Eaton et al. 1996, Hashimoto 1999b).
2.2.5.4 Auxiliary enzymes

Double bonds in naturally occurring unsaturated fatty acids are generally in a cis
configuration and can be found in both even- and odd-numbered positions. Since (2E)enoyl-CoA, with a double bond at the 2-position and in a trans configuration, is the only
unsaturated intermediate of the -oxidation cycle, metabolism beyond the pre-existing
double bonds illustrates the requirement for accessory or auxiliary enzymes, such as 3,52,4-dienoyl-CoA isomerase, 2,4-dienoyl-CoA reductase and 3-2-enoyl-CoA isomerase
(for reviews, see Osmundsen et al. 1991, Hiltunen et al. 1996, Hiltunen & Qin 2000). In
the oxidation of an odd-numbered double bond, stepwise -oxidation leads to cis-5enoyl-CoA, which is then dehydrogenated and isomerized to trans-3,cis-5-dienoyl-CoA.
This is followed by the conversion of 3,5-dienoyl-CoA to trans-2,trans-4-dienoyl-CoA
catalyzed by 3,5-2,4-dienoyl-CoA isomerase. Subsequently, trans-2,trans-4-dienoyl-CoA
undergoes NADPH-dependent reduction, which is catalyzed by 2,4-dienoyl-CoA
reductase, to 3-enoyl-CoA with the double bond in a trans configuration. 3-Enoyl-CoA
is subsequently converted to trans-2-enoyl-CoA by 3,2-enoyl-CoA isomerase. Fatty
30
acyl-CoAs with double bonds at even-numbered positions requires subsequent reactions
catalyzed first by 2,4-dienoyl-CoA reductase and then by 3,2-enoyl-CoA isomerase.
In the metabolism of 2-methyl-branched-chain acyl-CoAs, the peroxisomal oxidation system is stereoselective because only a (2S)-isomer is accepted by the
oxidases. -2-Methylacyl-CoA racemase is an auxiliary enzyme that catalyzes the
conversion of (2R)-pristanoyl-CoA and the bile acid intermediate, (25R)-isomer of
THCA-CoA, into their corresponding S-stereoisomers (Schmitz et al. 1994, 1995,
Schmitz & Conzelmann 1997, Ferdinandusse et al. 2002). -2-Methylacyl-CoA racemase
is present not only in peroxisomes but also in mitochondria, and it is encoded by a single
gene (Amery et al. 2000, Kotti et al. 2000).
2.3 Multifunctionality of MFE-2
2.3.1 Domain structure of various MFE-2s

The cDNA coding for MFE-2 was first identified in C. tropicalis. It showed that a partial
gene duplication event has occurred during the evolution of the gene. Namely, the
translated polypeptide contained a duplicate stretch in the NH2-terminus with
approximately 44 % amino acid sequence similarity (Nuttley et al. 1988). However, the
physiological activity of yeast MFE-2 was first identified with S. cerevisiae (Hiltunen et
al. 1992). It was shown that the -oxidation of fatty acids in yeast proceeds only via a
(3R)-hydroxyl intermediate. Additional deletion studies localized (2E)-enoyl-CoA
hydratase-2 into the COOH-terminus and the two copies of (3R)-hydroxyacyl-CoA
dehydrogenases into the NH2-terminal part of MFE-2 (Hiltunen et al. 1992).
Subsequently, this domain order was shown to be characteristic of other yeast MFE-2s
(Fig. 5) (Foss et al. 1995).
Characterization of porcine MFE-2 showed that the 32 kDa NH2-terminal peptide was
able to perform dehydrogenation via the same enantiomer as yeast MFE-2, and the
central part possessed (2E)-enoyl-CoA hydratase-2 activity (Leenders et al. 1996b).
Moreover, the COOH-terminal extension showed 40 % identity to SCP-2. The intronexon structure of the gene encoding the (3R)-hydroxyacyl-CoA dehydrogenase and (2E)enoyl-CoA hydratase-2 regions of mammalian MFE-2 is unique, but the gene structure of
the last three exons is similar to the gene coding for SCP-2 (Ohba et al. 1994, Mller et
al. 1999). This observation supports the hypothesis that the mammalian MFE-2 gene is
the result of gene fusion.
The domain compositions of other MFE-2-related proteins are different (Fig. 5). The
mycorrhizal fungus Glomus mosseae has the same domain structure as the yeast MFE-2,
with the exception that the SCP-2-like domain is fused to the hydratase-2 region
(Requena et al. 1999), as it is with mammalian MFE-2. In Drosophila melanogaster and
Caenohabditis elegans (C. elegans), the domains have been rearranged, so that either the
hydratase (C. elegans) or the SCP-2-like domain (Drosophila) is present as a separate
polypeptide (Breitling et al. 2001). All the variants have a PTS1 at the COOH-terminus.
31
Mammalian MFE-2
PTS1
Yeast MFE-2
PTS1
Glomus mosseae MFE-2
PTS1
Drosophila melanogaster
Caenohabditis elegans
PTS1
PTS1
PTS1
PTS1
Fig. 5. Domain organization of several MFE-2s. (3R)-hydroxyacyl-CoA dehydrogenase, (2E)enoyl-CoA hydratase-2 and SCP-2-like domain are represented as dark grey, white and light
grey, respectively. Every variant has a peroxisomal targeting signal, PTS1, at its COOHterminus. Domain sizes are not drawn to scale. (Modified from Breitling et al. 2001)
2.3.2 Catalytic properties of MFE-2

Mammalian MFE-2 was first identified as 17-hydroxysteroid dehydrogenase (17-HSD)
converting 17-estradiol and 5-androstene-3,17-diol into their less active keto-forms.
The enzyme performed oxidation 360-fold more efficiently than reduction. Therefore,
MFE-2 was first named 17-HSD type 4 (Leendrs et al. 1994, Adamski et al. 1995). In
view of the observation that yeast MFE-2 is also in vitro a 17-HSD, the potential
physiological role of MFE-2 as a 17-HSD is unclear (Adamski et al. 1995, Leenders et
al. 1996b, Qin et al. 2000). Furthermore, the catalytic efficiency (kcat/Km) of mammalian
and yeast MFE-2s with 17-estradiol was 1000 times lower than that of fatty acyl-CoAs.
Moreover, the observation that 17-HSD activity and the MFE-2 expression pattern do
not overlap in breast tissue supports the minor role of MFE-2 in steroid metabolism
(Miettinen et al. 1999).
The kinetic properties of the (3R)-hydroxyacyl-CoA dehydrogenase and (2E)-enoylCoA hydratase-2 activities of MFE-2 have been investigated as well and they are listed in
Tables 1 and 2, respectively. The maximal velocities of the dehydrogenase reaction of
mammalian MFE-2 doubled when the chain length of the substrate increased from C4 to
C16 (Dieuaide-Noubhani et al. 1996, Qin et al. 1997a). However, the dehydrogenase
region of yeast MFE-2 showed maximal velocity with 3-hydroxydecanoyl-CoA as well as
the lowest Km, indicating the highest catalytic efficiency with a fatty acyl tail of ten
carbon atoms (Qin et al. 1999). This result is, however, due to the combined action of two
dehydrogenases in the same polypeptide. Namely, further characterization of yeast MFE2 showed that the most NH2-terminal dehydrogenase, dehydrogenase A, is active towards
medium- and long-chain (3R)-hydroxyacyl-CoAs, while dehydrogenase B shows the
highest catalytic rate with short-chain (C4) substrates (Qin et al. 1999). The NH2-terminal
dehydrogenase region does not interfere with the hydratase-2 reaction, as demonstrated
by the kinetic properties of both full-length MFE-2 and the 46 kDa hydratase-2 fragment
isolated from human liver (Jiang et al. 1996). With both enzymes, the maximal velocities
32
Table 1. Kinetic properties of the dehydrogenase region reported for purified MFE-2 or
its variants from various species.
kcata (s-1)
Species
Km (M)
Reference
Human
MFE-2 (liver)
-3
0.2
Adamski et al. 1995
17-Estradiol
0.8
Adamski et al. 1995
5-Androstene-3,17-diol
0.9
Adamski et al. 1995
17-Estradiol
0.2x10
MFE-2
Porcine
MFE-2 (kidney)
-3
17-Estradiol
Acetoacetyl-CoA
0.3x10
0.3
Leenders et al. 1996b
4.4
34.8
MFE-2
-3
17-Estradiol
Acetoacetyl-CoA
Dehydrogenase fragment
0.2x10
0.4
3.9
35.3
b
-3
17-Estradiol
Acetoacetyl-CoA
0.1x10
0.3
0.7
31.1
Rat
b
MFE-2
3-Hydroxybutyroyl-CoA
0.6
Qin et al. 1997a
3-Hydroxydecanoyl-CoA
0.7
Qin et al. 1997a
3-Hydroxyhexadecanoyl-CoA
1.2
Dieuaide-Noubhani et al. 1996

-6
17-Estradiol
Qin et al. 1997a
2.1 x10
24R,25S-THCA-CoA
0.9
3.3
Candida tropicalis
Dehydrogenase fragment (A+/B+)
31
55
Qin et al. 1999
53
5.4
Qin et al. 1999
41
-3
17-Estradiol
6.2x10
Qin et al. 1999

Qin et al. 2000
24R,25S-THCA-CoA
0.1
Qin et al. 2000
24R,25R-THCA-CoA
0.3
Qin et al. 2000
Dehydrogenase fragment (A+/B-)
ND
33
5.4
Qin et al. 1999
36
24
Qin et al. 1999
Dehydrogenase fragment (A-/B+)
24
370
Qin et al. 1999
29
55
Qin et al. 1999
17
5.8
Qin et al. 1999
12
25
Qin et al. 1999
Enzyme activities are converted to catalytic activities by dividing the published values by the molecular weight
b
of the enzyme. Recombinant protein. ND means not detected. A+ or B+ indicates a functional dehydrogenase
A or dehydrogenase B domain, respectively.
33
Table 2. Kinetic properties of the hydratase-2 region reported for purified MFE-2 or its
variants from various species.
kcata (s-1)
Km (M)
trans-2-Hexenoyl-CoA
447
100
Jiang et al. 1996
trans-2-Octenoyl-CoA
603
40
Jiang et al. 1996
trans-2-Decenoyl-CoA
253
Jiang et al. 1996
trans-2-Dodecenoyl-CoA
199
Jiang et al. 1996
571
100
Jiang et al. 1996
697
30
Jiang et al. 1996
279
12
Jiang et al. 1996
trans-2-Dodecenoyl-CoA
216
Jiang et al. 1996
2.4
34.0
2.1
37.1
0.7
34.7
Species
Reference
Human
MFE-2 (liver)
Hydratase+SCP fragment (liver)
Porcine
MFE-2 (kidney)
Crotonyl-CoA
b
MFE-2
Crotonyl-CoA
Hydratase fragment
Crotonyl-CoA
Rat
b
MFE-2
Crotonyl-CoA
1.2
Crotonyl-CoA
1.3
Qin et al. 1997a

8.2
Qin et al. 1997a
161
trans-2-Hexadecenoyl-CoA
8.2
24R,25S-THCA-CoA
54
3-hydroxy-2-methyl-hexadecanoyl-CoA
9.2
Hydratase+SCP fragment (liver)

3-hydroxyoctanoyl-CoA
49
71
Li et al. 1990
42
22.5
Li et al. 1990
Hydratase+SCP fragment
Crotonyl-CoA
2.3
60
Qin et al. 1997b
23
8.7
Qin et al. 1997b
26
4.6
Qin et al. 1997b
Enzyme activities are converted to catalytic activities by dividing the published values by the molecular weight
b
of the enzyme. Recombinant protein.
34
increased with an increase in chain length up to eight carbon atoms and then started to
decrease gradually. Since the Km values decreased markedly with an increase in chain
length, the catalytic efficiency (kcat/Km) was highest with the C12 substrate. The rat
counterpart showed a similar profile, with the exception that the catalytic efficiencies
with longer substrates were ten times lower than that reported for the human variant (Li et
al. 1990, Qin et al. 1997b).
2.3.3 Tissue distribution

The multifunctionality of MFE-2 does not only lie in its multidomain structure and broad
substrate specificity but also in its tissue distribution and expression levels. The highest
MFE-2 activities and the strongest immunoreactions in human were found in liver
(hepatocytes) followed by heart, prostate and testis. Moderate expression occurred in
lung, skeletal muscle, kidney, pancreas, thymus, ovary, intestine and placenta. Weak
signals were observed in brain, spleen, colon and lymphocytes. (Adamski et al. 1995,
Carstensen et al. 1996, Fan et al. 1998). In human brain, MFE-2 appeared already in the
13th gestational week. Each neuron exhibited increased immunoreactivity along with
growth in size as age increased. Glial cells in white matter showed immunoreactivity after
the 30th gestational week (Itoh et al. 1999). In the developing mouse brain, the mRNA
levels of peroxisomal -oxidation enzymes, including MFE-2, reached a maximum on
postnatal day 5. Thereafter, the levels of mRNA studied decreased progressively, reaching
their steady-state levels on postnatal day 40 (Knoll et al. 2000). More interestingly,
palmitoyl-CoA oxidase and MFE-2 were shown to be essential for docosahexaenoic acid
(DHA, C22:6n-3) synthesis (Su et al. 2001). DHA is needed for normal brain and retinal
development. In the DHA synthetic pathway, C22:5n-3 is elongated to C24:5n-3, desaturated to
C24:6n-3 in microsomes and then retroconverted to docosahexaenoic acid by oxidase and
MFE-2 in peroxisomes.
Normal colonic mucosa has a high level of 17-estradiol metabolism, and the
expression of mRNA for MFE-2 was shown to be significantly decreased in tumours
compared to normal mucosa. Loss of expression of MFE-2 has also been demonstrated in
breast cancer (Krazeisen et al. 1999). Similarly, studies of the loss of heterozygosity at
tumour suppressor loci involved in sporadic breast cancer as well as in colorectal cancer
(Nishisho et al. 1991, Thomson et al. 1993) revealed allele loss at 5q21, which is the
location to which the MFE-2 gene has been assigned (Leenders et al. 1996a, Novikov et
al. 1997, Mller et al. 1999). On the contrary, high expression levels of MFE-2 were
consistently observed in prostate cancer cells, but it is not completely certain whether the
-oxidation of 17-estradiol driven by MFE-2 associates with hormone-refractory
prostate cancer (Castagnetta et al. 1997).
The full-length MFE-2 polypeptide is partially cleaved in vivo into separate (3R)hydroxyacyl-CoA dehydrogenase (34 kDa) and (2E)-enoyl-CoA hydratase-2 (45 kDa)
components (Adamski et al. 1992, Adamski et al. 1995, Dieuaide-Noubhani et al. 1997,
Qin et al. 1997a). The cleavage takes place only in peroxisomes (Markus et al. 1995).
There are different cleavage efficiencies: high in hormone target organs, such as uterus
35
and breast epithelium, but low in non-target tissues participating in the -oxidation of
fatty acids, such as liver and kidney (Kaufmann et al. 1995). It is not yet known whether
the release of a 45 kDa fragment is advantageous in hormone inactivation catalyzed by
the NH2-terminal 34 kDa fragment.
2.3.4 (3R)-Hydroxyacyl-CoA dehydrogenase, a member of the shortchain alcohol dehydrogenase/reductase superfamily

The (3R)-hydroxyacyl-CoA dehydrogenase region of MFE-2 belongs to the short-chain
alcohol dehydrogenase/reductase (SDR) superfamily. This is a large and diverse group of
NAD(H) or NADP(H)-dependent oxidoreductases found in bacteria, plants and animals
(Baker 1991, Krozowski 1992, Jrnvall et al. 1995, Bailey et al. 1997, Oppermann et al.
1997b, Jrnvall et al. 1999, Oppermann et al. 2001). At the present, more than 2000
sequences of the SDR family can be found in protein and nucleic acid databases, and the
crystal structures of close to twenty members of the family have been determined.
Although residue identity between the different forms usually does not amount to a level
of more than 15-30 %, all the known three-dimensional structures show a notably similar
one-domain / pattern, the SDR fold (Fig. 6).
Members of the SDR superfamily are identified through the occurrence of the several
distinct sequence motifs that they have in common (Persson et al. 1991, Jrnvall et al.
1995, Oppermann et al. 1997b, Oppermann et al. 2001). These amino acid elements are
restricted to certain segments in the sequence, indicating common fold, active site,
reaction mechanism and coenzyme and substrate-binding regions (Persson et al. 1991,
Filling et al. 2001, Filling et al. 2002). Essential parts of the coenzyme-binding site, as
determined by X-ray crystallographic studies (Ghosh et al. 1994, 1995, Tanaka et al.
1996) and amino acid sequence comparisons (Persson et al. 1991, Jrnvall et al. 1995),
are located in the NH2-terminal part, comprising a Rossmann fold structure (Rossmann et
al. 1974, Wierenga et al. 1985) with a conserved Gly-X-X-X-Gly-X-Gly pattern. This
dinucleotide-binding region is composed of units that create a parallel -sheet
sandwiched between two arrays of parallel -helices (Fig. 6). Additionally,
crystallographic and site-directed mutagenesis studies of various SDR enzymes revealed
another conserved motif, Tyr-X-X-X-Lys, essential for catalysis (see below).
Significantly, half of all the conserved residues are glycines (Borrs et al. 1989), which is
typical of distantly related proteins with a conserved fold.
Most SDRs are homodimeric or homotetrameric by quaternary structure. The dimeric
interface in homodimeric SDRs consists of a four-helix bundle, which is composed of
long parallel -helices, E and F, of two neighbouring subunits (Benach et al. 1998).
All the structures of homotetrameric SDRs determined so far exhibit two main subunit
interfaces; the four-helix bundle is responsible for constituting a dimer, and two dimers
simultaneously interact with each other via their COOH-terminal regions (Ghosh et al.
1994, Tanaka et al. 1996). However, these associations are not vital for a functional SDR
enzyme. Namely, porcine carbonyl reductase is a monomeric enzyme (Ghosh et al.
2001), whereas 3-hydroxysteroid dehydrogenase/carbonyl reductase is a homodimer,
36
but the dimeric interactions are solely dominated by the COOH-terminal regions (Grimm
et al. 2000), which is usually characteristic of homotetramers. Both enzymes have a basic
/ SDR fold, but the unique insertions before the -helix, F, comprise a subdomain
that packs against interfacial helices, eliminating the four-helix bundle interface
conserved in the superfamily.
Fig. 6. Crystal structure of rat type II hydroxyacyl-CoA dehydrogenase/amyloid- -binding

alcohol dehydrogenase (PDB code 1E6W, Powell et al. 2000). The conserved SDR fold consists
of the central -sheet, which is surrounded by two arrays of three -helices. The two long helices on the right side of the figure comprise a four-helix bundle with the neighbouring
monomer at the dimer interface. The molecule bound to the protein is NAD+. N and C
indicate NH2-terminus and COOH-terminus, respectively. The figure was prepared with the
Swiss-PDBViewer (Guex & Peitsch 1997).
Probably all SDRs share a common reaction mechanism (Fig. 7), which follows a
compulsory ordered pathway with the coenzyme binding first. In some cases, the binding
of the coenzyme induces changes in the structure (Benach et al. 1999), but sometimes
there is no influence on the protein conformation (Grimm et al. 2000). Upon binding of
the hydroxyl or carbonyl substrate, a substrate-binding loop, which is highly flexible in
most apo-SDRs, becomes well ordered and covers the substrate as well as the catalytic
centre from an aqueous environment (Chapman et al. 1999).
In addition to the tyrosine and lysine in the common motif, a conserved serine also
plays an important role in the catalysis (Fig. 7) (Ensor & Tai 1991, Albalat et al. 1992,
Obeid & White 1992, Chen et al. 1993, Cols et al. 1993, Tanaka et al. 1996, Benach et al.
1998, 1999, Powell et al. 2000). In the first step, the deprotonated phenolic group of
tyrosine forms a hydrogen bond with the hydroxyl group attached to position 3 of a fatty
acyl-CoA (Rozwarski et al. 1999) or an alcohol. In the second step, the deprotonated
tyrosine residue acts as a catalytic base to extract hydrogen from the hydroxyl group of
the substrate. Since the substrate is oriented in such a way that its -face is facing
tyrosine with its -face oriented toward the nicotinamide ring of NAD+, the -hydride ion,
liberated from position 3 of the substrate, can be directly transferred to position 4 of
37
Fig. 7. Proposed catalytic reaction mechanism of Drosophila alcohol dehydrogenase. (I) Apo
state: three water molecules hydrogen-bonded to a catalytic triad. (II) Binary state: NAD+ at
the active site and one water molecule hydrogen-bonded to a catalytic triad. (III) Ternary
state: binding of alcohol, proton transfer and hydride transfer. (IV) Ternary state: ketone
and NADH at the active site. Finally, the ketone and NADH leave the active site. (Modified
from Benach et al. 1999). The figure was prepared with ChemDraw (CambridgeSoft
Corporation, MA, USA).
the nicotinamide ring. In addition to the interaction with the nicotinamide ring of NAD+,
the serine residue stabilizes the reaction intermediate via its hydroxyl group (Oppermann
et al. 1997a). Since the phenolic group of the tyrosine side chain has a pKa value close to
10, the -amino group of lysine is needed to convert tyrosine to tyrosinate (pKa 7.6), to
facilitate catalysis at neutral pH (Chen et al. 1993). Additionally, lysine orients the
nicotinamide ring in the syn conformation through a bifurcated hydrogen bond to both the
2- and the 3-hydroxyl groups of the nicotinamide ribose moiety to allow B-face 4-pro-S
hydride transfer. Due to their important roles in catalysis, serine, lysine and tyrosine are
called the Ser-Tyr-Lys catalytic triad. Recently, the asparagine, located close to the active
site, was shown to be important in stabilizing the position of the catalytic lysine via a
conserved water molecule, extending the previously recognised catalytic triad to form a
tetrad of Asn-Ser-Tyr-Lys (Filling et al. 2002).
Alternatively, site-directed mutagenesis and modelling studies proposed that the
deprotonated serine may act as a catalytic base, with tyrosine serving as an electrophilic
catalyst, stabilizing the transition state for hydride transfer by hydrogen bonding to the
38
substrate carbonyl. Even in this case, the dual role of the lysine in the catalytic triad is to
properly orient the cofactor by forming hydrogen bonds to the nicotinamide ribose
moiety and to lower the pKa not only of the tyrosine but also of the serine via electrostatic
interaction. (Parikh et al. 1999, Winberg et al. 1999)
2.3.5 Sterol carrier protein type 2

The COOH-terminal domain of mammalian MFE-2, which consists of approximately 120
amino acid residues, is 40 % identical to SCP-2. SCP-2 is also called non-specific lipid
transfer protein (nsLTP), and its proposed multiple functions arise from its complex gene
structure, post-translational processing, intracellular localization and ligand specificity
(for reviews, see Seedorf et al. 2000, Gallegos et al. 2001). The SCP-2 gene has two
initiation sites coding for proteins that share a common 13 kDa SCP-2 COOH-terminus;
one site codes for the 58 kDa SCPx, which is partially post-translationally cleaved to 13
kDa SCP-2 and 45 kDa thiolase. The other site codes for the 15 kDa pro-SCP-2, which is
completely post-translationally cleaved to 13 kDa SCP-2. SCP-2 appears to be localized
in subcellular organelles intimately involved with fatty acid oxidation, peroxisomes and
mitochondria, with lesser amounts in the cytosol and near to the endoplasmic reticulum
(Keller et al. 1989), even though all the translated variants share identical PTS1 in their
COOH-terminus.
In vitro studies have shown that SCP-2 binds sterols, phospholipids, long-chain
isoprenoids (Schrder et al. 1991, Schrder et al. 1996), long-chain fatty acids (Schrder
et al. 1995), long-chain fatty acyl-CoAs (Frolov et al. 1996c) and branched-chain fatty
acyl-CoAs (Frolov et at. 1997). Additionally, SCP-2 promotes the exchange of a wide
variety of lipids and sterols between membranes (Frolov et al. 1996a, 1996b). The Kd
values of SCP-2 for saturated and unsaturated fatty acyl-CoAs, with the length of the acyl
tail between C10 and C20, were the same as for cholesterol, i.e. close to 2-4 nM. The
binding of fatty acids was 100 times weaker. The introduction of a 3-hydroxy or 3-keto
group into fatty acyl-CoA decreased the affinity 5-fold (Dansen et al. 1999). Interestingly,
upon interacting with long-chain fatty acyl-CoA, SCP-2 forms specific complexes with
acyl-CoA oxidase, the first enzyme of the peroxisomal -oxidation cycle (Wouters et al.
1998). Therefore, SCP-2 may facilitate peroxisomal -oxidation by supplying fatty acylCoA esters. Furthermore, human 13 kDa SCP-2 isolated from recombinant bacteria
contained a small amount of endogenously bound fatty acid (Stolowich et al. 1997).
However, complete deficiency of SCP-2 and SCPx in mice was associated with the
impaired catabolism of methyl-branched fatty acyl-CoAs (Seedorf et al. 1998). On the
other hand, the serum concentrations of VLCFAs and long-chain fatty acids were not
affected, which might be due to up-regulation of the liver fatty acid-binding protein
(Fuchs et al. 2001).
39
2.3.5.1 Other fatty acid/fatty acyl-CoA-binding proteins

Recent data show that long-chain fatty acids and their CoA derivatives directly or
indirectly regulate the activity of many cellular components and processes, such as
membrane receptors, enzymes, ion channels, cell differentiation, cellular development,
gene expression and cellular energy conversion (for reviews, see Glatz et al. 1995, Ek et
al. 1997, Hertz et al. 1998, McArthur et al. 1999). Therefore, the cellular pool of fatty
acids and fatty acyl-CoAs is restricted and their distribution and trafficking are modulated
by fatty acid-binding proteins (FABP), fatty acyl-CoA-binding proteins (ACBP) and
obviously also by non-specific lipid transfer protein (nsLTP, SCP-2). The small sizes of
all of these proteins, i.e. less than 15 kDa, indicate that their only function is to provide a
proper environment for the binding of hydrophobic substrates.
Most unesterified fatty acids in the cytoplasm are bound to cellular membranes.
Especially long-chain fatty acids are minimally soluble in water (Vorum et al. 1992) and
have a strong affinity for membranes. These properties restrict their movement through
the cytoplasm. Consequently, the transport and solubilization of fatty acids are facilitated
by FABPs. Members of the FABP family are approximately 14-15 kDa in size and
monomeric (Glatz et al. 1996, Weisiger 1996). The rate of fatty acid diffusion within liver
cells is directly proportional to the concentration of liver FABP (Luxon & Weisiger 1993,
Luxon 1996, Luxon et al. 1998). The fatty acid uptake from membranes involves
interaction between a positively charged -helical region of the FABP and negative
charges on the membrane surface, resulting in a conformational change that permits
direct transfer of fatty acid between the protein-binding site and the membrane (Herr et
al. 1995, 1996, Gericke et al. 1997, Corsico et al. 1998). Such interaction was also
demonstrated for SCP-2 to accept ligands from membranes (Stolowich et al. 1997, Huang
et al. 1999).
ACBP is a cytosolic protein with 86103 residues and a highly conserved amino acid
sequence. A total of 30 sequences have been recognized either as proteins or as gene
products (Kragelund et al. 1999). In mammals, the highest concentration of ACBP is
found in liver (Bovolin et al. 1990). In other tissues, ACBP is reported to be abundant in
specialized cells, such as the steroid-producing cells of adrenal cortex and testis. The
main function of ACBP appears to be the modulation of acyl-CoA concentrations within
the cell. By its ability to bind acyl-CoA molecules, ACBP mediates the product feedback
inhibition of long-chain acyl-CoA synthetase. ACBP binds medium- and long-chain acylCoA esters with very high affinity, with a preference for acyl-CoA esters of 14-22 carbons
atoms (Rasmussen et al. 1990, Frgeman et al. 1996, Rosendal et al. 1993), but it does
not bind fatty acids, acyl carnitines and cholesterol (Rosendal et al. 1993).
Despite their capability to bind fatty acids or their CoA derivatives, SCP-2, FABP and
ACBP are not sequence- or structure-related (Fig. 8), which indicates evolutionarily
different origins. ACBPs are -helical proteins with either four or seven helices arranged
differently with respect to each other (Andersen & Poulsen 1993, Lerche et al. 1997, van
Aalten et al. 2000). The acyl chain, which is buried in the hydrophobic groove, is
completely protected from the aqueous solvent by the acyl-CoA head group. The CoA
head forms a lid on the binding pocket by interacting with specific residues on the rim of
the binding cavity. In contrast to ACBP, FABP and SCP-2 are / proteins. FABPs are
40
Fig. 8. Various fatty acid/fatty acyl-CoA-binding proteins. Top panel: human FABP with
oleic acid (PDB code 1HMS, Young et al. 1994). Central panel: ACBP from Plasmodium
falciparum in complex with myristoyl-CoA (PDB code 1HBK, van Aalten et al. 2001). The
lowest panel: rabbit SCP-2 (PDB code 1C44, Choinowski et al. 2000). The figure was
prepared with the Swiss-PDBViewer (Guex & Peitsch 1997).
composed of ten antiparallel -strands, which form a barrel-like structure capped by two
short -helical segments (Sacchettini et al. 1989, Zanotti et al. 1992). The flattened barrel
provides a hydrophobic pocket, where the carboxylate of the fatty acid is located. Even
though the tertiary structures for all FABPs solved are conserved, the bound fatty acids
are very different in their conformations and interactions. In SCP-2 proteins, the putative
ligand-binding site is built up of both -sheet and -helices; the -sheet with a mixed
sheet structure is flanked on one side by -helices. This arrangement forms a
hydrophobic tunnel, providing an environment for apolar ligands, such as fatty acids and
fatty acyl-CoAs (Choinowski et al. 2000, Garca et al. 2000).
41
2.4 Peroxisomal -oxidation deficiencies

The inherited peroxisomal disorders in human are divided into two categories. One group
consists of peroxisome biogenesis disorders involving an absence of peroxisome
formation (Braverman et al. 1995, Lazarow & Moser 1995), while the other group is
composed of single peroxisomal protein deficiencies (Wanders & Tager 1998). Human
fatal genetic peroxisomal biogenesis disorders (PBDs) include the Zellweger syndrome
(ZS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD) and
rhizomelic chondrodysplasia punctata (RCDP) (for a review, see Gould & Valle 2000).
ZS is characterized by an array of neural, hepatic and renal defects. Individuals with ZS
exhibit severe neurological dysfunction and rarely survive their first year. By contrast,
NALD patients display similar but less severe phenotypes than ZS patients and can
survive for up to a decade. IRD patients are even more mildly affected, with some
surviving beyond their third decade (Moser et al. 1995). RCDP, by contrast, is
characterized by unique skeletal abnormalities (Moser et al. 1995).
Several disorders relevant to the peroxisomal -oxidation cycle include X-linked
adrenoleukodystrophy, palmitoyl-CoA oxidase deficiency, MFE-2 deficiency and thiolase
deficiency, and they all are associated with the accumulation of VLCFAs, resulting in
defects in the nervous system. Adrenomyeloneuropathy (AMN) and cerebral childhood
adrenoleukodystrophy (CCALD) are the main phenotypic variants of an X-linked
inherited
metabolic
disorder,
X-linked
adrenoleukodystrophy
(X-ALD).
Neuropathological and electrophysiological studies have shown that X-ALD is a disease
with mixed features of axonal degeneration, leading to myeloneuropathy, and a severe
inflammatory reaction in the cerebral white matter, resulting in demyelination of the
peripheral and central nervous system, respectively (for a review, see McGuinness &
Smith 1999). Other tissues, such as adrenal gland and testis, are also affected. X-ALD is
caused by mutations in the ABCD1 (ALD) gene encoding a peroxisomal ABC transporter
(Mosser et al. 1993), an adrenoleukodystrophy protein, which in the peroxisomal
membrane participates in the transport of VLCFAs across the peroxisome membrane into
the matrix (Smith et al. 2000). Therefore, the principal biochemical abnormality in XALD patients is the accumulation of VLCFAs in tissues and body fluids (Moser et al.
1995). To date, 406 X-ALD mutations have been identified with no apparent correlation
between genotype and phenotype (for a review, see Kemp et al. 2001).
So far, palmitoyl-CoA oxidase deficiency (pseudoneonatal adrenoleukodystrophy) has
been reported in only a few patients with a large deletion in the corresponding gene
(Fournier et al. 1994). All the patients show severe neurological abnormalities, including
hypotonia, hearing impairment and visual failure. In this respect, the absence of
functional oxidase leads to deficient oxidation of especially the CoA derivatives of
VLCFAs. This explains the elevated VLCFA levels in plasma and tissues from these
patients.
Among the single-enzyme deficiencies, MFE-2 deficiency is very common (Paton &
Pollard 2000). The clinical presentation of MFE-2 deficiency is severe and resembles
Zellweger syndrome in many respects. The MFE-2 disorder, however, can be
distinguished from ZS by its normal plasmalogen levels. Abnormalities include neonatal
hypotonia, craniofacial dysmorphia, developmental delay, neuronal migration defects or
42
demyelination, which result in early death, mostly within the first year of life. Mutations
are found in both the dehydrogenase and the hydratase-2-coding regions of the MFE-2
gene, but not in the SCP-2-like domain coding region. The defects include point
mutations and nucleotide deletions of variable size (Mller et al. 2001). The patients
show elevated plasma levels of VLCFAs and branched-chain fatty acids and in most
cases, accumulate bile acid intermediates. Consequently, the reduced ability of pristanic
acid -oxidation can also be used as one of the indicators of MFE-2 deficiency.
The situation with 3-ketoacyl-CoA thiolase deficiency is less clear. Only in one case
was peroxisomal thiolase shown to be absent according to immunoblot analyses (Schram
et al. 1987). Moreover, the finding indicated that not only VLCFAs but also abnormal bile
acids accumulated in this patient, which is reminiscent of SCPx deficiency (Antonenkov
et al. 1997, Seedorf et al. 1998) rather than straight-chain 3-ketoacyl-CoA thiolase
deficiency, as postulated here.
3 Outlines of the present study

Mammalian peroxisome contains two multifunctional enzymes, MFE-1 and MFE-2. Both
of them catalyze the second and third reaction of the -oxidation cycle, but via reciprocal
stereochemical routes. When this work was started, MFE-2 was cloned from various
species, including human (Adamski et al. 1995) and rat (Dieuaide-Noubhani et al. 1996,
Qin et al. 1997a). According to sequence alignments, MFE-2 consists of multiple
domains. The domain order was first resolved by deletion studies done with S. cerevisiae
MFE-2 (Hiltunen et al. 1992). Subsequent experiments with mammalian MFE-2 revealed
that the NH2-terminal (3R)-hydroxyacyl-CoA dehydrogenase region is followed by (2E)enoyl-CoA hydratase-2, and the SCP-2-like domain is located in the COOH-terminus.
Despite the fact that MFE-2 was shown to participate in hormone inactivation and in the
degradation of straight-chain and 2-methyl-branched-chain fatty acyl-CoAs in vitro,
nothing was known about the mode of action of any of the domains at the structural level.
Moreover, conserved amino acid residues in the NH2-terminal part of MFE-2 had been
shown to be critical for catalysis in the enzymes belonging to the SDR superfamily, but
no experiments had identified the residues needed in the water-adding reaction catalyzed
by hydratase-2. Furthermore, the role of the SCP-2-like domain for the functionality of
MFE-2 remained to be investigated; at least it was not needed for the oxidation of
medium straight-chain fatty acyl-CoAs catalyzed by the recombinantly produced
dehydrogenase or hydratase-2 region of porcine MFE-2 (Leenders et al. 1996b).
Therefore, in this work, the structure-function relationship of mammalian MFE-2 was
studied in terms of the following topics:
1.
2.
3.
Crystallization and structural determination of the NH2-terminal (3R)hydroxyacyl-CoA dehydrogenase region of rat MFE-2 (III),
Identification and characterization of amino acid residues critical for (2E)enoyl-CoA hydratase-2 activity in human MFE-2 (I),
Crystallization and structural determination of the SCP-2-like domain to reveal
its putative role in human MFE-2 (II).
4 Materials and methods

The materials and methods have been described in more detail in the original articles
referred to by their Roman numerals (I-III).
4.1 cDNA cloning
4.1.1 Cloning of the (3R)-hydroxyacyl-CoA dehydrogenase region from

rat MFE-2 (III)
Total RNA from livers of Wistar rats (Laboratory Animal Centre of the University of
Oulu) was isolated using the REX total RNA isolation kit. The cDNA encoding rat MFE2 was obtained from the isolated total RNA by reverse transcription with Moloney murine
leukemia virus reverse transcriptase (Gibco BRL, Gaithersburg, MD, USA). The coding
sequence for the (3R)-hydroxyacyl-CoA dehydrogenase region was amplified by PCR
using 5-primer (cacttcc ATG GCT TCG CCT CTG AGG TTC GAC G, where a lower
case sequence indicates mismatches to the MFE-2 sequence) and 3-primer
(catctggatcctca ATC TGC AGA TGC CAC TTG ACC G). After subcloning into the
pUC18 vector with a SureClone ligation kit (Amersham Pharmacia Biotech AB, Uppsala,
Sweden) for the verification of the nucleotide sequence, the insert was released by using
NcoI and BamHI restriction endonucleases (the restriction sites are underlined in the
primers) and subsequently subcloned into the pET3d expression vector (Novagen,
Madison, WI, USA), resulting in a plasmid pET3d::dhSCP-2L encoding
dehydrogenase region of rat MFE-2 (Fig. 9).
45
Fig. 9. The variants of MFE-2 used in this study. All the other proteins, except dh SCP-2L ,
which is from rat MFE-2, are from human protein.
4.1.2 Cloning of human MFE-2 (HsMFE-2) and its variants, HsMFE2(dh) and dhSCP-2L (I, II)
The open reading frame of human MFE-2 cDNA was obtained from total RNA isolated
from human fibroblasts (Chomczynski & Sacchi 1987) using Moloney murine leukemia
virus reverse transcriptase (Gibco BRL). The resulting cDNA was used as a template in
PCR reactions in order to amplify DNA fragments encoding full-length human MFE-2
(HsMFE-2), the residues 319-736 (lacking the coding region for the dehydrogenase
region, HsMFE-2(dh)) and the residues 618-736 (lacking the coding regions for the
dehydrogenase and hydratase-2 regions, dhSCP-2L) (Fig. 9). The primers in the PCR
reactions were as follows: 5-primer (cgcaggagctctagaagATG GGC TCA CCG CTG AGG
TTC GA) and 3-primer (cctagctcgagTCA GAG CTT GGC GTA GTC TTT AAG AA) for
HsMFE-2, 5-primer (catatgACA GCA ACA TCA GGA TTT GCT) and 3-primer
(ggatccTCA GAG CTT GGC GTA GTC TTT AAG) for HsMFE-2(dh), and 5-primer
(cacttccatg GAG GGC GGG AAG CTT CAG AGT) and 3-primer (cacctggatcc TCA
GAG CTT GGC GTA GTC TTT AA) for dhSCP-2L. The PCR products were
subsequently subcloned into the pUC18 vector using the SureClone Ligation kit
(Amersham Pharmacia Biotech AB), and the nucleotide sequences of the inserted DNAs
were verified to ensure that no mutations had been introduced. The SacI- and XhoIdigested fragment consisting of HsMFE-2 cDNA was isolated and subsequently cloned
into similarly digested plasmid pYE352 (Filppula et al. 1995). NdeI and BamHI as well
as NcoI and BamHI were used to release the HsMFE-2(dh) and dhSCP-2L inserts,
which were subcloned into the pET3a and pET3d expression vectors (Novagen),
respectively. This gave the following plasmids: pYE352::HsMFE-2, pET3a::HsMFE2(dh) and pET3d::dhSCP-2L.
46
4.2 Site-directed mutagenesis (I)

A QuickChange mutagenesis kit (Stratagene, La Jolla, CA, USA) was applied to
introduce point mutations in the pYE352::HsMFE-2 and pET3a::HsMFE-2(dh)
plasmids to identify the amino acid residues critical for (2E)-enoyl-CoA hydratase-2
activity. The mutated variants of pYE352::HsMFE-2 that were not able use oleic acid in
vivo (see below) but were able to dehydrogenate (3R)-hydroxyacyl-CoA substrates in
vitro were subjected to further characterization by introducing the same mutations in
pET3a::HsMFE-2(dh). This resulted in the following plasmids: pET3a::HsMFE2(dhY347A), pET3a::HsMFE-2(dhE366A) and pET3a::HsMFE-2(dhD510A) (see
Fig. 9). The mutations in the constructs were confirmed by nucleotide sequencing.
4.3 Complementation of Saccharomyces cerevisiae fox-2 with human

MFE-2 and its mutated variants (I)
The pYE352::HsMFE-2 and its mutated variants were transformed into S. cerevisiae fox2 cells, which lacked the endogenous gene for MFE-2 (Hiltunen et al. 1992), by the
lithium acetate method (Gietz et al. 1995) and selected on ura- plates. The transforms
growing on the ura- plates were streaked onto oleic plates. Utilization of oleic acid by the
transformed fox-2 cells was assessed by observing the clearing zones on the oleic acid
plates. For enzyme assays, transformed yeast cells were cultured at 30C on either a rich
or a synthetic medium as described (Qin et al. 1999). The harvested cells were stored
frozen at -70C until used.
4.4 Production of recombinant proteins (I, II)

The recombinant HsMFE-2(dh), HsMFE-2(dhY347A), HsMFE-2(dhE366A),
HsMFE-2(dhD510A) and dhSCP-2L (Fig. 9) were expressed in Escherichia coli (E.
coli) BL21(DE3)plysS cells following the suppliers instructions (Novagen). M9ZB
medium supplemented with 50 g/ml carbenicillin and 34 g/ml chloramphenicol was
used in the expression experiments. E. coli cells containing the plasmid of interest were
used to inoculate one litre of culture. The cells were allowed to grow under aerobic
conditions at 37C until A600 of 0.6 was reached. The expression of recombinant protein
was induced by adding IPTG to a final concentration of 0.4 mM. After two hours of
additional incubation, the bacterial cells were harvested, washed with cold buffer (120
mM NaCl, 16 mM potassium phosphate, pH 7.4, 0.02 % NaN3) and stored at -70C until
used.
47
4.4.1 Production of selenomethionine-labelled recombinant (3R)hydroxyacyl-CoA dehydrogenase (III)

E. coli strain of B834(DE3) was transformed with pET3d::dhSCP-2L. After the
transformation, a single, freshly grown colony of E. coli B834(DE3)(pET3d::dhSCP2L) was picked from a LB plate and grown in LB medium overnight at 37C. The cells
from this overnight culture were collected by centrifugation, washed with 20 ml of
selenomethionine (Se-Met) minimal medium [Se-Met-MM, 48 mM Na2HPO4, 22 mM
KH2PO4, 9 mM NaCl, 0.4 % (w/v) glucose, 2 mM MgSO4, 0.1 mM CaCl2, 8 mM
(NH4)2SO4, 1x BME vitamin solution (Gibco BRL), 0.5 mM L-Se-Met (CalBiochemNovaBiochem Corp., San Diego, CA, USA)], centrifuged once again and resuspended in
20 ml of Se-Met-MM. This 20 ml culture was then used as an inoculum for 2 liters of
prewarmed (30C) Se-Met-MM medium in the presence of 50 g/ml carbenicillin. The
cells were allowed to grow under aerobic conditions until A600 of 0.9 was reached. The
temperature was shifted from 37C to 20C, and the expression of dhSCP-2L was
induced by the addition of IPTG to a final concentration of 1 mM. After 20 hours of
additional incubation, the bacterial cells were harvested, washed with cold buffer (120
mM NaCl, 16 mM potassium phosphate, pH 7.4, 0.02 % NaN3) and stored at -70C until
used.
4.5 Protein purification (I-III)

The cell walls of E. coli cells were digested with lysozyme (100 g/ml), and the viscosity
of the cellular lysate was reduced by using DNaseI (25 g/ml) and RNaseA (25 g/ml).
Subsequently, the cell debris was sedimented by centrifugation, and the soluble protein
fraction was applied to the first column of the purification protocol. HsMFE-2(dh),
HsMFE-2(dhE366A), HsMFE-2(dhD510A), dhSCP-2L and dhSCP-2L (Fig. 9)
were purified using anion exchange, cation exchange and size exclusion chromatography
columns, including Q-Sepharose (II & III, Amersham Pharmacia Biotech AB), DEAESephacel (I, Amersham Pharmacia Biotech AB), Poros 10 SP (I, PerSeptive Biosystems,
Cambridge, MA, USA), Resource S (II & III, Amersham Pharmacia Biotech AB),
SuperdexTM 200 10/30 (I & III, Amersham Pharmacia Biotech AB) and SuperdexTM 75
10/30 (II, Amersham Pharmacia Biotech AB). Detailed descriptions of the purification
protocols are given in the original articles.
4.6 Enzyme assays (I, III)

The activities of (2E)-enoyl-CoA hydratase-2 and (3R)-hydroxyacyl-CoA dehydrogenase
or their combined activity were measured spectrophotometrically using a Shimadzu UV
3000 spectrophotometer. In the reaction mixture, the formation of the magnesium
48
complex of 3-ketodecanoyl-CoA was monitored at 303 nm (Hiltunen et al. 1989). The
kinetic constants (kcat and Km) for hydratase-2 were measured via the reduction of the
double bond in (2E)-decenoyl-CoA at 263 nm (Binstock & Schulz 1981) and using
variable concentrations (4-60 M) of the substrate. The pH dependence experiment was
carried out in 200 mM potassium phosphate buffer at pH values ranging from five to 10.
The kinetic data, the pKa values and their errors were calculated with the GraFit computer
software (Sigma, St. Louis, MO, USA).
4.7 Dynamic light scattering and CD-spectroscopic measurements (I)

The monodispersity and hydrodynamic radii of purified HsMFE-2(dh) and its mutated
variants were studied with a DynaPro-MSTC dynamic light scattering device (Protein
solution, Charlottsville, VA, USA) at 6C. The secondary structural elements were
analyzed using circular dichroism (CD) spectroscopy with a Jasco JHO
spectropolarimeter at 22C. The far-UV spectra of the recombinant proteins were
measured from 200 to 250 nm in 80 mM potassium phosphate buffer, pH 7.0.
4.8 Surface plasmon resonance measurements (II)

dhSCP-2L was immobilized on a carboxymethylated dextran matrix (CM5) chip with
standard amine coupling chemistry by flowing a protein solution in 10 mM phosphate
buffer (pH 4.8) over the chip in a Biacore 3000 instrument (Biacore AB, Uppsala,
Sweden). The amount of immobilized protein was 1900 resonance units. Kd values were
estimated with the steady-state affinity model according to the manufacturers procedure
implemented in BIA evaluation 3.1.
4.9 Crystallization, data collection and processing (II, III)

Initial crystallization screening was performed using the sparse matrix screening method
described by Jancarik & Kim (Jancarik & Kim 1991) and the hanging-drop and sittingdrop vapour diffusion methods. The crystallization conditions of crystals suitable for
structural determination have been described in more detail in the original articles.
dhSCP-2L was crystallized at 4C, and a data set was collected from a single
crystal using the oscillation method with 0.5 rotations per frame at a wavelength of
0.9785 and a MAR CCD detector at beamline BW7A at the EMBL outstation at the
DESY synchrotron, Hamburg, Germany. A multiwavelength anomalous dispersion
(MAD) experiment, with a Se-Met-labelled dhSCP-2L crystal grown at 22C, was
performed on beam line BM30, ESRF, Grenoble, France. The X-ray fluorescence from
49
the crystal was measured as a function of the incident X-ray energy near the Se- edge.
The wavelengths chosen for data collection were 2 = 0.97927 and 3 = 0.97243 ,
corresponding to a minimum of f and a maximum of f, respectively. A third, remote
energy was selected at 12653 eV (1 = 0.97958 ). The MAD data was collected from a
single crystal with a strategy of strict inverse beam settings, 1 rotation per frame and a
MAR345 detector. All three wavelengths were collected successively in portions of forty
frames that consisted of 20 frames from and 20 frames from + 180. In both cases,
dhSCP-2L and dhSCP-2L, the images were processed using DENZO and the
reflections merged by applying SCALEPACK of the HKL suite (Otwinowski & Minor
1997).
4.10 Structural determination, model building and refinement (II, III)

For dhSCP-2L, the initial phases were determined from a molecular replacement
solution obtained with AMoRe (Nawaza 1994) using rabbit SCP-2 (PDB code 1C44,
Choinowski et al. 2000) as the search model. Subsequently, the phases were used as an
input for the autobuilding procedure in warpNtrace (Perrakis et al. 1999). The resulting
structure was further refined and model built using CNS (Brnger 1998) and O (Jones et
al. 1991).
In the case of dhSCP-2L, the initial experimental phases were obtained and refined
by the program SOLVE (Telwilliger & Berendzen 1999). The phases were then improved
by the application of phase extension, 2-fold averaging and solvent flattening, in a single
run with the program DM (Cowtan & Zhang 1999) using the AUTOMASK option. This
allowed the calculation of better-quality maps, which were used as a starting point for
autobuilding with MAID (Levitt 2001). The resulting model was further improved with
model building in O (Jones et al. 1991) and refinement with CNS (Brnger 1998).
Throughout the refinement, structural integrity was monitored by WHATIF (Vriend
1991) and PROCHECK (Laskowski et al. 1993). The locations and types of structural
motifs were defined by the PROMOTIF (Hutchinson & Thornton 1996) and DSSP
(Kabsch & Sander 1983) programs. Interatomic contacts were analyzed by the LPC
software (Sobolev et al. 1999).
4.11 Other methods

Oligonucleotides were prepared with an Applied Biosystems DNA Synthesizer (PerkinElmer, Norwalk, CT, USA) or purchased from Amersham Pharmacia Biotech. Nucleotide
sequences were verified by the dideoxynucleotide or the dye terminator cycle sequencing
methods.
Proteins were separated on a SDS-polyacrylamide slab gel according to their
molecular weights (Laemmli 1970) in the presence of 1.8 M urea and using low
molecular weight standards (Bio-Rad Laboratories, Hercules, CA, USA) for calibration.
50
The protein concentrations of the samples, which were subjected to SDSpolyacrylamide gel electrophoresis (SDS-PAGE), were determined according to Bradford
(Bradford 1976) with the Bradford reagent (Bio-Rad Laboratories). For the purified
proteins, absorption at 280 nm was measured and used for fine adjustment of the protein
concentration.
To find out if the mutant variants of human MFE-2 were expressed in S. cerevisiae, the
proteins from SDS-PAGE were blotted electrophoretically onto a nitrocellulose filter
(Towbin et al. 1979). The transferred proteins were identified by using first antihydratase-2 antibody (1:1000 dilution) (Malila et al. 1993) and then affinity-purified goat
anti-rabbit IgG with horseradish peroxidase conjugate (Bio-Rad Laboratories) as the
secondary antibody. As a visual indicator, 4-chloro-1-naphthol (Sigma) was used as the
electron acceptor.
To identify the degree of Se-Met labelling mass spectrometric analyses were carried out
for the purified dhSCP-2L and Se-Met labelled dhSCP-2L. The experiments were
performed using a LCT (Micromass LTD) orthogonal time-of-flight mass spectrometer
with OpenLynx3 Data system. The diluted samples in acetonitrile-water solution (50:50)
containing 0.1% formic acid solution were directed by a Harward 5311 syringe pump into
the Z-spray electrospray source at a flow rate of 10 l/minute. The vaporizer temperature
was 140C and N2 was used both as nebulizer (80 l/hour) gas and desolvation (400 l/hour)
gas. The electrospray capillary was kept at 3.8 kV and the sample cone voltage at 35 V.
5 Results
5.1 Binary structure of the two-domain (3R)-hydroxyacyl-CoA
dehydrogenase region of rat MFE-2 (III)
Multiple-sequence alignment of several mammalian peroxisomal MFE-2s revealed
nonconserved amino acid residues (His311-Ser321, in the rat sequence) between the
dehydrogenase and hydratase-2 regions (Fig. 1, original article III). Based on this
information, plasmid pET3d::dhSCP-2L was constructed. This plasmid encodes the
Met1-Asp319 of rat MFE-2 and therefore lacks the coding regions for the hydratase-2
and SCP-2-like domains. This was in line with the results of the study, where the NH2terminal fragments of MFE-2, including Met1-Thr312 and Met1-Ala316, were isolated
from rat liver with (3R)-hydroxyacyl-CoA dehydrogenase activity (Dieuaide-Noubhani et
al. 1996, 1997). The purified dhSCP-2L showed similar catalytic efficiency (kcat of 3.7
s-1) as that obtained for the full-length recombinant rat MFE-2 (in this study). When
applied to a size exclusion column, the elution volume of dhSCP-2L corresponded to
the size of a homodimer.
For structural determination, dhSCP-2L was produced as a Se-Met-labelled protein
and purified. The mass-spectrometric analysis of native and Se-Met dhSCP-2L
indicated complete labelling, where all of the five methionines were replaced by Se-Met.
Subsequently, thin trigonal prismatic crystals 0.4 x 0.2 x 0.05 mm3 in size were obtained
from Se-Met dhSCP-2L within a few weeks.
The MAD dataset on the frozen Se-Met-labelled dhSCP-2L crystal consisted of
three different wavelengths with 5-fold redundancy and 92.1-99.2 % completeness, when
2.38 was used as the diffraction limit (Table 1, original article III). The crystal
belonged to the space group P21 with unit cell dimensions of a = 89.466, b = 82.748, c =
95.745 and = 94.201. Assuming four monomers per asymmetric unit, the Vm value of
the crystal was 2.55 3/Da, which is within the most probable range of values for proteins
(Matthews 1968). The initial experimental phases were obtained and refined by the
program SOLVE (Telwilliger & Berendzen 1999) from twelve of the twenty expected
selenium atoms per asymmetric unit using 2.6 resolution as the diffraction limit. With
52
Table 3. MAD-data collection statistics of dhSCP-2L with resolution shells.
Data set
Resolution
shell
Rmerge (%)
Completeness
(%)
I/ I
Unique
reflections
Remote
24.00 5.11
7.8
86.8
18.2
4995
5.11 4.06
7.3
89.4
17.8
5057
4.06 3.55
9.1
90.7
14.9
5106
3.55 3.23
9.8
91.5
14.2
5136
3.23 3.00
9.7
92.8
13.4
5202
3.00 2.82
11.4
93.2
11.5
5212
2.82 2.68
14.6
93.9
8.9
5259
2.68 2.56
20.0
93.7
6.9
5242
2.56 2.46
19.6
94.8
7.1
5292
2.46 2.38
21.2
94.4
6.1
5251
24.00 5.11
8.3
99.9
15.4
5744
5.11 4.06
7.7
99.6
16.4
5622
4.06 3.55
9.8
99.5
13.7
5606
3.55 3.23
10.2
99.0
13.5
5560
3.23 3.00
10.4
99.4
12.6
5563
3.00 2.82
12.2
99.2
11.1
5552
2.82 2.68
15.4
99.0
9.3
5545
2.68 2.56
19.9
98.8
7.4
5523
2.56 2.46
19.6
99.1
7.3
5536
2.46 2.38
21.1
98.4
6.6
5466
24.00 5.11
10.2
99.8
13.5
6294
5.11 4.06
9.9
99.7
13.5
6167
4.06 3.55
11.8
99.6
11.4
6148
3.55 3.23
12.4
99.6
10.9
6133
3.23 3.00
13.3
99.7
10.2
6130
3.00 2.82
15.7
99.4
9.3
6077
2.82 2.68
21.3
99.3
7.5
6092
2.68 2.56
22.3
99.3
6.3
6088
2.56 2.46
23.3
97.1
6.1
5936
2.46 2.38
17.8
30.0
4.7
1841
Inflection point
Peak
this resolution limit the completenesses were 91.5 %, 99.3 % and 99.6 % for the remote,
inflection point and peak data sets, respectively (Table 3). This, however, did not result in
interpretable maps and clear solvent boundaries. The figure-of-merit of the experimental
phases was 0.34. Since dhSCP-2L was shown to exist as a dimer in aqueous solution, a
search for non-crystallographic symmetry was initiated. Indeed, three solutions of the
self-rotation function, calculated with GLRF (Tong & Rossmann 1997), were found at
= 180, = 0, = 86 and = 180, = 27, = 23 and = 180, = 160, = 31
with peak heights of 10.2 , 2.1 and 2.0 , respectively. When applied to the list of
53
heavy atom sites obtained from SOLVE, the program FINDNCS (Lu 1999) was used to
both confirm the orientation of the non-crystallographic 2-fold axis ( = 180, = 0, =
86) found from the self-rotation function and to provide the translational component for
the DM run (Cowtan & Zhang 1999). When the local 2-fold axis, which connected two
dimers and therefore covered the whole asymmetric unit, was used in line with solvent
flattening and phase extension in a single DM run, the correlation coefficient between
masked map areas improved from 0.49 to 0.95. This allowed the calculation of better
maps, which were used as a starting point for autobuilding with MAID (Levitt 2001).
Eight selenium sites out of those 12 found by SOLVE were in the electron density of the
experimental maps and they corresponded to selenomethionines in the E and E of each
monomer (Fig. 1, original article III). The other four selenium sites, which were a little
bit off the density, belonged to Se-Mets preceding CT1 (Fig. 1, original article III).
Further iterations of refinement and model building with O (Jones et al. 1991) resulted in
a final model with R and free R-factors of 19.7 % and 23.6 %, respectively (Table 1,
original article III), with good stereochemistry, as judged from the Ramachandran plot.
The crystal structure reveals two identical homodimers per asymmetric unit with no
conformational changes. The two monomers of a dimer superimpose well with an rms
deviation of 0.21 using C-backbone. The main body of the dimer can be described as
being oval-shaped (Fig. 2, original article III) and consisting of monomers with an /
doubly wound structure (Fig. 10). Each monomer is built of a core of a -sheet of six
parallel -strands (A to F) with the following topology: -1, -1, 3, 1, 1, 1, where
represents a crossover connection between the strands (Fig. 3, original article III). The
central -sheet is sandwiched between two arrays of three parallel -helices (B, C, G
and D, E, F) on both sides (Fig. 10). This folding pattern is conserved in the enzymes
of the SDR superfamily, and it is usually referred to as the basic / SDR fold that
mainly covers the cofactor-binding site. The association of monomers into a dimer is
partly accomplished by the long helices, E and F, comprising the interfacial four-helix
Fig. 10. The overall fold of the two-domain rat (3R)-hydroxyacyl-CoA dehydrogenase
monomer. The bound NAD+ sits on the surface created by the COOH-terminal ends of the strands of the central -sheet. The -helices, E and F, form a four-helix bundle with the
neighbouring monomer at the dimer interface. The novel COOH-terminal (C) domain is not
seen in the other enzymes of the SDR superfamily. The figure was prepared with the SwissPDBViewer (Guex & Peitsch 1997).
54
bundle typical of dimeric and tetrameric SDR proteins. In dhSCP-2L, the E and F
helices from one monomer are in contact with the corresponding helices from the other
monomer in such a way that the helices from different monomers run nearly antiparallel.
In the E-E interface, large hydrophobic and polar side chains face each other, and the
backbone carbonyls are approximately 8 apart. In the F-F interface, a few large
hydrophobic side chains do not point towards the dimer interface. Consequently, the two
F helices are closer to each other (4 ) compared to the E-E interface.
All the SDR protein structures available from the PDB are one-domain enzymes and
the dimeric interactions are dominated solely by the four-helix bundle. In this respect, the
crystal structure of dhSCP-2L is unique because it is the first two-domain enzyme
(Fig. 10) that belongs to the SDR superfamily with a more advanced quaternary
association. The antiparallel -strands, G and H, act as a linker between the NH2terminal NAD(H)-binding domain (Fig. 2, original article III) and the novel COOHterminal domain. Because of the hairpin structure formed by the -strands G and H,
the COOH-terminal domain of monomer A continues to the other side of a dimer, where
it closely interacts with monomer B, and vice versa (Fig. 2, original article III). The point
at which the COOH-terminal domains of both monomers intersect is Trp249 in the strand H. The -strand I and three -helices, CT1, CT2 and H, in the COOHterminal domain are in close proximity with the active site cavity of the neighbouring
monomer (Fig. 5, original article III). This arrangement further strengthens the dimeric
interactions.
Fig. 11. The NAD+ and catalytic triad. The conformation of the bound NAD+ and the distances
of Ser151, Tyr164 and Lys168 are identical to those reported for other SDR enzymes. This
indicates that the hydride transfer catalyzed by the Ser-Tyr-Lys catalytic triad is valid for the
(3R)-hydroxyacyl-CoA dehydrogenase region of rat MFE-2 as well. The close contact between
Asp40 and the hydroxyl groups of the adenine ribose does not leave enough space for the
phosphate group in NADP(H). This guides specificity towards NAD(H). The figure was
prepared with the Swiss-PDBViewer (Guex & Peitsch 1997).
55
In each monomer, the bound NAD+ molecule is in an extended conformation and sits
on a surface created by the COOH-terminal ends of the -strands in the NH2-terminal
cofactor-binding domain (Fig. 3, original article III). The adenine and nicotinamide rings
are oriented roughly perpendicular to the planes of the respective riboses, resulting in an
anti conformation for the adenine ring and a syn conformation for the nicotinamide ring
(Fig. 11). Both ribose rings reveal 2E (C2-endo) puckering. The hydroxyl group of
Tyr164 is hydrogen-bonded (2.6 ) to the 2-hydroxyl group on the nicotinamide ribose.
Thus, the tyrosine is in close proximity with the nicotinamide ring (3.0 ) (Fig. 11). The
-amino group of Lys168 forms a hydrogen bond (3.0 ) with the 3-hydroxyl of the
nicotinamide ribose (Fig. 11), an interaction needed to orient the nicotinamide ring in the
syn conformation. The arrangement of Ser151, Tyr164 and Lys168 around NAD+ and the
syn conformation of the nicotinamide ring strongly support the B-face 4-pro-S hydride
transfer reaction, which is preserved within the enzymes in the SDR superfamily.
5.2 Site-directed mutagenesis studies on (2E)-enoyl-CoA hydratase-2

derived from human MFE-2 (I)
The amino acid sequence alignment of various hydratase-2 domains was used to identify
the conserved protic residues putatively responsible for (2E)-enoyl-CoA hydratase-2
activity (Fig. 2, original article I). The comparison revealed that the hydratase-2 region
contains 12 conserved protic amino acid residues. Additionally, the most conserved part
of hydratase-2 (residues 452-612 in human MFE-2) yielded significant similarity to five
dehydratases of the -subunit of fungal fatty acid synthetase complexes and three
domains of the fatty acid synthetases of prokaryotic microorganisms. Further
characterization of the conserved region allowed the identification of a motif [YF]X(1,2)-[LVIG]-[STGC]-G-D-X-N-P-[LIV]-H-X(5)-[AS], which was named the
hydratese-2 motif (Fig. 2, original article I).
Because the amino acid residues crucial for catalysis are generally highly conserved
and the dehydration-hydration of 2 carboxylates has been shown to take place through
acid-base catalysis, the conserved protic residues in the human MFE-2 were mutated to
alanine and tested in vivo in yeast. Both fox-2 cells transformed with pYE352::HsMFE-2
and wild-type S. cerevisiae UTL-7A cells were able to use oleic acid as a carbon source
(see Materials and methods). However, five mutated variants of the 12 identified protic
residues failed to utilize oleic acid (Fig. 3, original article I), even though all of them
were properly translated as judged by the immunoblotting experiments. In vitro
characterization revealed that the three noncomplementing variants, Y347A, E366A and
D510A, had lost only their hydratase-2 but not dehydrogenase activity (Table 3, original
article I). Therefore, these three mutants were subjected to a further exploration of the
catalytic properties of the hydratase-2 reaction. For this purpose, deleted variants, lacking
the dehydrogenase region, of human MFE-2 were produced as recombinant proteins and
purified. HsMFE-2(dh), HsMFE-2(dhE366A) and HsMFE-2(dhD510A) showed
similar chromatographic properties, but the HsMFE-2(dhY347A) variant could not be
purified with any of the different approaches applied. The composition of secondary
56
structures and the quaternary association of HsMFE-2(dh) and its variants were shown
to be practically identical, as demonstrated by the light scattering and CD measurements
(Fig. 5, original article I).
The kinetic variables were measured in the direction of hydration using (2E)-decenoylCoA as a substrate. The Km and kcat of HsMFE-2(dh) were 8.1 1 M and 196 7 s-1,
which agree with the values estimated for HsMFE-2 isolated from human liver (Jiang et
al. 1996). The kcat value of HsMFE-2(dhE366A) was nearly 100-fold lower than that of
HsMFE-2(dh) at pH 5, but the Km values were practically the same (Table 4, original
article I). When the kcat values were plotted against pH, the curves were bell-shaped (Fig.
6, original article I), with apparent values of pKa1 of 8.2 0.1 (6.5 0.1) and pKa2 of 9.7
0.2 (9.6 0.2). The values in parenthesis are for HsMFE-2(dhE366A). The pH
dependence of catalytic efficiency (kcat/Km) showed different profiles for HsMFE-2(dh)
and HsMFE-2(dhE366A), the catalytic efficiency of HsMFE-2(dhE366A) being 10
(pH 7.0) to 100 (pH 5.0) times lower than that of HsMFE-2(dh). HsMFE-2(dhD510A)
was enzymatically inactive (Table 4, original article I). This demonstrates the importance
of Glu366 and Asp510 for catalysis.
5.3 Crystal structure of the liganded SCP-2-like domain of human

MFE-2 (II)
Multiple amino acid sequence alignment of MFE-2s was used to identify the COOHterminal SCP-2-like domain (SCP-2L) (data not shown). Subsequently, the fragment
Glu618-Leu736 (dhSCP-2L) of human MFE-2 (Fig. 1, original article II) was
expressed in E. coli, purified and crystallized. A dataset of frozen trigonal prismatic
crystals 0.25 0.20 0.40 mm3 in size was collected using synchrotron radiation. The
data was 98.3 % complete with 3.6-fold redundancy to 1.75 resolution (Table 2,
original article II). The data collection statistics are given in Table 4. The liganded
structure of dhSCP-2L was solved at 1.75 resolution by applying molecular
replacement techniques.
Table 4. Data collection statistics of d h SCP-2L with resolution shells.
Resolution shell
Rmerge (%)
Completeness (%)
I/ I
Unique reflections
20.00 3.76
2.3
95.1
42.3
1238
3.76 2.99
2.2
98.0
40.1
1173
2.99 2.61
3.0
97.9
29.5
1176
2.61 2.37
4.3
99.1
20.4
1148
2.37 2.20
6.7
98.6
9.4
1179
2.20 2.07
6.5
99.1
13.3
1156
2.07 1.97
9.1
99.5
9.0
1154
1.97 1.89
15.2
99.6
4.6
1167
1.89 1.81
19.1
99.4
4.2
1136
1.81 1.75
25.9
97.1
3.4
1132
57
Fig. 12. Stereo view of dhSCP-2L. The spatial arrangement of the central -sheet and the
-helices results in a hydrophobic tunnel that traverses the protein. The ligand bound to the
protein is Triton X-100. The arrow indicates a peroxisomal targeting signal, which became
solvent-exposed upon ligand binding and movement of the COOH-terminal helix, helix E.
The figure was prepared with the Swiss-PDBViewer (Guex & Peitsch 1997).
dhSCP-2L has an /-fold composed of five -helices and -strands (Fig. 12). The
overall dimensions of monomeric dhSCP-2L are 39 32 32 3, and it is thus more
spherical in shape than rabbit SCP-2 (Choinowski et al. 2000), which was used as a
search model in the molecular replacement experiment. Five -strands with a mixed sheet
structure of -1, -1, +3, +1 topology form the core of the protein. The solvent-exposed
side of the -sheet layer is mainly populated by polar residues, while the side facing the
interior of the protein is composed of hydrophobic amino acids. Moreover, the central sheet is covered on one side by five -helices (Fig. 12), which are all amphipathic, with
the polar residues facing the solvent and the apolar ones facing the interior of the protein.
The last helix, helix E (Met105-Tyr117), is functionally in a central position with respect
to both ligand binding (see Discussion) and PTS1, which is located at its COOHterminal end (Fig. 12). In contrast to human (Garca et al. 2000) and rabbit (Choinowski
et al. 2000) SCP-2 structures, the peroxisomal targeting signal (-Ala-Lys-LeuOH) is
ordered and fully solvent-exposed in dhSCP-2L.
The hydrophobic tunnel formed by the spatial arrangement of the central -sheet and
the -helices is occupied by an ordered triton molecule. Although Triton X-100 is not a
natural ligand of dhSCP-2L, it could be considered a model molecule for lipids
binding to SCP-2 or SCP-2L proteins. Triton X-100 is positioned at the binding site in
such a way that the hydrophobic end lies deep inside the hydrophobic tunnel, while the
hydrophilic end extends outside the protein (Fig. 6, original article II). Most of the
contacts between the triton molecule and dhSCP-2L are hydrophobic or aromatic
(Table 1, original article II), and the surface plasmon resonance measurements gave a Kd
value of 400 M for Triton X-100. Only one hydrogen bond is formed by the Gln108 and
O55 of the triton molecule near the entrance of the tunnel. The additional cavities close to
the exit of the tunnel and between the helices C and D suggest that molecules larger than
Triton X-100 could bind in the tunnel. However, the tunnel as such, with a diameter of 9
58
and a length of 18 , is large enough to accommodate ligands of the size of various
fatty acids or their CoA derivatives, such as straight-chain and branched-chain fatty acyl
groups.
6 Discussion
6.1 Structural studies on the (3R)-hydroxyacyl-CoA dehydrogenase
region of rat MFE-2 (III)
The NH2-terminal (3R)-hydroxyacyl-CoA dehydrogenase fragment of MFE-2 proteins
belongs to the SDR superfamily. This relationship was already demonstrated by the
amino acid sequence analysis with porcine (Leenders et al. 1994) and human (Adamski et
al. 1995) MFE-2s. The most conserved motifs in this family are Gly-X-X-X-Gly-X-Gly
in the cofactor-binding site and Tyr-X-X-X-Lys, which is part of the active site.
Conservation of these critical residues suggests that the short-chain alcohol
dehydrogenases are functionally related, especially in respect to the stereochemical
course of the catalyzed reaction and the chirality of the accepted substrates.
Crystallographic studies showed the architecture of the active site to be consistent with
the observed stereochemistry of the enzymes (Ghosh et al. 1991, 1994, Tanaka et al.
1996). Additionally, yeast MFE-2 was shown to follow the same stereochemical course
by accepting only the R-isomer of the hydroxyl group of a substrate in vitro (Hiltunen et
al. 1992).
To study the structural basis of the rat (3R)-hydroxyacyl-CoA dehydrogenase region
(dhSCP-2L) of MFE-2, the corresponding fragment was expressed in E. coli. Purified
dhSCP-2L had a kcat value of 3.7 s-1, which is comparable to the kcat value of 3.4 s-1
obtained for full-length recombinant rat MFE-2 (this study). Similar results have been
found for porcine MFE-2 (Leenders et al. 1996b). This showed that the dehydrogenase
produced as itself had similar catalytic properties as when it was part of full-length MFE2.
The crystal structure of dhSCP-2L showed structural similarities with the other
SDR enzymes. Especially the central -sheet (A to F) and the two arrays of three
parallel -helices (B, C, G and D, E, F) surrounding it are virtually identical in
spatial arrangement. This conserved SDR fold covers the regions for cofactor binding and
contains the catalytic triad and -helices, E and F, for dimeric interactions. To date, all
the members of the SDR superfamily have been one-domain enzymes with the conserved
60
SDR fold and, sometimes, short variable amino acid stretches, approximately ten residues
long, in the COOH-terminus. The COOH-terminal extension in dhSCP-2L is much
longer, including about 60 residues with a folding pattern found neither in previously
characterized SDR, nor in other proteins, giving rise to the first two-domain member of
the SDR protein family. The characterized COOH-terminal domain is involved in lining
the active site cavity of the neighbouring monomer. This kind of quaternary association
makes the dimeric interactions more extensive when compared to other dimeric SDR
enzymes. Furthermore, the COOH-terminal domain folds into a circle and provides an
entrance towards the amino acid residues putatively critical for catalysis. Additionally, the
positive clusters in this domain demonstrate interaction sites for the negatively charged
phosphates of the fatty acyl-CoA molecule.
The bound NAD+ is in an extended conformation, as judged from the distance (14.3 )
between the C6 of the adenine and the C2 of the nicotinamide in the syn conformation.
This value agrees with the distances reported for the other crystal structures of SDR
proteins. Furthermore, when compared to other SDR enzymes, the positions of Ser151,
Tyr164 and Lys168 in respect to extended nicotinamide dinucleotide suggest the
occurrence of hydride transfer on the si face of the nicotinamide ring. In this reaction
mechanism, the tyrosine residue acts as a catalytic base to extract hydrogen from the
hydroxyl group of the substrate, while the serine stabilizes the reaction intermediate via
its hydroxyl group. Subsequently, the -hydride ion, liberated from position 3 of the
substrate, is directly transferred to position 4 of the nicotinamide ring.
In dhSCP-2L, the glycine-rich loop of 12 residues between the -strand B and the
-helix C could be linked to substrate preference. This glycine-rich loop, located at the
bottom of the active site cavity, is present among the (3R)-hydroxyacyl-CoA
dehydrogenases accepting substrates of long chain lengths. However, dehydrogenases
acting on short-chain substrates and the non-peroxisomal SDR dehydrogenases lack this
loop region (Qin et al. 2000), suggesting a role in the accommodation of long-chain
substrates.
6.2 Importance of two protic residues for (2E)-enoyl-CoA hydratase-2

activity (I)
The physiological importance of MFE-2 is well demonstrated by the incapability of yeast
fox-2 cells to utilize fatty acids, especially long-chain fatty acids, such as oleic acid (cisC18:1(9)), as a carbon source (Hiltunen et al. 1992). An even more striking feature of the
patients with MFE-2 deficiency is their failure to thrive, resulting in death in early
infancy. A similar phenotype compared to patients with MFE-2 deficiency was observed
with MFE-2 knock-out mice (Baes et al. 2000). In both cases, increased plasma levels
of VLCFAs and branched-chain fatty acids were demonstrated. Despite the extensive
characterization of MFE-2 genetic errors, surprisingly little was known about the
catalytic properties or mechanism of the hydratase-2 reaction when catalyzed by MFE-2.
Since the hydratase-1 reaction catalyzed by either the multifunctional -oxidation
complex of E. coli (He & Yang 1997) or mitochondrial hydratase-1 from rat liver (Kiema
61
et al. 1999) follows a two-residue mechanism involving protic residues, it was
hypothesized that acid-base catalysis is valid for hydratase-2. Furthermore, in the
biosynthesis of unsaturated fatty acids in E. coli, the reaction catalyzed by 3hydroxydecanoyl thiol ester dehydratase was shown to involve the participation of both a
histidine and an aspartic acid residue (Leesong et al. 1996).
In the first approach, multiple amino acid sequence analysis was used to identify the
conserved protic residues within hydratase-2 proteins. Subsequently, these residues were
mutated to alanine, and the ability of the mutated variants to utilize oleic acid in vivo was
tested. Three amino acid residues, Tyr347, Glu366 and Asp510, were identified as critical
only for the hydratase-2 activity of MFE-2. In the second step, the recombinant variants
affecting only hydratase-2 activity were subjected to further characterization in vitro.
Purified HsMFE-2(dh), HsMFE-2(dhE366A) and HsMFE-2(dhD510A) exhibited
dimeric subunit composition similar to the 46 kDa degradation product of MFE-2 from
either human (Jiang et al. 1996) or rat (Li et al. 1990) liver. HsMFE-2(dhY347A)
behaved chromatographically differently and was therefore left uncharacterized. The
enzymatic inactivation of D510A and the decrease in the catalytic efficiency of E366A
resulting from the unfolding of the polypeptide were ruled out by investigating secondary
structural elements with a CD spectropolarimeter using HsMFE-2 as a reference. The pH
dependence curve of kcat/Km of HsMFE-2(dh) was shown to be bell-shaped, suggesting
that two protic residues participate in the catalysis. The estimated pKa2 values were about
the same for both HsMFE-2(dh) and HsMFE-2(dhE366A), whereas the apparent pKa1
of HsMFE-2(dhE366A) dropped from 8.2 to 6.5. Furthermore, the 100-fold decrease in
catalytic efficiency at low pH was not caused by a change in substrate binding because
the Km values remained unchanged over the pH range tested. This suggests that the
negatively charged side-chain of Glu366 acts as a base in catalysis. Additionally,
alignment of HsMFE-2(dh) with the other known hydratase-2 proteins of the oxidation pathway revealed a new fingerprint of hydratase-2. The identified novel
hydratase-2 motif is also conserved in the R-specific dehydratases of fatty acid de novo
synthesis in fungi and some prokaryotes. Even though the catalytic properties of HsMFE2(dhD510A) could not be analyzed because of the overall inactivity, the location of
Asp510 within the conserved hydratase-2 motif indicates its important role in the
hydratase-2 reaction. As a consequence, Asp510 either acts as an acid in the catalysis or
affects the binding of the substrate.
6.3 Ligand binding to the SCP-2-like domain of human MFE-2 (II)

The structure of dhSCP-2L complexed with Triton X-100 demonstrates a hydrophobic
tunnel that traverses the protein molecule and accommodates the bound ligand. The
hydrophobic tunnel was also described in the unliganded rabbit SCP-2 crystal structure
(Choinowski et al. 2000), and the authors hypothesized the putative entrance and exit of
the tunnel. In dhSCP-2L, the triton molecule enters the tunnel through the entrance
built up by the helices D and E and the -strand V. Compared to rabbit SCP-2, the tunnel
is similar in length but wider. Moreover, the positions of the loop between the -strands I
62
and II and the COOH-terminal helix are different in dhSCP-2L and rabbit SCP-2 (Fig.
3, original article II), indicating conformational changes upon ligand binding.
Furthermore, the amino acid residues that form the entrance are conserved in SCP-2 or
SCP-2-like proteins (Fig. 1, original article II). This conservation might reflect functional
similarity within this family.
Human SCP-2 was shown to interact strongly with acyl-CoAs with carbon chain
length of 24 or 26 with Kd of 2-4 nM (Frolov et al. 1996c, Dansen et al. 1999). Similarly,
the surface plasmon resonance binding experiments of various fatty acyl-CoAs
demonstrated the strongest interaction between dhSCP-2L and long- and very-longchain fatty acyl-CoAs (unpublished results). In the mode of binding, the positive cluster
(Arg97-Arg101) near the entrance of the tunnel could serve as a potential interaction site
for the phosphate groups of the CoA molecule. This would indicate that both the
pantetheine group and the fatty acyl tail of a fatty acyl-CoA molecule are localized in the
tunnel. Due to the limited space of the tunnel, the -end of an acyl tail longer than eight
carbons should protrude out of the tunnel. The hydrophobic face of dhSCP-2L, which
also contains the exit of the tunnel, is the potential interaction site with the hydratase-2
domain in full-length MFE-2. This interface could provide a hydrophobic environment
for the longer fatty acyl tails. Such a mode of binding has been observed in (2E)-enoylCoA hydratase-1 (Engel et al. 1998), where the -end of the fatty acid group longer than
C6 enters the hydrophobic region between the subunits of the enzyme. Unfortunately,
attemps to incorporate fatty acyl-CoAs into the crystal of dhSCP-2L to test this
hypothesis, have so far failed.
dhSCP-2L has PTS1 in the extreme COOH-terminus. Proteins with this targeting
signal mediate with the soluble receptor protein, Pex5p, in cytosol. Subsequently, upon
translocation into peroxisome, the Pex5p-cargo protein complex interacts with the
peroxins in peroxisomal membrane (Elgersma et al. 1996, Albertini et al. 1997). So far, a
number of structures of proteins containing PTS1 have been reported, but the structure of
PTS1 has only been defined in rat 3,5-2,4-dienoyl-CoA isomerase (PDB code 1dci,
Modis et al. 1998) and rabbit SCP-2 (PDB code 1c44, Choinowski et al. 2000). However,
both structures are unliganded proteins, and PTS1 is buried in a pocket between two
dimers in dienoyl-CoA isomerase or bound to the surface of the bulk of SCP-2. In the
liganded structure of dhSCP-2L, the COOH-terminal residues have adopted different
conformations. Namely, PTS1 (-Ala-Lys-LeuOH) is ordered and fully solvent-exposed,
being thus able to interact with a receptor molecule of the peroxisomal import system.
Compared to unliganded SCP-2, the exposure of PTS1 results from the movement of the
COOH-terminal helix upon ligand binding. This observation supports the hypothesis
about ligand-assisted protein import into peroxisomes.
7 Conclusions
Mammalian MFE-2 consists of three functional regions: an NH2-terminal (3R)hydroxyacyl-CoA dehydrogenase region followed by an (2E)-enoyl-CoA hydratase-2
domain and a COOH-terminal SCP-2-like domain. The full-length MFE-2 is partially
cleaved in vivo into separate dehydrogenase (34 kDa) and hydratase-2 (45 kDa)
components. As the catalytic properties are similar before and after cleavage, the domains
in MFE-2, obviously do not need structural support from each other to be functional.
Consequently, in this study, both the dehydrogenase region and the SCP-2-like domain
were able to produce as separate recombinant proteins for crystallization experiments.
Additionally, the recombinant 45-kDa hydratase-2 fragment was used to study the
catalytic properties of hydratase-2 reaction.
The crystal structures of both the rat MFE-2 dehydrogenase region and the human
MFE-2 SCP-2-like domain were solved. The dehydrogenase region of MFE-2 belongs to
the SDR superfamily and the structure of rat dehydrogenase revealed the basic / SDR
fold. This fold is composed of a central -sheet of six parallel -strands sandwiched
between two arrays of parallel -helices on both sides, and it is mainly responsible for
cofactor binding. The long -helices, E and F, of one subunit were shown to comprise
a four-helix bundle with the neighbouring subunit at the dimer interface, which is typical
of dimeric SDR enzymes. However, the dimeric interactions are more extensive in rat
dehydrogenase. Namely, the separate COOH-terminal domain, which is not seen among
the known SDR structures, lines the active site cavity of the neighbouring monomer. The
structure revealed a glycine-rich loop that could be linked to substrate preference. This
loop, which is located at the bottom of the active site cavity in rat dehydrogenase, is
absent in dehydrogenases acting on short-chain substrates, suggesting a role for it in the
accommodation of long-chain fatty acyl-CoAs. Additionally, the conformation of the
bound NAD+ in relation to conserved Ser151, Tyr164 and Lys168 found in other SDR
enzymes allows interpretation of the reaction mechanism, which involves B-face 4-pro-S
hydride transfer.
The SCP-2-like domain was shown to be monomeric and to have the same fold as the
previously determined crystal structure of rabbit SCP-2. Both proteins are composed of a
-sheet covered on one side by -helices. The structure showed a hydrophobic tunnel
traversing the protein similar to rabbit SCP-2. Nevertheless, the tunnel was, this time,
64
occupied by an ordered Triton X-100 molecule, an analogue of a lipid molecule. This
demonstrated the ligand-binding site and, consequently, the entrance and exit of the
tunnel. The ligand binding to the human SCP-2-like domain caused changes in the
structure. Especially, the COOH-terminal helix, helix E, had moved relative to its position
in the unliganded rabbit SCP-2 structure. Therefore, the PTS1 located after helix E
became solvent-exposed and thus able to interact with Pex5p, the soluble receptor
molecule of the peroxisomal import system. This suggests ligand-assisted protein import
into peroxisomes.
The role of the SCP-2-like domain in MFE-2, however, remains to be resolved. SCP-2
and SCP-2-like domain with similar folds may associate with the degradation of longchain and very-long-chain fatty acids. When occupied by long-chain fatty acyl-CoA,
SCP-2 formed specific complexes with acyl-CoA oxidase, the first enzyme of the
peroxisomal -oxidation cycle. Furthermore, the peroxisomal thiolase, SCPx, which has
SCP-2 as a COOH-terminal domain, cleaves long-chain 3-ketoacyl-CoAs. Consequently,
the SCP-2-like domain, in MFE-2, could be needed to provide additional space for
binding longer substrates, as it has been shown that one of the physiological roles of
MFE-2 is the degradation of VLCFAs.
Site-directed mutagenesis studies indicated the importance of conserved protic
residues for the hydration reaction catalyzed by the central hydratase-2 region or the
folding of MFE-2. In vitro characterization of the enzymatic properties of human
recombinant hydratase-2 revealed that the hydratase-2 reaction involves an acid and a
base, as demonstrated by the bell-shaped curve of the pH dependence of catalytic
efficiency. Glu366 and Asp510 were shown to be the amino acid residues essential for
catalysis, with Glu366 putatively acting as a base. The importance of Asp510 for the
hydratase-2 reaction was further supported by its localization in a novel conserved
hydratase-2 motif. This motif was also found in the dehydratase region of the -subunit of
the fungal fatty acid synthetase complexes. Similar observations are often made regarding
the amino acid residues around an active site indicating conservation of a reaction
mechanism in otherwise distantly related enzymes. A deeper understanding of the
mechanism of the hydratase-2 reaction could be inferred if the high-resolution structure
of hydratase-2 were available.
8 References
van Aalten DM, DiRusso CC, Knudsen J & Wierenga RK (2000) Crystal structure of FadR, a fatty
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Studies of Peroxisome

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Studies of Peroxisome

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STRUCTURE-FUNCTION

STUDIES OF THE MAMMALIAN

Academic Dissertation to be presented with the assent of

ALSO AVAILABLE IN PRINTED FORMAT

Haapalainen, Antti, Structure-function studies of the mammalian peroxisomal

Keywords: -oxidation, dehydrogenase, hydratase, SCP-2, SDR

Oulu, August 2002

List of original articles

3 Outlines of the present study .........................................................................................43

2 Review of the literature

2.1.1 Transport of fatty acids

2.1.2 Compartmentalization of fatty acid oxidation

2.1.3 Activation of fatty acids prior to -oxidation

2.2 Peroxisomal -oxidation system

2.2.2 Peroxisomal targeting signals

2.2.2.1 Additional targeting signals

2.2.3 Protein translocation into peroxisomes

2.2.4 Transport of fatty acyl-CoAs across peroxisomal membrane

2.2.5 Peroxisomal -oxidation cycle

2.2.5.2 Second and third steps are catalyzed by two multifunctional

Fig. 4. -Oxidation of branched-chain fatty acyl-CoAs. In addition to very-long-chain fatty

1997) and 5-androstene-3,17-diol (Leenders et al. 1994, Adamski et al. 1995).

2.2.5.3 3-Ketoacyl-CoA thiolases

2.2.5.4 Auxiliary enzymes

2.3 Multifunctionality of MFE-2

2.3.1 Domain structure of various MFE-2s

Glomus mosseae MFE-2

2.3.2 Catalytic properties of MFE-2

Adamski et al. 1995

Adamski et al. 1995

Adamski et al. 1995

Leenders et al. 1996b

Leenders et al. 1996b

Leenders et al. 1996b

Leenders et al. 1996b

Leenders et al. 1996b

Leenders et al. 1996b

Qin et al. 1997a

Qin et al. 1997a

Dieuaide-Noubhani et al. 1996

Qin et al. 1997a

Dieuaide-Noubhani et al. 1996

Qin et al. 1999

Qin et al. 1999

Qin et al. 1999

Qin et al. 2000

Qin et al. 2000

Dehydrogenase fragment (A+/B-)

Qin et al. 1999

Qin et al. 1999

Qin et al. 1999

Qin et al. 1999

Qin et al. 1999

Qin et al. 1999

Jiang et al. 1996

Jiang et al. 1996

Jiang et al. 1996

Jiang et al. 1996

Jiang et al. 1996

Jiang et al. 1996

Jiang et al. 1996

Jiang et al. 1996

Leenders et al. 1996b

Leenders et al. 1996b