1
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Sridhar S, Kiema T, Schmitz W, Widersten M, Wierenga RK. Structural enzymology studies with the substrate 3S-hydroxybutanoyl-CoA: bifunctional MFE1 is a less efficient dehydrogenase than monofunctional HAD. FEBS Open Bio 2024; 14:655-674. [PMID: 38458818 PMCID: PMC10988713 DOI: 10.1002/2211-5463.13786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/08/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Multifunctional enzyme, type-1 (MFE1) catalyzes the second and third step of the β-oxidation cycle, being, respectively, the 2E-enoyl-CoA hydratase (ECH) reaction (N-terminal part, crotonase fold) and the NAD+-dependent, 3S-hydroxyacyl-CoA dehydrogenase (HAD) reaction (C-terminal part, HAD fold). Structural enzymological properties of rat MFE1 (RnMFE1) as well as of two of its variants, namely the E123A variant (a glutamate of the ECH active site is mutated into alanine) and the BCDE variant (without domain A of the ECH part), were studied, using as substrate 3S-hydroxybutanoyl-CoA. Protein crystallographic binding studies show the hydrogen bond interactions of 3S-hydroxybutanoyl-CoA as well as of its 3-keto, oxidized form, acetoacetyl-CoA, with the catalytic glutamates in the ECH active site. Pre-steady state binding experiments with NAD+ and NADH show that the kon and koff rate constants of the HAD active site of monomeric RnMFE1 and the homologous human, dimeric 3S-hydroxyacyl-CoA dehydrogenase (HsHAD) for NAD+ and NADH are very similar, being the same as those observed for the E123A and BCDE variants. However, steady state and pre-steady state kinetic data concerning the HAD-catalyzed dehydrogenation reaction of the substrate 3S-hydroxybutanoyl-CoA show that, respectively, the kcat and kchem rate constants for conversion into acetoacetyl-CoA by RnMFE1 (and its two variants) are about 10 fold lower as when catalyzed by HsHAD. The dynamical properties of dehydrogenases are known to be important for their catalytic efficiency, and it is discussed that the greater complexity of the RnMFE1 fold correlates with the observation that RnMFE1 is a slower dehydrogenase than HsHAD.
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Affiliation(s)
- Shruthi Sridhar
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluFinland
| | | | - Werner Schmitz
- Theodor Boveri Institute of Biosciences (Biocenter)University of WürzburgGermany
| | | | - Rik K. Wierenga
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluFinland
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Dalwani S, Lampela O, Leprovost P, Schmitz W, Juffer A, Wierenga RK, Venkatesan R. Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis β-oxidation trifunctional enzyme. J Struct Biol 2021; 213:107776. [PMID: 34371166 DOI: 10.1016/j.jsb.2021.107776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme. The α -chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) activities and the β -chain provides the 3-ketoacyl-CoA thiolase (KAT) activity. Enzyme kinetic data reported here show that medium and long chain enoyl-CoA molecules are preferred substrates for MtTFE. Modelling studies indicate how the linear medium and long chain acyl chains of these substrates can bind to each of the active sites. In addition, crystallographic binding studies have identified three new CoA binding sites which are different from the previously known CoA binding sites of the three TFE active sites. Structure comparisons provide new insights into the properties of ECH, HAD and KAT active sites of MtTFE. The interactions of the adenine moiety of CoA with loop-2 of the ECH active site cause a conformational change of this loop by which a competent ECH active site is formed. The NAD+ binding domain (domain C) of the HAD part of MtTFE has only a few interactions with the rest of the complex and adopts a range of open conformations, whereas the A-domain of the ECH part is rigidly fixed with respect to the HAD part. Two loops, the CB1-CA1 region and the catalytic CB4-CB5 loop, near the thiolase active site and the thiolase dimer interface, have high B-factors. Structure comparisons suggest that a competent and stable thiolase dimer is formed only when complexed with the α -chains, highlighting the importance of the assembly for the proper functioning of the complex.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Outi Lampela
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Pierre Leprovost
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Werner Schmitz
- Theoder-Boveri-Institut für Biowissenschaften der Universität Würzburg, Würzburg, Germany
| | - Andre Juffer
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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3
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Crystal structure of human mitochondrial trifunctional protein, a fatty acid β-oxidation metabolon. Proc Natl Acad Sci U S A 2019; 116:6069-6074. [PMID: 30850536 DOI: 10.1073/pnas.1816317116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Membrane-bound mitochondrial trifunctional protein (TFP) catalyzes β-oxidation of long chain fatty acyl-CoAs, employing 2-enoyl-CoA hydratase (ECH), 3-hydroxyl-CoA dehydrogenase (HAD), and 3-ketothiolase (KT) activities consecutively. Inherited deficiency of TFP is a recessive genetic disease, manifesting in hypoketotic hypoglycemia, cardiomyopathy, and sudden death. We have determined the crystal structure of human TFP at 3.6-Å resolution. The biological unit of the protein is α2β2 The overall structure of the heterotetramer is the same as that observed by cryo-EM methods. The two β-subunits make a tightly bound homodimer at the center, and two α-subunits are bound to each side of the β2 dimer, creating an arc, which binds on its concave side to the mitochondrial innermembrane. The catalytic residues in all three active sites are arranged similarly to those of the corresponding, soluble monofunctional enzymes. A structure-based, substrate channeling pathway from the ECH active site to the HAD and KT sites is proposed. The passage from the ECH site to the HAD site is similar to those found in the two bacterial TFPs. However, the passage from the HAD site to the KT site is unique in that the acyl-CoA intermediate can be transferred between the two sites by passing along the mitochondrial inner membrane using the hydrophobic nature of the acyl chain. The 3'-AMP-PPi moiety is guided by the positively charged residues located along the "ceiling" of the channel, suggesting that membrane integrity is an essential part of the channel and is required for the activity of the enzyme.
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Abstract
The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid β-oxidation process. Mutations in the two TFP subunits cause mitochondrial trifunctional protein deficiency and acute fatty liver of pregnancy that can lead to death. Here we report a 4.2-Å cryo-electron microscopy α2β2 tetrameric structure of the human TFP. The tetramer has a V-shaped architecture that displays a distinct assembly compared with the bacterial TFPs. A concave surface of the TFP tetramer interacts with the detergent molecules in the structure, suggesting that this region is involved in associating with the membrane. Deletion of a helical hairpin in TFPβ decreases its binding to the liposomes in vitro and reduces its membrane targeting in cells. Our results provide the structural basis for TFP function and have important implications for fatty acid oxidation related diseases.
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5
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Suzuki R, Fujimoto Z, Kaneko S, Hasegawa T, Kuno A. Enhanced Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant. J Appl Glycosci (1999) 2018; 65:1-8. [PMID: 34354506 PMCID: PMC8056907 DOI: 10.5458/jag.jag.jag-2017_011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 11/04/2022] Open
Abstract
Glycoside hydrolases require carboxyl groups as catalysts for their activity. A retaining xylanase from Streptomyces olivaceoviridis E-86 belonging to glycoside hydrolase family 10 possesses Glu128 and Glu236 that respectively function as acid/base and nucleophile. We previously developed a unique mutant of the retaining xylanase, N127S/E128H, whose deglycosylation is triggered by azide. A crystallographic study reported that the transient formation of a Ser–His catalytic dyad in the reaction cycle possibly reduced the azidolysis reaction. In the present study, we engineered a catalytic dyad with enhanced stability by site-directed mutagenesis and crystallographic study of N127S/E128H. Comparison of the Michaelis complexes of N127S/E128H with pNP-X2 and with xylopentaose showed that Ser127 could form an alternative hydrogen bond with Thr82, which disrupts the formation of the Ser–His catalytic dyad. The introduction of T82A mutation in N127S/E128H produces an enhanced first-order rate constant (6 times that of N127S/E128H). We confirmed the presence of a stable Ser–His hydrogen bond in the Michaelis complex of the triple mutant, which forms the productive tautomer of His128 that acts as an acid catalyst. Because the glycosyl azide is applicable in the bioconjugation of glycans by using click chemistry, the enzyme-assisted production of the glycosyl azide may contribute to the field of glycobiology.
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Affiliation(s)
- Ryuichiro Suzuki
- 1 Department of Biological Production, Akita Prefectural University.,2 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University
| | - Zui Fujimoto
- 3 Advanced Analysis Center, National Agriculture and Food Research Organization (NARO)
| | - Satoshi Kaneko
- 4 Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus
| | - Tsunemi Hasegawa
- 2 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University
| | - Atsushi Kuno
- 5 Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST)
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Natarajan SK, Ibdah JA. Role of 3-Hydroxy Fatty Acid-Induced Hepatic Lipotoxicity in Acute Fatty Liver of Pregnancy. Int J Mol Sci 2018; 19:ijms19010322. [PMID: 29361796 PMCID: PMC5796265 DOI: 10.3390/ijms19010322] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
Acute fatty liver of pregnancy (AFLP), a catastrophic illness for both the mother and the unborn offspring, develops in the last trimester of pregnancy with significant maternal and perinatal mortality. AFLP is also recognized as an obstetric and medical emergency. Maternal AFLP is highly associated with a fetal homozygous mutation (1528G>C) in the gene that encodes for mitochondrial long-chain hydroxy acyl-CoA dehydrogenase (LCHAD). The mutation in LCHAD results in the accumulation of 3-hydroxy fatty acids, such as 3-hydroxy myristic acid, 3-hydroxy palmitic acid and 3-hydroxy dicarboxylic acid in the placenta, which are then shunted to the maternal circulation leading to the development of acute liver injury observed in patients with AFLP. In this review, we will discuss the mechanistic role of increased 3-hydroxy fatty acid in causing lipotoxicity to the liver and in inducing oxidative stress, mitochondrial dysfunction and hepatocyte lipoapoptosis. Further, we also review the role of 3-hydroxy fatty acids in causing placental damage, pancreatic islet β-cell glucolipotoxicity, brain damage, and retinal epithelial cells lipoapoptosis in patients with LCHAD deficiency.
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Affiliation(s)
- Sathish Kumar Natarajan
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA.
| | - Jamal A Ibdah
- Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA.
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65212, USA.
- Harry S. Truman Memorial Veterans Medical Center, Columbia, MO 65201, USA.
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7
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Kasaragod P, Midekessa GB, Sridhar S, Schmitz W, Kiema TR, Hiltunen JK, Wierenga RK. Structural enzymology comparisons of multifunctional enzyme, type-1 (MFE1): the flexibility of its dehydrogenase part. FEBS Open Bio 2017; 7:1830-1842. [PMID: 29226071 PMCID: PMC5715344 DOI: 10.1002/2211-5463.12337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/13/2017] [Accepted: 10/14/2017] [Indexed: 12/23/2022] Open
Abstract
Multifunctional enzyme, type‐1 (MFE1) is a monomeric enzyme with a 2E‐enoyl‐CoA hydratase and a 3S‐hydroxyacyl‐CoA dehydrogenase (HAD) active site. Enzyme kinetic data of rat peroxisomal MFE1 show that the catalytic efficiencies for converting the short‐chain substrate 2E‐butenoyl‐CoA into acetoacetyl‐CoA are much lower when compared with those of the homologous monofunctional enzymes. The mode of binding of acetoacetyl‐CoA (to the hydratase active site) and the very similar mode of binding of NAD+ and NADH (to the HAD part) are described and compared with those of their monofunctional counterparts. Structural comparisons suggest that the conformational flexibility of the HAD and hydratase parts of MFE1 are correlated. The possible importance of the conformational flexibility of MFE1 for its biocatalytic properties is discussed. Database Structural data are available in PDB database under the accession number 5MGB.
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Affiliation(s)
- Prasad Kasaragod
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine University of Oulu Finland
| | - Getnet B Midekessa
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine University of Oulu Finland
| | - Shruthi Sridhar
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine University of Oulu Finland
| | - Werner Schmitz
- Theodor Boveri Institute of Biosciences (Biocenter) University of Würzburg Germany
| | - Tiila-Riikka Kiema
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine University of Oulu Finland
| | - Jukka K Hiltunen
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine University of Oulu Finland
| | - Rik K Wierenga
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine University of Oulu Finland
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8
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Barman A, Smitherman C, Souffrant M, Gadda G, Hamelberg D. Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins. J Chem Inf Model 2015; 56:139-47. [DOI: 10.1021/acs.jcim.5b00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Arghya Barman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Crystal Smitherman
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Michael Souffrant
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Departments
of Chemistry and ‡Biology and the §Centers for Diagnostics and Therapeutics and ∥Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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9
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Mugo AN, Kobayashi J, Mikami B, Yoshikane Y, Yagi T, Ohnishi K. Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD⁺-dependent dismutase from Mesorhizobium loti. Biochem Biophys Res Commun 2014; 456:35-40. [PMID: 25446130 DOI: 10.1016/j.bbrc.2014.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/11/2014] [Indexed: 10/24/2022]
Abstract
5-Formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase (FHMPCDH) from Mesorhizobium loti is the fifth enzyme in degradation pathway I for pyridoxine. The enzyme catalyzes a dismutation reaction: the oxidation of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) to 3-hydroxy-2-methylpyridine 4,5-dicarboxylic acid with NAD(+) and reduction of FHMPC to 4-pyridoxic acid with NADH. FHMPCDH belongs to the l-3-hydroxyacyl-CoA dehydrogenase (HAD) family. The crystal structure was determined by molecular replacement and refined to a resolution of 1.55Å (R-factor of 16.4%, Rfree=19.4%). There were two monomers in the asymmetric unit. The overall structure of the monomer consisted of N- and C-terminal domains connected by a short linker loop. The monomer was similar to members of the HAD family (RMSD=1.9Å). The active site was located between the domains and highly conserved to that of human heart l-3-hydroxyacyl-CoA dehydrogenase (HhHAD). His-Glu catalytic dyad, a serine and two asparagine residues of HhHAD were conserved. Ser116, His137 and Glu149 in FHMPCDH are connected by a hydrogen bonding network forming a catalytic triad. The functions of the active site residues in the reaction mechanism are discussed.
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Affiliation(s)
- Andrew Njagi Mugo
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Jun Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Yu Yoshikane
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Toshiharu Yagi
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan.
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10
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Eltayeb MM, Arima J, Mori N. Alanine-scanning mutation approach for classification of the roles of conserved residues in the activity and substrate affinity of l-carnitine dehydrogenase. Biotechnol Lett 2014; 36:309-17. [DOI: 10.1007/s10529-013-1357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/11/2013] [Indexed: 11/29/2022]
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11
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Identification of residues essential for the activity and substrate affinity of L-carnitine dehydrogenase. Mol Biotechnol 2013; 55:268-76. [PMID: 23794271 DOI: 10.1007/s12033-013-9678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recently, two L-carnitine dehydrogenases from soil isolates Rhizobium sp. (Rs-CDH) and Xanthomonas translucens (Xt-CDH) have demonstrated to exhibit mutually differing affinities toward L-carnitine. To identify residues important for affinity to the substrate, we compared the primary structure of Xt-CDH and Rs-CDH with the recognized 3D structure of 3-hydroxyacyl-CoA dehydrogenase (PDB code: 1F0Y). Then, six residues of Xt-CDH (Phe143, Gly188, Ile190, Ala191, Gly223, and Ala224) and the corresponding residues of Rs-CDH (Tyr140, Ala185, Val187, Gly188, Ser220, and Phe221) were selected for further mutagenesis. The residues of Xt-CDH were replaced with that of Rs-CDH at the corresponding position and vice versa. All Rs-CDH mutants exhibited slight effects on substrate affinity, except for the double mutants Rs-V187I/G188A, which was devoid of enzyme activity. All Xt-CDH mutants showed different K m values. Xt-F143Y caused a higher increase in the K m value. Furthermore, the kinetic parameters of 10 mutants at Xt-F143 and Rs-Y140 were investigated. All Rs-Y140 mutants, except aromatic residues (Phe, Trp), produced proteins that were almost entirely devoid of enzyme activity and with disrupted affinity to L-carnitine. All Xt-F143 variants showed a marked reduction (P ≤ 0.05) in enzyme activity. Overall, our results suggest that the aromatic rings of Tyr140 in Rs-CDH and Phe143 of Xt-CDH are essential for substrate recognition.
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12
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Kasaragod P, Schmitz W, Hiltunen JK, Wierenga RK. The isomerase and hydratase reaction mechanism of the crotonase active site of the multifunctional enzyme (type-1), as deduced from structures of complexes with 3S-hydroxy-acyl-CoA. FEBS J 2013; 280:3160-75. [PMID: 23351063 DOI: 10.1111/febs.12150] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/10/2013] [Accepted: 01/15/2013] [Indexed: 01/20/2023]
Abstract
The multifunctional enzyme, type-1 (MFE1) is involved in several lipid metabolizing pathways. It catalyses: (a) enoyl-CoA isomerase and (b) enoyl-CoA hydratase (EC 4.2.1.17) reactions in its N-terminal crotonase part, as well as (3) a 3S-hydroxy-acyl-CoA dehydrogenase (HAD; EC 1.1.1.35) reaction in its C-terminal 3S-hydroxy-acyl-CoA dehydrogenase part. Crystallographic binding studies with rat peroxisomal MFE1, using unbranched and branched 2E-enoyl-CoA substrate molecules, show that the substrate has been hydrated by the enzyme in the crystal and that the product, 3S-hydroxy-acyl-CoA, remains bound in the crotonase active site. The fatty acid tail points into an exit tunnel shaped by loop-2. The thioester oxygen is bound in the classical oxyanion hole of the crotonase fold, stabilizing the enolate reaction intermediate. The structural data of these enzyme product complexes suggest that the catalytic base, Glu123, initiates the isomerase reaction by abstracting the C2-proton from the substrate molecule. Subsequently, in the hydratase reaction, Glu123 completes the catalytic cycle by reprotonating the C2 atom. A catalytic water, bound between the OE1-atoms of the two catalytic glutamates, Glu103 and Glu123, plays an important role in the enoyl-CoA isomerase and the enoyl-CoA hydratase reaction mechanism of MFE1. The structural variability of loop-2 between MFE1 and its monofunctional homologues correlates with differences in the respective substrate preferences and catalytic rates.
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Affiliation(s)
- Prasad Kasaragod
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Oulu, Finland
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13
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Cantu DC, Dai T, Beversdorf ZS, Reilly PJ. Structural classification and properties of ketoacyl reductases, hydroxyacyl dehydratases and enoyl reductases. Protein Eng Des Sel 2012; 25:803-11. [DOI: 10.1093/protein/gzs050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Identification of important residues in diketoreductase from Acinetobacter baylyi by molecular modeling and site-directed mutagenesis. Biochimie 2011; 94:471-8. [PMID: 21893158 DOI: 10.1016/j.biochi.2011.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/23/2011] [Indexed: 11/21/2022]
Abstract
Diketoreductase (DKR) from Acinetobacter baylyi exhibits a unique property of double reduction of a β, δ-diketo ester with excellent stereoselectivity, which can serve as an efficient biocatalyst for the preparation of an important chiral intermediate for cholesterol lowering statin drugs. Taken the advantage of high homology between DKR and human heart 3-hydroxyacyl-CoA dehydrogenase (HAD), a molecular model was created to compare the tertiary structures of DKR and HAD. In addition to the possible participation of His-143 in the enzyme catalysis by pH profile, three key amino acid residues, Ser-122, His-143 and Glu-155, were identified and mutated to explore the possibility of involving in the catalytic process. The catalytic activities for mutants S122A/C, H143A/K and E155Q were below detectable level, while their binding affinities to the diketo ester substrate and cofactor NADH did not change obviously. The experimental results were further supported by molecular docking, suggesting that Ser-122 and His-143 were essential for the proton transfer to the carbonyl functional groups of the substrate. Moreover, Glu-155 was crucial for maintaining the proper orientation and protonation of the imidazole ring of His-143 for efficient catalysis.
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15
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Asada Y, Kuroishi C, Ukita Y, Sumii R, Endo S, Matsunaga T, Hara A, Kunishima N. Dimeric Crystal Structure of Rabbit l-Gulonate 3-Dehydrogenase/λ-Crystallin: Insights into the Catalytic Mechanism. J Mol Biol 2010; 401:906-20. [DOI: 10.1016/j.jmb.2010.06.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/24/2010] [Accepted: 06/30/2010] [Indexed: 10/19/2022]
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16
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Arent S, Christensen CE, Pye VE, Nørgaard A, Henriksen A. The multifunctional protein in peroxisomal beta-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. J Biol Chem 2010; 285:24066-77. [PMID: 20463021 PMCID: PMC2911295 DOI: 10.1074/jbc.m110.106005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 04/12/2010] [Indexed: 11/06/2022] Open
Abstract
Plant fatty acids can be completely degraded within the peroxisomes. Fatty acid degradation plays a role in several plant processes including plant hormone synthesis and seed germination. Two multifunctional peroxisomal isozymes, MFP2 and AIM1, both with 2-trans-enoyl-CoA hydratase and l-3-hydroxyacyl-CoA dehydrogenase activities, function in mouse ear cress (Arabidopsis thaliana) peroxisomal beta-oxidation, where fatty acids are degraded by the sequential removal of two carbon units. A deficiency in either of the two isozymes gives rise to a different phenotype; the biochemical and molecular background for these differences is not known. Structure determination of Arabidopsis MFP2 revealed that plant peroxisomal MFPs can be grouped into two families, as defined by a specific pattern of amino acid residues in the flexible loop of the acyl-binding pocket of the 2-trans-enoyl-CoA hydratase domain. This could explain the differences in substrate preferences and specific biological functions of the two isozymes. The in vitro substrate preference profiles illustrate that the Arabidopsis AIM1 hydratase has a preference for short chain acyl-CoAs compared with the Arabidopsis MFP2 hydratase. Remarkably, neither of the two was able to catabolize enoyl-CoA substrates longer than 14 carbon atoms efficiently, suggesting the existence of an uncharacterized long chain enoyl-CoA hydratase in Arabidopsis peroxisomes.
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Affiliation(s)
- Susan Arent
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Caspar E. Christensen
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Valerie E. Pye
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Allan Nørgaard
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
| | - Anette Henriksen
- From the Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark
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17
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Parkot J, Gröger H, Hummel W. Purification, cloning, and overexpression of an alcohol dehydrogenase from Nocardia globerula reducing aliphatic ketones and bulky ketoesters. Appl Microbiol Biotechnol 2009; 86:1813-20. [DOI: 10.1007/s00253-009-2385-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/24/2009] [Accepted: 11/24/2009] [Indexed: 10/20/2022]
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18
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Asada Y, Kuroishi C, Ukita Y, Sumii R, Endo S, Matsunaga T, Hara A, Kunishima N. Crystallization and preliminary X-ray crystallographic analysis of rabbit L-gulonate 3-dehydrogenase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:228-30. [PMID: 18323616 PMCID: PMC2374150 DOI: 10.1107/s1744309108004326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 02/13/2008] [Indexed: 11/10/2022]
Abstract
Rabbit L-gulonate 3-dehydrogenase was crystallized using the oil-microbatch method at 295 K. X-ray diffraction data were collected to 1.70 A resolution from a crystal at 100 K using synchrotron radiation. The crystal belongs to the C-centred monoclinic space group C2, with unit-cell parameters a = 71.81, b = 69.08, c = 65.64 A, beta = 102.7 degrees. Assuming the presence of a monomeric protomer in the asymmetric unit gives a V(M) value of 2.21 A(3) Da(-1) and a solvent content of 44.4%. A cocrystal with NADH, which was isomorphous to the apo form, was also prepared and diffraction data were collected to 1.85 A resolution using Cu Kalpha radiation at 100 K.
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Affiliation(s)
- Yukuhiko Asada
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Chizu Kuroishi
- SR System Biology Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoko Ukita
- SR System Biology Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Rie Sumii
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Mitahora-higashi, Gifu 502-8585, Japan
| | - Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Mitahora-higashi, Gifu 502-8585, Japan
| | - Toshiyuki Matsunaga
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Mitahora-higashi, Gifu 502-8585, Japan
| | - Akira Hara
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Mitahora-higashi, Gifu 502-8585, Japan
| | - Naoki Kunishima
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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19
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Faye A, Esnous C, Price NT, Onfray MA, Girard J, Prip-Buus C. Rat Liver Carnitine Palmitoyltransferase 1 Forms an Oligomeric Complex within the Outer Mitochondrial Membrane. J Biol Chem 2007; 282:26908-26916. [PMID: 17650509 DOI: 10.1074/jbc.m705418200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carnitine palmitoyltransferase (CPT) 1A catalyzes the rate-limiting step in the transport of long chain acyl-CoAs from cytoplasm to the mitochondrial matrix by converting them to acylcarnitines. Located within the outer mitochondrial membrane, CPT1A activity is inhibited by malonyl-CoA, its allosteric inhibitor. In this study, we investigate for the first time the quaternary structure of rat CPT1A. Chemical cross-linking studies using intact mitochondria isolated from fed rat liver or from Saccharomyces cerevisiae expressing CPT1A show that CPT1A self-assembles into an oligomeric complex. Size exclusion chromatography experiments using solubilized mitochondrial extracts suggest that the fundamental unit of its quaternary structure is a trimer. When studied in blue native-PAGE, the CPT1A hexamer could be observed, however, suggesting that under these native conditions CPT1A trimers might be arranged as dimers. Moreover, the oligomeric state of CPT1A was found unchanged by starvation and by streptozotocin-induced diabetes, conditions characterized by changes in malonyl-CoA sensitivity of CPT1A. Finally, gel filtration analysis of several yeast-expressed chimeric CPTs demonstrates that the first 147 N-terminal residues of CPT1A, encompassing its two transmembrane segments, trigger trimerization independently of its catalytic C-terminal domain. Deletion of residues 1-82, including transmembrane 1, did not abrogate oligomerization, but the latter is limited to a trimer by the presence of the large catalytic C-terminal domain on the cytosolic face of mitochondria. Based on these findings, we proposed that the oligomeric structure of CPT1A would allow the newly formed acylcarnitines to gain direct access into the intermembrane space, hence facilitating substrate channeling.
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Affiliation(s)
- Audrey Faye
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), 75014 Paris, France; INSERM, U567, Paris 75014, France
| | - Catherine Esnous
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), 75014 Paris, France; INSERM, U567, Paris 75014, France
| | - Nigel T Price
- Department of Cell Biochemistry, Hannah Research Institute, Ayr KA6 5HL, Scotland, United Kingdom
| | - Marie Anne Onfray
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), 75014 Paris, France; INSERM, U567, Paris 75014, France
| | - Jean Girard
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), 75014 Paris, France; INSERM, U567, Paris 75014, France
| | - Carina Prip-Buus
- Institut Cochin, Université Paris Descartes, CNRS (UMR8104), 75014 Paris, France; INSERM, U567, Paris 75014, France.
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20
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Liu X, Deng G, Chu X, Li N, Wu L, Li D. Formation of an enolate intermediate is required for the reaction catalyzed by 3-hydroxyacyl-CoA dehydrogenase. Bioorg Med Chem Lett 2007; 17:3187-90. [PMID: 17383181 DOI: 10.1016/j.bmcl.2007.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 03/06/2007] [Accepted: 03/08/2007] [Indexed: 01/24/2023]
Abstract
Fluorinated substrate analogs were synthesized and incubated with rat liver 3-hydroxyacyl-CoA dehydrogenase, which reveals that the formation of an enolate intermediate is required for the reaction catalyzed by the enzyme.
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Affiliation(s)
- Xiaojun Liu
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, PR China
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21
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Taskinen JP, Kiema TR, Hiltunen JK, Wierenga RK. Structural Studies of MFE-1: the 1.9Å Crystal Structure of the Dehydrogenase Part of Rat Peroxisomal MFE-1. J Mol Biol 2006; 355:734-46. [PMID: 16330050 DOI: 10.1016/j.jmb.2005.10.085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 10/26/2005] [Accepted: 10/26/2005] [Indexed: 10/25/2022]
Abstract
The 1.9 A structure of the C-terminal dehydrogenase part of the rat peroxisomal monomeric multifunctional enzyme type 1 (MFE-1) has been determined. In this construct (residues 260-722 and referred to as MFE1-DH) the N-terminal hydratase part of MFE-1 has been deleted. The structure of MFE1-DH shows that it consists of an N-terminal helix, followed by a Rossmann-fold domain (domain C), followed by two tightly associated helical domains (domains D and E), which have similar topology. The structure of MFE1-DH is compared with the two known homologous structures: human mitochondrial 3-hydroxyacyl-CoA dehydrogenase (HAD; sequence identity is 33%) (which is dimeric and monofunctional) and with the dimeric multifunctional alpha-chain (alphaFOM; sequence identity is 28%) of the bacterial fatty acid beta-oxidation alpha2beta2-multienzyme complex. Like MFE-1, alphaFOM has an N-terminal hydratase part and a C-terminal dehydrogenase part, and the structure comparisons show that the N-terminal helix of MFE1-DH corresponds to the alphaFOM linker helix, located between its hydratase and dehydrogenase part. It is also shown that this helix corresponds to the C-terminal helix-10 of the hydratase/isomerase superfamily, suggesting that functionally it belongs to the N-terminal hydratase part of MFE-1.
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Affiliation(s)
- Jukka P Taskinen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, P.O. Box 3000, FIN-90014, Finland
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22
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Li A, Itoh T, Taguchi T, Xiang T, Ebizuka Y, Ichinose K. Functional studies on a ketoreductase gene from Streptomyces sp. AM-7161 to control the stereochemistry in medermycin biosynthesis. Bioorg Med Chem 2005; 13:6856-63. [PMID: 16169737 DOI: 10.1016/j.bmc.2005.07.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Revised: 07/25/2005] [Accepted: 07/26/2005] [Indexed: 10/25/2022]
Abstract
Medermycin shows the same trans (3S,15R) configuration as actinorhodin in the pyran ring crucial for its bioactivity. One medermycin biosynthetic gene, med-ORF12, is assumed to be involved in the stereochemical control at C-3. Functional complementation suggested that it plays a similar role as actVI-ORF1 previously proved to determine the stereospecificity at C-3 in actinorhodin biosynthesis. Co-expression of med-ORF12 with actinorhodin early biosynthetic genes further demonstrated that med-ORF12 encodes a ketoreductase responsible for the enantioselective reduction at C-3 in the formation of the pyran ring.
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Affiliation(s)
- Aiying Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
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23
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Bhaumik P, Koski MK, Glumoff T, Hiltunen JK, Wierenga RK. Structural biology of the thioester-dependent degradation and synthesis of fatty acids. Curr Opin Struct Biol 2005; 15:621-8. [PMID: 16263264 DOI: 10.1016/j.sbi.2005.10.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 07/14/2005] [Accepted: 10/21/2005] [Indexed: 12/30/2022]
Abstract
The fatty acid degradation and synthesis pathways consist of the same four chemical transformations. These transformations are facilitated by conjugating the fatty acid, via a thioester bond, to coenzyme A or acyl carrier protein in, respectively, the degradation and synthesis pathways. These pathways are compartmentalized in the peroxisomes, mitochondria and cytosol of eukaryotic cells. Current structural knowledge of the enzymes comprising these pathways shows that the approximately 130 entries in the RCSB Protein Data Bank can be grouped into seven superfamilies. Multifunctional enzymes are important in both pathways.
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Affiliation(s)
- Prasenjit Bhaumik
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Linnanmaa, PO Box 3000, FIN-90014 Oulu, Finland
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24
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Yang SY, He XY, Schulz H. 3-Hydroxyacyl-CoA dehydrogenase and short chain 3-hydroxyacyl-CoA dehydrogenase in human health and disease. FEBS J 2005; 272:4874-83. [PMID: 16176262 DOI: 10.1111/j.1742-4658.2005.04911.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Hydroxyacyl-CoA dehydrogenase (HAD) functions in mitochondrial fatty acid beta-oxidation by catalyzing the oxidation of straight chain 3-hydroxyacyl-CoAs. HAD has a preference for medium chain substrates, whereas short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD) acts on a wide spectrum of substrates, including steroids, cholic acids, and fatty acids, with a preference for short chain methyl-branched acyl-CoAs. Therefore, HAD should not be referred to as SCHAD. SCHAD is not a member of the HAD family, but instead, belongs to the short chain dehydrogenase/reductase superfamily. Previously reported cases of SCHAD deficiency are due to an inherited HAD deficiency. SCHAD, also known as 17beta-hydroxysteroid dehydrogenase type 10, is important in brain development and aging. Abnormal levels of SCHAD in certain brain regions may contribute to the pathogenesis of some neural disorders. The human SCHAD gene and its protein product, SCHAD, are potential targets for intervention in conditions, such as Alzheimer's disease, Parkinson's disease, and an X-linked mental retardation, that may arise from the impaired degradation of branched chain fatty acid and isoleucine.
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Affiliation(s)
- Song-Yu Yang
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, 10314, USA.
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25
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Taguchi T, Kunieda K, Takeda-Shitaka M, Takaya D, Kawano N, Kimberley MR, Booker-Milburn KI, Stephenson GR, Umeyama H, Ebizuka Y, Ichinose K. Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics. Bioorg Med Chem 2004; 12:5917-27. [PMID: 15498668 DOI: 10.1016/j.bmc.2004.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 08/16/2004] [Accepted: 08/17/2004] [Indexed: 10/26/2022]
Abstract
Two ketoreductases, RED1 and RED2, are involved in the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2) and dihydrogranaticin in S. violaceoruber Tu22, respectively. They are responsible for the stereospecific reductions of the bicyclic intermediate to give (S)- or (R)-DNPA, although there is no similarity between their amino acid sequences. Biotransformation using synthetic analogous substrates revealed that the substrate specificities are quite different. Homology modelling studies and site directed mutagenesis showed remarkable differences in three-dimensional structures and catalytic mechanisms between RED1 and RED2.
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Affiliation(s)
- Takaaki Taguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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26
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Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K. Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex. EMBO J 2004; 23:2745-54. [PMID: 15229654 PMCID: PMC514956 DOI: 10.1038/sj.emboj.7600298] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Accepted: 06/04/2004] [Indexed: 12/29/2022] Open
Abstract
The atomic view of the active site coupling termed channelling is a major subject in molecular biology. We have determined two distinct crystal structures of the bacterial multienzyme complex that catalyzes the last three sequential reactions in the fatty acid beta-oxidation cycle. The alpha2beta2 heterotetrameric structure shows the uneven ring architecture, where all the catalytic centers of 2-enoyl-CoA hydratase (ECH), L-3-hydroxyacyl-CoA dehydrogenase (HACD) and 3-ketoacyl-CoA thiolase (KACT) face a large inner solvent region. The substrate, anchored through the 3'-phosphate ADP moiety, allows the fatty acid tail to pivot from the ECH to HACD active sites, and finally to the KACT active site. Coupling with striking domain rearrangements, the incorporation of the tail into the KACT cavity and the relocation of 3'-phosphate ADP bring the reactive C2-C3 bond to the correct position for cleavage. The alpha-helical linker specific for the multienzyme contributes to the pivoting center formation and the substrate transfer through its deformation. This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex.
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Affiliation(s)
- Momoyo Ishikawa
- Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan
| | - Daisuke Tsuchiya
- Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan
| | - Takuji Oyama
- Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan
| | - Yasuo Tsunaka
- Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan
| | - Kosuke Morikawa
- Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan
- Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan. Tel.: +81 66 872 8211; Fax: +81 66 872 8210; E-mail:
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27
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Napal L, Dai J, Treber M, Haro D, Marrero PF, Woldegiorgis G. A single amino acid change (substitution of the conserved Glu-590 with alanine) in the C-terminal domain of rat liver carnitine palmitoyltransferase I increases its malonyl-CoA sensitivity close to that observed with the muscle isoform of the enzyme. J Biol Chem 2003; 278:34084-9. [PMID: 12826662 DOI: 10.1074/jbc.m305826200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carnitine palmitoyltransferase I (CPTI) catalyzes the conversion of long-chain fatty acyl-CoAs to acylcarnitines in the presence of l-carnitine. To determine the role of the highly conserved C-terminal glutamate residue, Glu-590, on catalysis and malonyl-CoA sensitivity, we separately changed the residue to alanine, lysine, glutamine, and aspartate. Substitution of Glu-590 with aspartate, a negatively charged amino acid with only one methyl group less than the glutamate residue in the wild-type enzyme, resulted in complete loss in the activity of the liver isoform of CPTI (L-CPTI). A change of Glu-590 to alanine, glutamine, and lysine caused a significant 9- to 16-fold increase in malonyl-CoA sensitivity but only a partial decrease in catalytic activity. Substitution of Glu-590 with neutral uncharged residues (alanine and glutamine) and/or a basic positively charged residue (lysine) significantly increased L-CPTI malonyl-CoA sensitivity to the level observed with the muscle isoform of the enzyme, suggesting the importance of neutral and/or positive charges in the switch of the kinetic properties of L-CPTI to the muscle isoform of CPTI. Since a conservative substitution of Glu-590 to aspartate but not glutamine resulted in complete loss in activity, we suggest that the longer side chain of glutamate is essential for catalysis and malonyl-CoA sensitivity. This is the first demonstration whereby a single residue mutation in the C-terminal region of the liver isoform of CPTI resulted in a change of its kinetic properties close to that observed with the muscle isoform of the enzyme and provides the rationale for the high malonyl-CoA sensitivity of muscle CPTI compared with the liver isoform of the enzyme.
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Affiliation(s)
- Laura Napal
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, Beaverton, Oregon 97006-8921, USA
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28
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Treber M, Dai J, Woldegiorgis G. Identification by mutagenesis of conserved arginine and glutamate residues in the C-terminal domain of rat liver carnitine palmitoyltransferase I that are important for catalytic activity and malonyl-CoA sensitivity. J Biol Chem 2003; 278:11145-9. [PMID: 12540837 DOI: 10.1074/jbc.m210566200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carnitine palmitoyltransferase I (CPTI) catalyzes the conversion of long chain fatty acyl-CoAs to acylcarnitines in the presence of l-carnitine. To determine the role of the conserved glutamate residue, Glu-603, on catalysis and malonyl-CoA sensitivity, we separately changed the residue to alanine, histidine, glutamine, and aspartate. Substitution of Glu-603 with alanine or histidine resulted in complete loss of L-CPTI activity. A change of Glu-603 to glutamine caused a significant decrease in catalytic activity and malonyl-CoA sensitivity. Substitution of Glu-603 with aspartate, a negatively charged amino acid with only one methyl group less than the glutamate residue in the wild type enzyme, resulted in partial loss in CPTI activity and a 15-fold decrease in malonyl-CoA sensitivity. The mutant L-CPTI with a replacement of the conserved Arg-601 or Arg-606 with alanine also showed over 40-fold decrease in malonyl-CoA sensitivity, suggesting that these two conserved residues may be important for substrate and inhibitor binding. Since a conservative substitution of Glu-603 to aspartate or glutamine resulted in partial loss of activity and malonyl-CoA sensitivity, it further suggests that the negative charge and the longer side chain of glutamate are essential for catalysis and malonyl-CoA sensitivity. We predict that this region of L-CPTI spanning these conserved C-terminal residues may be the region of the protein involved in binding the CoA moiety of palmitoyl-CoA and malonyl-CoA and/or the putative low affinity acyl-CoA/malonyl-CoA binding site.
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Affiliation(s)
- Michelle Treber
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health & Science University, Beaverton, Oregon 97006-8921
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29
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Zheng G, Dai J, Woldegiorgis G. Identification by mutagenesis of a conserved glutamate (Glu487) residue important for catalytic activity in rat liver carnitine palmitoyltransferase II. J Biol Chem 2002; 277:42219-23. [PMID: 12200419 DOI: 10.1074/jbc.m202914200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mitochondrial membranes express two active but distinct carnitine palmitoyltransferases: carnitine palmitoyltransferase I (CPTI), which is malonyl coA-sensitive and detergent-labile; and carnitine palmitoyltransferase II (CPTII), which is malonyl coA-insensitive and detergent-stable. To determine the role of the highly conserved C-terminal acidic residues glutamate 487 (Glu(487)) and glutamate 500 (Glu(500)) on catalytic activity in rat liver CPTII, we separately mutated these residues to alanine, aspartate, or lysine, and the effect of the mutations on CPTII activity was determined in the Escherichia coli-expressed mutants. Substitution of Glu(487) with alanine, aspartate, or lysine resulted in almost complete loss in CPTII activity. Because a conservative substitution mutation of this residue, Glu(487) with aspartate (E487D), resulted in a 97% loss in activity, we predicted that Glu(487) would be at the active-site pocket of CPTII. The substantial loss in CPTII activity observed with the E487K mutant, along with the previously reported loss in activity observed in a child with a CPTII deficiency disease, establishes that Glu(487) is crucial for maintaining the configuration of the liver isoform of the CPTII active site. Substitution of the conserved Glu(500) in CPTII with alanine or aspartate reduced the V(max) for both substrates, suggesting that Glu(500) may be important in stabilization of the enzyme-substrate complex. A conservative substitution of Glu(500) to aspartate resulted in a significant decrease in the V(max) for the substrates. Thus, Glu(500) may play a role in substrate binding and catalysis. Our site-directed mutagenesis studies demonstrate that Glu(487) in the liver isoform of CPTII is essential for catalysis.
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Affiliation(s)
- Guolu Zheng
- Department of Biochemistry and Molecular Biology, OGI School of Science and Engineering, Oregon Health & Science University, Beaverton 97006-8921, USA
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30
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Metzler DE, Metzler CM, Sauke DJ. The Organization of Metabolism. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50020-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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