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Trisrivirat D, Sutthaphirom C, Pimviriyakul P, Chaiyen P. Dual activities of oxidation and oxidative decarboxylation by flavoenzymes. Chembiochem 2022; 23:e202100666. [PMID: 35040514 DOI: 10.1002/cbic.202100666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Indexed: 11/07/2022]
Abstract
Specific flavoenzyme oxidases catalyze oxidative decarboxylation in addition to their classical oxidation reactions in the same active sites. The mechanisms underlying oxidative decarboxylation by these enzymes and how they control their two activities are not clearly known. This article reviews the current state of knowledge of four enzymes from the l-amino acid oxidase and l-hydroxy acid oxidase families, including l-tryptophan 2-monooxygenase, l-phenylalanine 2-oxidase and l-lysine oxidase/monooxygenase and lactate monooxygenase which catalyze substrate oxidation and oxidative decarboxylation. Apart from specific interactions to allow substrate oxidation by the flavin cofactor, specific binding of oxidized product in the active sites appears to be important for enabling subsequent decarboxylation by these enzymes. Based on recent findings of l-lysine oxidase/monooxygenase, we propose that nucleophilic attack of H2O2 on the imino acid product is the mechanism enabling oxidative decarboxylation.
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Affiliation(s)
- Duangthip Trisrivirat
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | - Chalermroj Sutthaphirom
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | | | - Pimchai Chaiyen
- Vidyasirimedhi Institute of Science and Technology (VISTEC), School of Biomolecular Science and Engineering, 555 Moo 1 Payupnai, 21210, Wangchan District, THAILAND
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2
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Pekarsky A, Mihalyi S, Weiss M, Limbeck A, Spadiut O. Depletion of Boric Acid and Cobalt from Cultivation Media: Impact on Recombinant Protein Production with Komagataella phaffii. Bioengineering (Basel) 2020; 7:bioengineering7040161. [PMID: 33322107 PMCID: PMC7763993 DOI: 10.3390/bioengineering7040161] [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: 10/09/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
The REACH regulation stands for “Registration, Evaluation, Authorization and Restriction of Chemicals” and defines certain substances as harmful to human health and the environment. This urges manufacturers to adapt production processes. Boric acid and cobalt dichloride represent such harmful ingredients, but are commonly used in yeast cultivation media. The yeast Komagataella phaffii (Pichia pastoris) is an important host for heterologous protein production and compliance with the REACH regulation is desirable. Boric acid and cobalt dichloride are used as boron and cobalt sources, respectively. Boron and cobalt support growth and productivity and a number of cobalt-containing enzymes exist. Therefore, depletion of boric acid and cobalt dichloride could have various negative effects, but knowledge is currently scarce. Herein, we provide an insight into the impact of boric acid and cobalt depletion on recombinant protein production with K. phaffii and additionally show how different vessel materials affect cultivation media compositions through leaking elements. We found that boric acid could be substituted through boron leakiness from borosilicate glassware. Furthermore, depletion of boric acid and cobalt dichloride neither affected high cell density cultivation nor cell morphology and viability on methanol. However, final protein quality of three different industrially relevant enzymes was affected in various ways.
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Affiliation(s)
- Alexander Pekarsky
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
| | - Sophia Mihalyi
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
| | - Maximilian Weiss
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-I2AC, 1060 Vienna, Austria; (M.W.); (A.L.)
| | - Andreas Limbeck
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-I2AC, 1060 Vienna, Austria; (M.W.); (A.L.)
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
- Correspondence: ; Tel.: +43-1-58801-166473
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3
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Yeh HW, Lin KH, Lyu SY, Li YS, Huang CM, Wang YL, Shih HW, Hsu NS, Wu CJ, Li TL. Biochemical and structural explorations of α-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction. Acta Crystallogr D Struct Biol 2019; 75:733-742. [PMID: 31373572 PMCID: PMC6677016 DOI: 10.1107/s2059798319009574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/03/2019] [Indexed: 11/05/2022] Open
Abstract
p-Hydroxymandelate oxidase (Hmo) is a flavin mononucleotide (FMN)-dependent enzyme that oxidizes mandelate to benzoylformate. How the FMN-dependent oxidation is executed by Hmo remains unclear at the molecular level. A continuum of snapshots from crystal structures of Hmo and its mutants in complex with physiological/nonphysiological substrates, products and inhibitors provides a rationale for its substrate enantioselectivity/promiscuity, its active-site geometry/reactivity and its direct hydride-transfer mechanism. A single mutant, Y128F, that extends the two-electron oxidation reaction to a four-electron oxidative decarboxylation reaction was unexpectedly observed. Biochemical and structural approaches, including biochemistry, kinetics, stable isotope labeling and X-ray crystallography, were exploited to reach these conclusions and provide additional insights.
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Affiliation(s)
- Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Man Huang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hao-Wei Shih
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan
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4
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Conformational flexibility related to enzyme activity: evidence for a dynamic active-site gatekeeper function of Tyr(215) in Aerococcus viridans lactate oxidase. Sci Rep 2016; 6:27892. [PMID: 27302031 PMCID: PMC4908395 DOI: 10.1038/srep27892] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/26/2016] [Indexed: 01/15/2023] Open
Abstract
L-Lactate oxidase (LOX) belongs to a large family of flavoenzymes that catalyze oxidation of α-hydroxy acids. How in these enzymes the protein structure controls reactivity presents an important but elusive problem. LOX contains a prominent tyrosine in the substrate binding pocket (Tyr(215) in Aerococcus viridans LOX) that is partially responsible for securing a flexible loop which sequesters the active site. To characterize the role of Tyr(215), effects of substitutions of the tyrosine (Y215F, Y215H) were analyzed kinetically, crystallographically and by molecular dynamics simulations. Enzyme variants showed slowed flavin reduction and oxidation by up to 33-fold. Pyruvate release was also decelerated and in Y215F, it was the slowest step overall. A 2.6-Å crystal structure of Y215F in complex with pyruvate shows the hydrogen bond between the phenolic hydroxyl and the keto oxygen in pyruvate is replaced with a potentially stronger hydrophobic interaction between the phenylalanine and the methyl group of pyruvate. Residues 200 through 215 or 216 appear to be disordered in two of the eight monomers in the asymmetric unit suggesting that they function as a lid controlling substrate entry and product exit from the active site. Substitutions of Tyr(215) can thus lead to a kinetic bottleneck in product release.
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5
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Martin V, Giorello F, Fariña L, Minteguiaga M, Salzman V, Boido E, Aguilar PS, Gaggero C, Dellacassa E, Mas A, Carrau F. De Novo Synthesis of Benzenoid Compounds by the Yeast Hanseniaspora vineae Increases the Flavor Diversity of Wines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4574-4583. [PMID: 27193819 DOI: 10.1021/acs.jafc.5b05442] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Benzyl alcohol and other benzenoid-derived metabolites of particular importance in plants confer floral and fruity flavors to wines. Among the volatile aroma components in Vitis vinifera grape varieties, benzyl alcohol is present in its free and glycosylated forms. These compounds are considered to originate from grapes only and not from fermentative processes. We have found increased levels of benzyl alcohol in red Tannat wine compared to that in grape juice, suggesting de novo formation of this metabolite during vinification. In this work, we show that benzyl alcohol, benzaldehyde, p-hydroxybenzaldehyde, and p-hydroxybenzyl alcohol are synthesized de novo in the absence of grape-derived precursors by Hanseniaspora vineae. Levels of benzyl alcohol produced by 11 different H. vineae strains were 20-200 times higher than those measured in fermentations with Saccharomyces cerevisiae strains. These results show that H. vineae contributes to flavor diversity by increasing grape variety aroma concentration in a chemically defined medium. Feeding experiments with phenylalanine, tryptophan, tyrosine, p-aminobenzoic acid, and ammonium in an artificial medium were tested to evaluate the effect of these compounds either as precursors or as potential pathway regulators for the formation of benzenoid-derived aromas. Genomic analysis shows that the phenylalanine ammonia-lyase (PAL) and tyrosine ammonia lyase (TAL) pathways, used by plants to generate benzyl alcohols from aromatic amino acids, are absent in the H. vineae genome. Consequently, alternative pathways derived from chorismate with mandelate as an intermediate are discussed.
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Affiliation(s)
- Valentina Martin
- Sección Enología, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
| | - Facundo Giorello
- Sección Enología, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
| | - Laura Fariña
- Sección Enología, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
- Departamento de Biología, Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable , 11600 Montevideo, Uruguay
| | - Manuel Minteguiaga
- Catedra de Farmacognosia y Productos Naturales, Departamento de Quimica Orgánica, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
| | - Valentina Salzman
- Laboratorio de Biología Celular de Membranas, Institut Pasteur de Montevideo , 11400 Montevideo, Uruguay
- Laboratorio de Biología Celular de Membranas, IIB-INTECH, CONICET, Universidad Nacional de San Martin , San Martin, Argentina
| | - Eduardo Boido
- Sección Enología, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
| | - Pablo S Aguilar
- Laboratorio de Biología Celular de Membranas, Institut Pasteur de Montevideo , 11400 Montevideo, Uruguay
- Laboratorio de Biología Celular de Membranas, IIB-INTECH, CONICET, Universidad Nacional de San Martin , San Martin, Argentina
| | - Carina Gaggero
- Departamento de Biología, Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable , 11600 Montevideo, Uruguay
| | - Eduardo Dellacassa
- Catedra de Farmacognosia y Productos Naturales, Departamento de Quimica Orgánica, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
| | - Albert Mas
- Deptamento de Bioquímica y Biotecnología, Faculty of Oneology, University Rovira i Virgili , 43007 Tarragona, Spain
| | - Francisco Carrau
- Sección Enología, Departamento Ciencia y Tecnología Alimentos, Facultad de Quimica, Universidad de la Republica , 11800 Montevideo, Uruguay
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Functional Characterization of a Novel Member of the Amidohydrolase 2 Protein Family, 2-Hydroxy-1-Naphthoic Acid Nonoxidative Decarboxylase from Burkholderia sp. Strain BC1. J Bacteriol 2016; 198:1755-1763. [PMID: 27068590 DOI: 10.1128/jb.00250-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The gene encoding a nonoxidative decarboxylase capable of catalyzing the transformation of 2-hydroxy-1-naphthoic acid (2H1NA) to 2-naphthol was identified, recombinantly expressed, and purified to homogeneity. The putative gene sequence of the decarboxylase (hndA) encodes a 316-amino-acid protein (HndA) with a predicted molecular mass of 34 kDa. HndA exhibited high identity with uncharacterized amidohydrolase 2 proteins of various Burkholderia species, whereas it showed a modest 27% identity with γ-resorcylate decarboxylase, a well-characterized nonoxidative decarboxylase belonging to the amidohydrolase superfamily. Biochemically characterized HndA demonstrated strict substrate specificity toward 2H1NA, whereas inhibition studies with HndA indicated the presence of zinc as the transition metal center, as confirmed by atomic absorption spectroscopy. A three-dimensional structural model of HndA, followed by docking analysis, identified the conserved metal-coordinating and substrate-binding residues, while their importance in catalysis was validated by site-directed mutagenesis. IMPORTANCE Microbial nonoxidative decarboxylases play a crucial role in the metabolism of a large array of carboxy aromatic chemicals released into the environment from a variety of natural and anthropogenic sources. Among these, hydroxynaphthoic acids are usually encountered as pathway intermediates in the bacterial degradation of polycyclic aromatic hydrocarbons. The present study reveals biochemical and molecular characterization of a 2-hydroxy-1-naphthoic acid nonoxidative decarboxylase involved in an alternative metabolic pathway which can be classified as a member of the small repertoire of nonoxidative decarboxylases belonging to the amidohydrolase 2 family of proteins. The strict substrate specificity and sequence uniqueness make it a novel member of the metallo-dependent hydrolase superfamily.
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7
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Lederer F, Vignaud C, North P, Bodevin S. Trifluorosubstrates as mechanistic probes for an FMN-dependent l-2-hydroxy acid-oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1215-1221. [PMID: 27155230 DOI: 10.1016/j.bbapap.2016.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 11/29/2022]
Abstract
A controversy exists with respect to the mechanism of l-2-hydroxy acid oxidation by members of a family of FMN-dependent enzymes. A so-called carbanion mechanism was initially proposed, in which the active site histidine abstracts the substrate α-hydrogen as a proton, followed by electron transfer from the carbanion to the flavin. But an alternative mechanism was not incompatible with some results, a mechanism in which the active site histidine instead picks up the substrate hydroxyl proton and a hydride transfer occurs. Even though more recent experiments ruling out such a mechanism were published (Rao & Lederer (1999) Protein Science 7, 1531-1537), a few authors have subsequently interpreted their results with variant enzymes in terms of a hydride transfer. In the present work, we analyse the reactivity of trifluorolactate, a substrate analogue, with the flavocytochrome b2 (Fcb2) flavodehydrogenase domain, compared to its reactivity with an NAD-dependent lactate dehydrogenase (LDH), for which this compound is known to be an inhibitor (Pogolotti & Rupley (1973) Biochem. Biophys. Res. Commun, 55, 1214-1219). Indeed, electron attraction by the three fluorine atoms should make difficult the removal of the α-H as a hydride. We also analyse the reactivity of trifluoropyruvate with the FMN- and NAD-dependent enzymes. The results substantiate a different effect of the fluorine substituents on the two enzymes compared to their normal substrates. In the discussion we analyse the conclusions of recent papers advocating a hydride transfer mechanism for the family of l-2-hydroxy acid oxidizing FMN-dependent enzymes.
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Affiliation(s)
- Florence Lederer
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France; Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Caroline Vignaud
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Paul North
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Sabrina Bodevin
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
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8
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Gillet N, Ruiz-Pernía JJ, de la Lande A, Lévy B, Lederer F, Demachy I, Moliner V. QM/MM study of l-lactate oxidation by flavocytochrome b2. Phys Chem Chem Phys 2016; 18:15609-18. [DOI: 10.1039/c6cp00395h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Free energy surfaces calculated from a state-of-the-art computational methodology highlight the role of active site residues in l-lactate oxidation by flavocytochrome b2.
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Affiliation(s)
- N. Gillet
- Laboratoire de Chimie-Physique
- CNRS UMR 8000
- Université Paris Sud
- 91405 Cedex Orsay
- France
| | - J. J. Ruiz-Pernía
- Departament de Química Física i Analítica
- Universitat Jaume I
- 12071 Castellón
- Spain
| | - A. de la Lande
- Laboratoire de Chimie-Physique
- CNRS UMR 8000
- Université Paris Sud
- 91405 Cedex Orsay
- France
| | - B. Lévy
- Laboratoire de Chimie-Physique
- CNRS UMR 8000
- Université Paris Sud
- 91405 Cedex Orsay
- France
| | - F. Lederer
- Laboratoire de Chimie-Physique
- CNRS UMR 8000
- Université Paris Sud
- 91405 Cedex Orsay
- France
| | - I. Demachy
- Laboratoire de Chimie-Physique
- CNRS UMR 8000
- Université Paris Sud
- 91405 Cedex Orsay
- France
| | - V. Moliner
- Departament de Química Física i Analítica
- Universitat Jaume I
- 12071 Castellón
- Spain
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9
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Cao Y, Han S, Yu L, Qian H, Chen JZ. MD and QM/MM studies on long-chain L-α-hydroxy acid oxidase: substrate binding features and oxidation mechanism. J Phys Chem B 2014; 118:5406-17. [PMID: 24801764 DOI: 10.1021/jp5022399] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long-chain L-α-hydroxy acid oxidase (LCHAO) is a flavin mononucleotide (FMN)-dependent oxidase that dehydrogenates l-α-hydroxy acids to keto acids. There were two different mechanisms, named as hydride transfer (HT) mechanism and carbanion (CA) mechanism, respectively, proposed about the catalytic process for the FMN-dependent L-α-hydroxy acid oxidases on the basis of biochemical data. However, crystallographic and kinetic studies could not provide enough evidence to prove one of the mechanisms or eliminate the alternative. In the present studies, theoretical computations were carried out to study the molecular mechanism for LCHAO-catalyzed dehydrogenation of L-lactate. Our molecular dynamics (MD) simulations indicated that L-lactate prefers to bind with LCHAO in a hydride transfer mode rather than a carbanion mode. Quantum mechanics/molecular mechanics (QM/MM) calculations were further carried out to obtain the optimized structures of reactants, transition states, and products at the level of ONIOM-EE (B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p):AMBER). Quantum chemical studies indicated that LCHAO-catalyzed dehydrogenation of L-lactate would be a stepwise catalytic reaction in a hydride transfer mechanism but not a carbanion mechanism. MD simulations, binding free energy calculations, and QM/MM computations were also implemented on the complex between L-lactate and Y129F mutant LCHAO. By comparing the Y129F mutant system with the wild-type system, it was further confirmed that the key residue Tyr129 in the active site of LCHAO would not affect L-lactate's binding to LCHAO but play an important role on the catalytic reaction process through an H-bond interaction.
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Affiliation(s)
- Yang Cao
- Institute of Materia Medica, College of Pharmaceutical Sciences, Zijingang Campus, Zhejiang University , 866 Yuhangtang Rd., Hangzhou, Zhejiang 310058, China
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10
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Mowat CG, Gazur B, Campbell LP, Chapman SK. Flavin-containing heme enzymes. Arch Biochem Biophys 2010; 493:37-52. [DOI: 10.1016/j.abb.2009.10.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/13/2009] [Accepted: 10/13/2009] [Indexed: 11/25/2022]
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11
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Bourhis JM, Vignaud C, Pietrancosta N, Guéritte F, Guénard D, Lederer F, Lindqvist Y. Structure of human glycolate oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1246-53. [PMID: 20054120 PMCID: PMC2802872 DOI: 10.1107/s1744309109041670] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 10/12/2009] [Indexed: 11/10/2022]
Abstract
Glycolate oxidase, a peroxisomal flavoenzyme, generates glyoxylate at the expense of oxygen. When the normal metabolism of glyoxylate is impaired by the mutations that are responsible for the genetic diseases hyperoxaluria types 1 and 2, glyoxylate yields oxalate, which forms insoluble calcium deposits, particularly in the kidneys. Glycolate oxidase could thus be an interesting therapeutic target. The crystal structure of human glycolate oxidase (hGOX) in complex with 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole (CCPST) has been determined at 2.8 A resolution. The inhibitor heteroatoms interact with five active-site residues that have been implicated in catalysis in homologous flavodehydrogenases of L-2-hydroxy acids. In addition, the chlorophenyl substituent is surrounded by nonconserved hydrophobic residues. The present study highlights the role of mobility in ligand binding by glycolate oxidase. In addition, it pinpoints several structural differences between members of the highly conserved family of flavodehydrogenases of L-2-hydroxy acids.
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Affiliation(s)
- Jean-Marie Bourhis
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Caroline Vignaud
- Laboratoire d’Enzymologie et Biochimie Structurales, CNRS FRE 2930, Gif-sur-Yvette, France
| | - Nicolas Pietrancosta
- Laboratoire d’Enzymologie et Biochimie Structurales, CNRS FRE 2930, Gif-sur-Yvette, France
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Françoise Guéritte
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Daniel Guénard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Florence Lederer
- Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud, Orsay, France
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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12
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Gadda G. Hydride transfer made easy in the reaction of alcohol oxidation catalyzed by flavin-dependent oxidases. Biochemistry 2009; 47:13745-53. [PMID: 19053234 DOI: 10.1021/bi801994c] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Choline oxidase (E.C. 1.1.3.17; choline-oxygen 1-oxidoreductase) catalyzes the two-step, four-electron oxidation of choline to glycine betaine with betaine aldehyde as enzyme-associated intermediate and molecular oxygen as final electron acceptor. Biochemical, structural, and mechanistic studies on the wild-type and a number of mutant forms of choline oxidase from Arthrobacter globiformis have recently been carried out, allowing for the delineation at molecular and atomic levels of the mechanism of alcohol oxidation catalyzed by the enzyme. First, the alcohol substrate is activated to its alkoxide species by the removal of the hydroxyl proton in the enzyme-substrate complex. The resulting activated alkoxide is correctly positioned for catalysis through electrostatic and hydrogen bonding interactions with a number of active site residues. After substrate activation and correct positioning are attained, alcohol oxidation occurs in a highly preorganized enzyme-substrate complex through quantum mechanical transfer of a hydride ion from the alpha-carbon of the chelated, alkoxide species to the N(5) atom of the enzyme-bound flavin. This mechanism in its essence is shared by another class of alcohol oxidizing enzymes that utilize a catalytic zinc to stabilize an alkoxide intermediate and NAD(P)(+) as the organic cofactor that accepts the hydride ion, whose paradigm example is alcohol dehydrogenase. It will be interesting to experimentally evaluate the attractive hypothesis of whether the mechanism of choline oxidase can be extended to other flavin-dependent enzymes as well as enzymes that utilize cofactors other than flavins in the oxidation of alcohols.
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Affiliation(s)
- Giovanni Gadda
- Departments of Chemistry and Biology, and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA.
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13
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Murray MS, Holmes RP, Lowther WT. Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design. Biochemistry 2008; 47:2439-49. [PMID: 18215067 DOI: 10.1021/bi701710r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human glycolate oxidase (GO) catalyzes the FMN-dependent oxidation of glycolate to glyoxylate and glyoxylate to oxalate, a key metabolite in kidney stone formation. We report herein the structures of recombinant GO complexed with sulfate, glyoxylate, and an inhibitor, 4-carboxy-5-dodecylsulfanyl-1,2,3-triazole (CDST), determined by X-ray crystallography. In contrast to most alpha-hydroxy acid oxidases including spinach glycolate oxidase, a loop region, known as loop 4, is completely visible when the GO active site contains a small ligand. The lack of electron density for this loop in the GO-CDST complex, which mimics a large substrate, suggests that a disordered to ordered transition may occur with the binding of substrates. The conformational flexibility of Trp110 appears to be responsible for enabling GO to react with alpha-hydroxy acids of various chain lengths. Moreover, the movement of Trp110 disrupts a hydrogen-bonding network between Trp110, Leu191, Tyr134, and Tyr208. This loss of interactions is the first indication that active site movements are directly linked to changes in the conformation of loop 4. The kinetic parameters for the oxidation of glycolate, glyoxylate, and 2-hydroxy octanoate indicate that the oxidation of glycolate to glyoxylate is the primary reaction catalyzed by GO, while the oxidation of glyoxylate to oxalate is most likely not relevant under normal conditions. However, drugs that exploit the unique structural features of GO may ultimately prove to be useful for decreasing glycolate and glyoxylate levels in primary hyperoxaluria type 1 patients who have the inability to convert peroxisomal glyoxylate to glycine.
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Affiliation(s)
- Michael S Murray
- Center for Structural Biology and Department of Biochemistry, Wake Forest University Health Sciences, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA
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14
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Fitzpatrick PF. Carbanion versus hydride transfer mechanisms in flavoprotein-catalyzed dehydrogenations. Bioorg Chem 2004; 32:125-39. [PMID: 15110192 DOI: 10.1016/j.bioorg.2003.02.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2003] [Indexed: 11/26/2022]
Abstract
The present understanding of the mechanisms by which flavoproteins oxidize amino acid or hydroxy acids to the respective imino or keto acids is reviewed. The observation that many of these enzymes catalyze the elimination of HBr or HCl from the appropriate beta-halogenated substrate was long considered evidence for a carbanion intermediate. Recent structural and mechanistic studies are not compatible with the intermediacy of carbanions in the reactions catalyzed by d-amino acid oxidase and flavocytochrome b(2). In contrast, the data are most consistent with mechanisms involving direct hydride transfer.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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Sobrado P, Fitzpatrick PF. Solvent and primary deuterium isotope effects show that lactate CH and OH bond cleavages are concerted in Y254F flavocytochrome b2, consistent with a hydride transfer mechanism. Biochemistry 2004; 42:15208-14. [PMID: 14690431 PMCID: PMC1630681 DOI: 10.1021/bi035546n] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Yeast flavocytochrome b(2) catalyzes the oxidation of lactate to pyruvate; because of the wealth of structural and mechanistic information available, this enzyme has served as the model for the family of flavoproteins catalyzing oxidation of alpha-hydroxy acids. Primary deuterium and solvent isotope effects have now been used to analyze the effects of mutating the active site residue Tyr254 to phenylalanine. Both the V(max) and the V/K(lactate) values decrease about 40-fold in the mutant enzyme. The primary deuterium isotope effects on the V(max) and the V/K(lactate) values increase to 5.0, equivalent to the intrinsic isotope effect for the wild-type enzyme. In addition, both the V(max) and the V/K(lactate) values exhibit solvent isotope effects of 1.5. Measurement of the solvent isotope effect with deuterated lactate establishes that the primary and solvent isotope effects arise from the same chemical step, consistent with concerted cleavage of the lactate OH and CH bonds. The pH dependence of the mutant enzyme is not significantly different from that of the wild-type enzyme; this is most consistent with a requirement that the side chain of Tyr254 be uncharged for catalysis. The results support a hydride transfer mechanism for the mutant protein and, by extension, wild-type flavocytochrome b(2) and the other flavoproteins catalyzing oxidation of alpha-hydroxy acids.
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Affiliation(s)
| | - Paul F. Fitzpatrick
- * Address correspondence to this author at the Department of Biochemistry and Biophysics, 2128 TAMU, College Station, TX 77843-2128. Phone: 979-845-5487. Fax: 979-845-4946. E-mail:
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Current awareness on yeast. Yeast 2002; 19:285-92. [PMID: 11816036 DOI: 10.1002/yea.821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (3 weeks journals - search completed 5th. Dec. 2001)
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