1
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Tülek A, Günay E, Servili B, Eşsiz Ş, Binay B, Yildirim D. Sustainable production of formic acid from CO2 by a novel immobilized mutant formate dehydrogenase. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.123090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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2
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Popinako А, Pometun А, Nilov D, Dibrova D, Khrustalev V, Khrustaleva T, Iurchenko T, Nikolaeva А, Švedas V, Boyko K, Tishkov V, Popov V. The role of Tyr102 residue in the functioning of bacterial NAD+-dependent formate dehydrogenase of Pseudomonas sp. 101. Biochem Biophys Res Commun 2022; 616:134-139. [DOI: 10.1016/j.bbrc.2022.05.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
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3
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Pometun AA, Parshin PD, Galanicheva NP, Shaposhnikov LA, Atroshenko DL, Pometun EV, Burmakin VV, Kleymenov SY, Savin SS, Tishkov VI. Effect of Additional Amino Acid Replacements on the Properties of Multi-point Mutant Bacterial Formate Dehyderogenase PseFDH SM4S. Acta Naturae 2022; 14:82-91. [PMID: 35441051 PMCID: PMC9013435 DOI: 10.32607/actanaturae.11665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Formate dehydrogenase from Pseudomonas sp. 101 bacterium (PseFDH, EC 1.2.1.2)
is a research model for the elucidation of the catalytic mechanism of 2-oxyacid
D-specific dehydrogenases enzyme superfamily. The enzyme is actively used for
regeneration of the reduced form of NAD(P)H in chiral synthesis with
oxidoreductases. A multi-point mutant PseFDH SM4S with an improved thermal and
chemical stability has been prepared earlier in this laboratory. To further
improve the properties of the mutant, additional single-point replacements have
been introduced to generate five new PseFDH mutants. All new enzymes have been
highly purified, and their kinetic properties and thermal stability studied
using analysis of thermal inactivation kinetics and differential scanning
calorimetry. The E170D amino acid change in PseFDH SM4S shows an increase in
thermal stability 1.76- and 10-fold compared to the starting mutant and the
wild-type enzyme, respectively.
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Affiliation(s)
- A. A. Pometun
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
- Innovations and High Technologies MSU Ltd., Moscow, 109559 Russia
| | - P. D. Parshin
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
- Innovations and High Technologies MSU Ltd., Moscow, 109559 Russia
| | - N. P. Galanicheva
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
| | - L. A. Shaposhnikov
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
| | - D. L. Atroshenko
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
- Innovations and High Technologies MSU Ltd., Moscow, 109559 Russia
| | - E. V. Pometun
- Sechenov First Moscow State Medical University, Moscow, 119991 Russia
| | - V. V. Burmakin
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
| | - S. Yu. Kleymenov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071 Russia
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334 Russia
| | - S. S. Savin
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
- Innovations and High Technologies MSU Ltd., Moscow, 109559 Russia
| | - V. I. Tishkov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991 Russia
- Innovations and High Technologies MSU Ltd., Moscow, 109559 Russia
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4
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Yilmazer B, Isupov MN, De Rose SA, Bulut H, Benninghoff JC, Binay B, Littlechild JA. Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme. J Struct Biol 2020; 212:107657. [DOI: 10.1016/j.jsb.2020.107657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
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5
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Abstract
We have analyzed the reaction catalyzed by formate dehydrogenase using transition path sampling. This system has recently received experimental attention using infrared spectroscopy and heavy-enzyme studies. Some of the experimental results point to the possible importance of protein motions that are coupled to the chemical step. We found that the residue Val123 that lies behind the nicotinamide ring occasionally comes into van der Waals contact with the acceptor and that in all reactive trajectories, the barrier-crossing event is preceded by this contact, meaning that the motion of Val123 is part of the reaction coordinate. Experimental results have been interpreted with a two-dimensional formula for the chemical rate, which cannot capture effects such as the one we describe.
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Affiliation(s)
- Dimitri Antoniou
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd., Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd., Tucson, Arizona 85721, United States
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6
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Bulut H, Valjakka J, Yuksel B, Yilmazer B, Turunen O, Binay B. Effect of Metal Ions on the Activity of Ten NAD-Dependent Formate Dehydrogenases. Protein J 2020; 39:519-530. [PMID: 33043425 DOI: 10.1007/s10930-020-09924-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 11/25/2022]
Abstract
NAD-dependent formate dehydrogenase (FDH) enzymes are frequently used in industrial and scientific applications. FDH is a reversible enzyme that reduces the NAD molecule to NADH and produces CO2 by oxidation of the formate ion, whereas it causes CO2 reduction in the reverse reaction. Some transition metal elements - Fe3+, Mo6+ and W6 + - can be found in the FDH structure of anaerobic and archaeal microorganisms, and these enzymes require cations and other redox-active cofactors for their FDH activity. While NAD-dependent FDHs do not necessarily require any metal cations, the presence of various metal cations can still affect FDH activities. To study the effect of 11 different metal ions, NAD-dependent FDH enzymes from ten different microorganisms were tested: Ancylobacter aquaticus (AaFDH), Candida boidinii (CboFDH), Candida methylica (CmFDH), Ceriporiopsis subvermispora (CsFDH), Chaetomium thermophilum (CtFDH), Moraxella sp. (MsFDH), Myceliophthora thermophila (MtFDH), Paracoccus sp. (PsFDH), Saccharomyces cerevisiae (ScFDH) and Thiobacillus sp. (TsFDH). It was found that metal ions (mainly Cu2+ and Zn2+) could have quite strong inhibition effects on several enzymes in the forward reaction, whereas several cations (Li+, Mg2+, Mn2+, Fe3+ and W6+) could increase the forward reaction of two FDHs. The highest activity increase (1.97 fold) was caused by Fe3+ in AaFDH. The effect on the reverse reaction was minimal. The modelled structures of ten FDHs showed that the active site is formed by 15 highly conserved amino acid residues spatially settling around the formate binding site in a conserved way. However, the residue differences at some of the sites close to the substrate do not explain the activity differences. The active site space is very tight, excluding water molecules, as observed in earlier studies. Structural examination indicated that smaller metal ions might be spaced close to the active site to affect the reaction. Metal ion size showed partial correlation to the effect on inhibition or activation. Affinity of the substrate may also affect the sensitivity to the metal's effect. In addition, amino acid differences on the protein surface may also be important for the metal ion effect.
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Affiliation(s)
- Huri Bulut
- Medical Biochemistry Department, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Busra Yuksel
- Molecular Biology and Genetics Department, Istanbul Technical University, Istanbul, Turkey
| | - Berin Yilmazer
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
| | - Ossi Turunen
- School of Forest Sciences, Faculty of Science and Forestry, University of Eastern Finland, Joensuu, Finland
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
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7
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Robescu MS, Rubini R, Beneventi E, Tavanti M, Lonigro C, Zito F, Filippini F, Cendron L, Bergantino E. From the Amelioration of a NADP
+
‐dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice. ChemCatChem 2020. [DOI: 10.1002/cctc.201902089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Marina Simona Robescu
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
| | - Rudy Rubini
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
| | - Elisa Beneventi
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
| | - Michele Tavanti
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
| | - Chiara Lonigro
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR7099, CNRS, IBPC, Université Paris Diderot Sorbonne Paris Cité 13 rue Pierre et Marie Curie 75005 Paris France
| | - Francesca Zito
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires UMR7099, CNRS, IBPC, Université Paris Diderot Sorbonne Paris Cité 13 rue Pierre et Marie Curie 75005 Paris France
| | - Francesco Filippini
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
| | - Laura Cendron
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
| | - Elisabetta Bergantino
- Synthetic Biology and Biotechnology Unit Department of Biology University of Padova via U. Bassi 58B/viale G. Colombo 3 I-35131 Padova Italy
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8
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Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W. Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. BMC Evol Biol 2018; 18:199. [PMID: 30577795 PMCID: PMC6303947 DOI: 10.1186/s12862-018-1309-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/27/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data for various representatives of the family, the long and complex evolution and broad sequence diversity hinder functional annotations for uncharacterized members. RESULTS We report an in-depth phylogenetic analysis, followed by mapping of available biochemical and structural data on the reconstructed phylogenetic tree. The analysis suggests that some subfamilies comprising enzymes with similar yet broad substrate specificity profiles diverged early in the evolution of 2HADHs. Based on the phylogenetic tree, we present a revised classification of the family that comprises 22 subfamilies, including 13 new subfamilies not studied biochemically. We summarize characteristics of the nine biochemically studied subfamilies by aggregating all available sequence, biochemical, and structural data, providing comprehensive descriptions of the active site, cofactor-binding residues, and potential roles of specific structural regions in substrate recognition. In addition, we concisely present our analysis as an online 2HADH enzymes knowledgebase. CONCLUSIONS The knowledgebase enables navigation over the 2HADHs classification, search through collected data, and functional predictions of uncharacterized 2HADHs. Future characterization of the new subfamilies may result in discoveries of enzymes with novel metabolic roles and with properties beneficial for biotechnological applications.
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Affiliation(s)
- Dorota Matelska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA
| | - Jagoda Jabłońska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Marcin J Domagalski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA
| | - Jan Kutner
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.,Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA. .,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, USA. .,Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland.
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9
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Roca M, Ruiz-Pernía JJ, Castillo R, Oliva M, Moliner V. Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase. Phys Chem Chem Phys 2018; 20:25722-25737. [PMID: 30280169 DOI: 10.1039/c8cp04244f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial topics. In the present work, the hydride transfer step in the formate dehydrogenase (FDH EC 1.2.1.2) enzyme is studied by means of molecular dynamic (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials in order to explore any correlation between dynamics, tunnelling effects and the rate constant. The temperature dependence of the kinetic isotope effects (KIEs), which is one of the few tests that can be studied by experiments and simulations to shed light on this debate, has been computed and the results have been compared with previous experimental data. The classical mechanical free energy barrier and the number of recrossing trajectories seem to be temperature-independent while the quantum vibrational corrections and the tunnelling effects are slightly temperature-dependent over the interval of 5-45 °C. The computed primary KIEs are in very good agreement with previous experimental data, being almost temperature-independent within the standard deviations. The modest dependence on the temperature is due to just the quantum vibrational correction contribution. These results, together with the analysis of the evolution of the collective variables such as the electrostatic potential or the electric field created by the protein on the key atoms involved in the reaction, confirm that while the protein is well preorganised, some changes take place along the reaction that favour the hydride transfer and the product release. Coordinates defining these movements are, in fact, part of the real reaction coordinate.
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Affiliation(s)
- Maite Roca
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | | | - Raquel Castillo
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Mónica Oliva
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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10
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Pala U, Yelmazer B, Çorbacıoğlu M, Ruupunen J, Valjakka J, Turunen O, Binay B. Functional effects of active site mutations in NAD+-dependent formate dehydrogenases on transformation of hydrogen carbonate to formate. Protein Eng Des Sel 2018; 31:327-335. [DOI: 10.1093/protein/gzy027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/20/2018] [Indexed: 12/21/2022] Open
Affiliation(s)
- Uğur Pala
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Berin Yelmazer
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Meltem Çorbacıoğlu
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Jouni Ruupunen
- Faculty of Medicine and Health Technology, University of Tampere, Tampereen yliopisto, Finland
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, University of Tampere, Tampereen yliopisto, Finland
| | - Ossi Turunen
- Faculty of Science and Forestry, School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
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11
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Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W. Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. Biochemistry 2018; 57:963-977. [PMID: 29309127 PMCID: PMC6469932 DOI: 10.1021/acs.biochem.7b01137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site.
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Affiliation(s)
- Jan Kutner
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Dorota Matelska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 93 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Katarzyna B. Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Olga Gasiorowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Piotr Sroka
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Maria W. Gorna
- Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 93 Zwirki i Wigury, 02-089 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
| | - Krzysztof Wozniak
- Laboratory for Structural and Biochemical Research, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 101 Zwirki i Wigury, 02-089 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States,Department of Chemistry, University of Warsaw, 1 Ludwika Pasteura, 02-093 Warsaw, Poland,Corresponding Authors: (K.G.)., (K.W.)., . Phone: (434) 243-6865. Fax: (434) 243-2981 (W.M.)
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12
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Structural basis for double cofactor specificity in a new formate dehydrogenase from the acidobacterium Granulicella mallensis MP5ACTX8. Appl Microbiol Biotechnol 2015; 99:9541-54. [PMID: 26104866 DOI: 10.1007/s00253-015-6695-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 10/23/2022]
Abstract
Formate dehydrogenases (FDHs) are considered particularly useful enzymes in biocatalysis when the regeneration of the cofactor NAD(P)H is required, that is, in chiral synthesis with dehydrogenases. Their utilization is however limited to the recycling of NAD(+), since all (apart one) of the FDHs characterized so far are strictly specific for this cofactor, and this is a major drawback for their otherwise wide applicability. Despite the many attempts performed to modify cofactor specificity by protein engineering different NAD(+)-dependent FDHs, in the general practice, glucose or phosphite dehydrogenases are chosen for the recycling of NADP(+). We report on the functional and structural characterization of a new FDH, GraFDH, identified by mining the genome of the extremophile prokaryote Granulicella mallensis MP5ACTX8. The new enzyme displays a valuable stability in the presence of many organic cosolvents as well as double cofactor specificity, with NADP(+) preferred over NAD(+) at acidic pH values, at which it also shows the highest stability. The quite low affinities for both cofactors as well as for the substrate formate indicate, however, that the native enzyme requires optimization to be applied as biocatalytic tool. We also determined the crystal structure of GraFDH both as apoprotein and as holoprotein, either in complex with NAD(+) or NADP(+). Noticeably, the latter represents the first structure of an FDH enzyme in complex with NADP(+). This fine picture of the structural determinants involved in cofactor selectivity will possibly boost protein engineering of the new enzyme or other homolog FDHs in view of their biocatalytic exploitation for NADP(+) recycling.
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13
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Kargov IS, Kleimenov SY, Savin SS, Tishkov VI, Alekseeva AA. Improvement of the soy formate dehydrogenase properties by rational design. Protein Eng Des Sel 2015; 28:171-8. [PMID: 25744036 DOI: 10.1093/protein/gzv007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/27/2015] [Indexed: 11/13/2022] Open
Abstract
Previous experiments on substitution of the residue Phe290 to Asp, Asn and Ser in NAD(+)-dependent formate dehydrogenase from soya Glycine max (SoyFDH) showed important role of the residue in enzyme thermal stability and catalytic properties (Alekseeva et al. Prot. Eng. Des. Sel., 2012a; 25: :781-88). In this work, we continued site-directed mutagenesis experiments of the Phe290 and the residue was changed to Ala, Thr, Tyr, Glu and Gln. All amino acid changes resulted in increase of catalytic constant from 2.9 to 3.5-4.7 s(-1). The substitution Phe290Ala led to KM (NAD+) decrease from 13.3 to 8.6 μM, and substitutions Phe290Tyr and Phe290Glu resulted in decrease and increase of KM (HCOO-) from 1.5 to 0.9 and -2.9 mM, respectively. The highest improvement of catalytic properties was observed for SoyFDH Phe290Ala which showed 2-fold higher catalytic efficiency with both substrates. Stability of mutants was examined by study of thermal inactivation kinetics and differential scanning calorimetry (DSC). All five amino acids provided increase of thermal stability of mutant SoyFDH in comparison with wild-type enzyme. Mutant SoyFDH Phe290Glu showed the highest improvement-the stabilization effect was 43 at 56°C. The DSC data agree with results of thermal inactivation kinetics. Substitutions Phe290Tyr, Phe290Thr, Phe290Gln and Phe290Glu provided Tm value increase 0.6°-6.6°. SoyFDH Phe290Glu and previously prepared SoyFDH Phe290Asp show similar thermal stability as enzymes from Candida boidinii and Mycobacterium vaccae N10 and have higher catalytic efficiency with NAD(+) compared with all described FDHs. Therefore, these mutants are very perspective enzymes for coenzyme regeneration in processes of chiral synthesis with dehydrogenases.
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Affiliation(s)
- I S Kargov
- Department of Chemical Enzymology, Chemistry Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia Innovations and High Technologies MSU Ltd, 109559 Moscow, Russia
| | - S Y Kleimenov
- A.N.Bach Institute of Biochemistry, Russian Academy of Sciences, 119074 Moscow, Russia Koltzov Institute of Developmental Biology, Russian Academy of Science, 119334 Moscow, Russia
| | - S S Savin
- Department of Chemical Enzymology, Chemistry Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia Innovations and High Technologies MSU Ltd, 109559 Moscow, Russia
| | - V I Tishkov
- Department of Chemical Enzymology, Chemistry Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia Innovations and High Technologies MSU Ltd, 109559 Moscow, Russia A.N.Bach Institute of Biochemistry, Russian Academy of Sciences, 119074 Moscow, Russia
| | - A A Alekseeva
- Department of Chemical Enzymology, Chemistry Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia Innovations and High Technologies MSU Ltd, 109559 Moscow, Russia A.N.Bach Institute of Biochemistry, Russian Academy of Sciences, 119074 Moscow, Russia
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14
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Choe H, Ha JM, Joo JC, Kim H, Yoon HJ, Kim S, Son SH, Gengan RM, Jeon ST, Chang R, Jung KD, Kim YH, Lee HH. Structural insights into the efficient CO2-reducing activity of an NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA. ACTA ACUST UNITED AC 2015; 71:313-23. [PMID: 25664741 DOI: 10.1107/s1399004714025474] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/20/2014] [Indexed: 11/11/2022]
Abstract
CO2 fixation is thought to be one of the key factors in mitigating global warming. Of the various methods for removing CO2, the NAD-dependent formate dehydrogenase from Candida boidinii (CbFDH) has been widely used in various biological CO2-reduction systems; however, practical applications of CbFDH have often been impeded owing to its low CO2-reducing activity. It has recently been demonstrated that the NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA (TsFDH) has a higher CO2-reducing activity compared with CbFDH. The crystal structure of TsFDH revealed that the biological unit in the asymmetric unit has two conformations, i.e. open (NAD(+)-unbound) and closed (NAD(+)-bound) forms. Three major differences are observed in the crystal structures of TsFDH and CbFDH. Firstly, hole 2 in TsFDH is blocked by helix α20, whereas it is not blocked in CbFDH. Secondly, the sizes of holes 1 and 2 are larger in TsFDH than in CbFDH. Thirdly, Lys287 in TsFDH, which is crucial for the capture of formate and its subsequent delivery to the active site, is an alanine in CbFDH. A computational simulation suggested that the higher CO2-reducing activity of TsFDH is owing to its lower free-energy barrier to CO2 reduction than in CbFDH.
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Affiliation(s)
- Hyunjun Choe
- Department of Chemical Engineering, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Jung Min Ha
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Jeong Chan Joo
- Department of Chemical Engineering, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Hyunook Kim
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Seonghoon Kim
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Sang Hyeon Son
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Robert M Gengan
- Department of Chemistry, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Seung Taeg Jeon
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Kwang Deog Jung
- Energy Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Yong Hwan Kim
- Department of Chemical Engineering, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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15
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Mordkovich NN, Voeikova TA, Novikova LM, Smirnov IA, Il’in VK, Soldatov PE, Tyurin-Kuz’min AY, Smolenskaya TS, Veiko VP, Shakulov RS, Debabov VG. Effect of NAD+-dependent formate dehydrogenase on anaerobic respiration of Shewanella oneidensis MR-1. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713040061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Alekseeva AA, Serenko AA, Kargov IS, Savin SS, Kleymenov SY, Tishkov VI. Engineering catalytic properties and thermal stability of plant formate dehydrogenase by single-point mutations. Protein Eng Des Sel 2012; 25:781-8. [PMID: 23100543 DOI: 10.1093/protein/gzs084] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The analysis of the 3D model structure of the ternary complex of recombinant formate dehydrogenase from soya Glycine max (EC 1.2.1.2., SoyFDH) with bound NAD+ and an inhibitor azide ion revealed the presence of hydrophobic Phe290 in the coenzyme-binding domain. This residue should shield the enzyme active site from solvent. On the basis of the alignment of plant FDHs sequences, Asp, Asn and Ser were selected as candidates to substitute Phe290. Computer modeling indicated the formation of two (Ser and Asn) or three (Asp) new hydrogen bonds in such mutants. The mutant SoyFDHs were expressed in Escherichia coli, purified and characterized. All amino acid substitutions increased K(м)(HCOO-) from 1.5 to 4.1-5.0 mM, whereas the K(м)(NAD+) values remained almost unchanged in the range from 9.1 to 14.0 μM, which is close to wt-SoyFDH (13.3 μM). The catalytic constants for F290N, F290D and F290S mutants of SoyFDH equaled 2.8, 5.1 and 4.1 s⁻¹, respectively; while that of the wild-type enzyme was 2.9 s⁻¹. The thermal stability of all mutant SoyFDHs was much higher compared with the wild-type enzyme. The differential scanning calorimetry data were in agreement with the results of thermal inactivation kinetics. The mutations F290S, F290N and F290D introduced into SoyFDH increased the T(m) values by 2.9°C, 4.3°C and 7.8°C, respectively. The best mutant F290D exhibited thermal stability similar to that of FDH from the plant Arabidopsis thaliana and exceeded that of the enzymes from the yeast Candida boidinii and the bacterium Moraxella sp. C1.
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Affiliation(s)
- Anastasia A Alekseeva
- Department of Chemical Enzymology, Chemistry Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
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17
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Vardi-Kilshtain A, Major DT, Kohen A, Engel H, Doron D. Hybrid Quantum and Classical Simulations of the Formate Dehydrogenase Catalyzed Hydride Transfer Reaction on an Accurate Semiempirical Potential Energy Surface. J Chem Theory Comput 2012; 8:4786-96. [DOI: 10.1021/ct300628e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandra Vardi-Kilshtain
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
| | - Amnon Kohen
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Hamutal Engel
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
| | - Dvir Doron
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University,
Ramat-Gan 52900, Israel
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18
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Nilov DK, Shabalin IG, Popov VO, Švedas VK. Molecular modeling of formate dehydrogenase: the formation of the Michaelis complex. J Biomol Struct Dyn 2012; 30:170-9. [DOI: 10.1080/07391102.2012.677768] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Nilov DK, Shabalin IG, Popov VO, Svedas VK. Investigation of formate transport through the substrate channel of formate dehydrogenase by steered molecular dynamics simulations. BIOCHEMISTRY (MOSCOW) 2011; 76:172-4. [PMID: 21568849 DOI: 10.1134/s0006297911020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Steered molecular dynamics simulation has revealed the mechanism of formate transport via the substrate channel of formate dehydrogenase. It is shown that the structural organization of the channel promotes the transport of formate anion in spite of the fact that the channel is too narrow even for such a small molecule. The conformational mobility of Arg284 residue, one of the residues forming the wall of the substrate channel, provides for the binding and delivery of formate to the active site.
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Affiliation(s)
- D K Nilov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
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20
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Crable BR, Plugge CM, McInerney MJ, Stams AJM. Formate formation and formate conversion in biological fuels production. Enzyme Res 2011; 2011:532536. [PMID: 21687599 PMCID: PMC3112519 DOI: 10.4061/2011/532536] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 03/23/2011] [Indexed: 11/20/2022] Open
Abstract
Biomethanation is a mature technology for fuel production. Fourth generation biofuels research will focus on sequestering CO(2) and providing carbon-neutral or carbon-negative strategies to cope with dwindling fossil fuel supplies and environmental impact. Formate is an important intermediate in the methanogenic breakdown of complex organic material and serves as an important precursor for biological fuels production in the form of methane, hydrogen, and potentially methanol. Formate is produced by either CoA-dependent cleavage of pyruvate or enzymatic reduction of CO(2) in an NADH- or ferredoxin-dependent manner. Formate is consumed through oxidation to CO(2) and H(2) or can be further reduced via the Wood-Ljungdahl pathway for carbon fixation or industrially for the production of methanol. Here, we review the enzymes involved in the interconversion of formate and discuss potential applications for biofuels production.
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Affiliation(s)
- Bryan R Crable
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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21
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Bekhouche M, Blum LJ, Doumèche B. Ionic Liquid-Inspired Cations Covalently Bound to Formate Dehydrogenase Improve its Stability and Activity in Ionic Liquids. ChemCatChem 2011. [DOI: 10.1002/cctc.201000390] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Shabalin IG, Serov AE, Skirgello OE, Timofeev VI, Samygina VR, Popov VO, Tishkov VI, Kuranova IP. Recombinant formate dehydrogenase from Arabidopsis thaliana: Preparation, crystal growth in microgravity, and preliminary X-ray diffraction study. CRYSTALLOGR REP+ 2010. [DOI: 10.1134/s1063774510050159] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Maeda Y, Doubayashi D, Ootake T, Oki M, Mikami B, Uchida H. Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1064-6. [PMID: 20823527 DOI: 10.1107/s1744309110028605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/17/2010] [Indexed: 05/26/2023]
Abstract
Formate oxidase (FOD), which catalyzes the oxidation of formate to yield carbon dioxide and hydrogen peroxide, belongs to the glucose-methanol-choline oxidoreductase (GMCO) family. FOD from Aspergillus oryzae RIB40, which has a modified FAD as a cofactor, was crystallized at 293 K by the hanging-drop vapour-diffusion method. The crystal was orthorhombic and belonged to space group C222(1). Diffraction data were collected from a single crystal to 2.4 A resolution.
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Affiliation(s)
- Yoshifumi Maeda
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 9-1 Bunkyo 3-chome, Fukui-shi 910-8507, Japan
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