1
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Jiang HW, Chen Q, Pan J, Zheng GW, Xu JH. Rational Engineering of Formate Dehydrogenase Substrate/Cofactor Affinity for Better Performance in NADPH Regeneration. Appl Biochem Biotechnol 2020; 192:530-543. [PMID: 32405732 DOI: 10.1007/s12010-020-03317-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022]
Abstract
Formate dehydrogenases are critical tools for nicotinamide cofactor regeneration, but their limited catalytic efficiency (kcat/Km) is a major drawback. A formate dehydrogenase from Burkholderia stabilis 15516 (BstFDH) was the first native NADP+-dependent formate dehydrogenase reported and has the highest kcat/Km toward NADP+ (kcat/KmNADP+) compared with other FDHs that can utilize NADP+ as a hydrogen acceptor. However, the substrate and cofactor affinities of BstFDH are inferior to those of other FDHs, making its practical application difficult. Herein, we engineered recombinant BstFDH to enhance its HCOO- and NADP+ affinities. Based on sequence information analysis and homologous modeling results, I124, G146, S262, and A287 were found to affect the binding affinity for HCOO- and NADP+. By combining these mutations, we identified a BstFDH variant (G146M/A287G) that reduced KmNADP+ to 0.09 mM, with a concomitant decrease in KmHCOO-, and gave 1.6-fold higher kcat/KmNADP+ than the wild type (WT). Furthermore, BstFDH I124V/G146H/A287G, with the lowest KmHCOO- of 8.51 mM, showed a catalytic efficiency that was 2.3-fold higher than that of the wild type and a decreased KmNADP+ of 0.11 mM. These results are beneficial for improving the performance of NADP+-dependent formate dehydrogenase in the NADPH regeneration of various bioreductive reactions and provide a useful guide for engineering of the substrate and cofactor affinity of other enzymes.
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Affiliation(s)
- He-Wen Jiang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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2
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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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3
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The physiology and biotechnology of dark fermentative biohydrogen production. Biotechnol Adv 2018; 36:2165-2186. [DOI: 10.1016/j.biotechadv.2018.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 02/02/2023]
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4
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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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5
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Sultana S, Chandra Sahoo P, Martha S, Parida K. A review of harvesting clean fuels from enzymatic CO2 reduction. RSC Adv 2016. [DOI: 10.1039/c6ra05472b] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This review has summarised single enzyme, multi enzymatic and semiconducting nanomaterial integrated enzymatic systems for CO2 conversion to clean fuels.
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Affiliation(s)
- Sabiha Sultana
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Prakash Chandra Sahoo
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Satyabadi Martha
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
| | - Kulamani Parida
- Centre for Nano Science and Nano Technology
- ITER
- Siksha ‘O’ Anusandhan University
- Bhubaneswar – 751030
- India
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6
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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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7
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Mattozzi MD, Ziesack M, Voges MJ, Silver PA, Way JC. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metab Eng 2013; 16:130-9. [PMID: 23376595 DOI: 10.1016/j.ymben.2013.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/08/2013] [Accepted: 01/17/2013] [Indexed: 01/11/2023]
Abstract
The 3-hydroxypropionate (3-HPA) bicycle is unique among CO2-fixing systems in that none of its enzymes appear to be affected by oxygen. Moreover, the bicycle includes a number of enzymes that produce novel intermediates of biotechnological interest, and the CO2-fixing steps in this pathway are relatively rapid. We expressed portions of the 3-HPA bicycle in a heterologous organism, E. coli K12. We subdivided the 3-HPA bicycle into four sub-pathways: (1) synthesis of propionyl-CoA from acetyl-CoA, (2) synthesis of succinate from propionyl-CoA, (3) glyoxylate production and regeneration of acetyl-CoA, and (4) assimilation of glyoxylate and propionyl-CoA to form pyruvate and regenerate acetyl-CoA. We expressed the novel enzymes of the 3-HPA bicycle in operon form and used phenotypic tests for activity. Sub-pathway 1 activated a propionate-specific biosensor. Sub-pathway 2, found in non-CO2-fixing bacteria, was reassembled in E. coli using genes from diverse sources. Sub-pathway 3, operating in reverse, generated succinyl-CoA sufficient to rescue a sucAD(-) double mutant of its diaminopimelic acid (DAP) auxotrophy. Sub-pathway 4 was able to reduce the toxicity of propionate and allow propionate to contribute to cell biomass in a prpC(-)(2 methylcitrate synthase) mutant strain. These results indicate that all of the sub-pathways of the 3-HPA bicycle can function to some extent in vivo in a heterologous organism, as indicated by growth tests. Overexpression of certain enzymes was deleterious to cell growth, and, in particular, expression of MMC-CoA lyase caused a mucoid phenotype. These results have implications for metabolic engineering and for bacterial evolution through horizontal gene transfer.
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Affiliation(s)
- Matthew d Mattozzi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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8
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Zou Y, Zhang H, Brunzelle JS, Johannes TW, Woodyer R, Hung JE, Nair N, van der Donk WA, Zhao H, Nair SK. Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration. Biochemistry 2012; 51:4263-70. [PMID: 22564171 DOI: 10.1021/bi2016926] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent conversion of phosphite to phosphate and represents the first biological catalyst that has been shown to conduct the enzymatic oxidation of phosphorus. Despite investigation for more than a decade into both the mechanism of its unusual reaction and its utility in cofactor regeneration, there has been a lack of any structural data for PTDH. Here we present the cocrystal structure of an engineered thermostable variant of PTDH bound to NAD(+) (1.7 Å resolution), as well as four other cocrystal structures of thermostable PTDH and its variants with different ligands (all between 1.85 and 2.3 Å resolution). These structures provide a molecular framework for understanding prior mutational analysis and point to additional residues, located in the active site, that may contribute to the enzymatic activity of this highly unusual catalyst.
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Affiliation(s)
- Yaozhong Zou
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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9
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Hoelsch K, Sührer I, Heusel M, Weuster-Botz D. Engineering of formate dehydrogenase: synergistic effect of mutations affecting cofactor specificity and chemical stability. Appl Microbiol Biotechnol 2012; 97:2473-81. [PMID: 22588502 DOI: 10.1007/s00253-012-4142-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 12/01/2022]
Abstract
Formate dehydrogenases (FDHs) are frequently used for the regeneration of cofactors in biotransformations employing NAD(P)H-dependent oxidoreductases. Major drawbacks of most native FDHs are their strong preference for NAD(+) and their low operational stability in the presence of reactive organic compounds such as α-haloketones. In this study, the FDH from Mycobacterium vaccae N10 (MycFDH) was engineered in order to obtain an enzyme that is not only capable of regenerating NADPH but also stable toward the α-haloketone ethyl 4-chloroacetoacetate (ECAA). To change the cofactor specificity, amino acids in the conserved NAD(+) binding motif were mutated. Among these mutants, MycFDH A198G/D221Q had the highest catalytic efficiency (k cat/K m) with NADP(+). The additional replacement of two cysteines (C145S/C255V) not only conferred a high resistance to ECAA but also enhanced the catalytic efficiency 6-fold. The resulting quadruple mutant MycFDH C145S/A198G/D221Q/C255V had a specific activity of 4.00 ± 0.13 U mg(-1) and a K m, NADP(+) of 0.147 ± 0.020 mM at 30 °C, pH 7. The A198G replacement had a major impact on the kinetic constants of the enzyme. The corresponding triple mutant, MycFDH C145S/D221Q/C255V, showed the highest specific activity reported to date for a NADP(+)-accepting FDH (v max, 10.25 ± 1.63 U mg(-1)). However, the half-saturation constant for NADP(+) (K m, NADP(+) , 0.92 ± 0.10 mM) was about one order of magnitude higher than the one of the quadruple mutant. Depending on the reaction setup, both novel MycFDH variants could be useful for the production of the chiral synthon ethyl (S)-4-chloro-3-hydroxybutyrate [(S)-ECHB] by asymmetric reduction of ECAA with NADPH-dependent ketoreductases.
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Affiliation(s)
- Kathrin Hoelsch
- Institute of Biochemical Engineering, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany.
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10
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Hall M, Bommarius AS. Enantioenriched Compounds via Enzyme-Catalyzed Redox Reactions. Chem Rev 2011; 111:4088-110. [DOI: 10.1021/cr200013n] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mélanie Hall
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, Georgia 30332, United States
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
| | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, Georgia 30332, United States
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11
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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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12
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Fröhlich P, Albert K, Bertau M. Formate dehydrogenase - a biocatalyst with novel applications in organic chemistry. Org Biomol Chem 2011; 9:7941-50. [DOI: 10.1039/c1ob06064c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Durante-Rodríguez G, Valderrama JA, Mancheño JM, Rivas G, Alfonso C, Arias-Palomo E, Llorca O, García JL, Díaz E, Carmona M. Biochemical characterization of the transcriptional regulator BzdR from Azoarcus sp. CIB. J Biol Chem 2010; 285:35694-705. [PMID: 20826820 DOI: 10.1074/jbc.m110.143503] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The BzdR transcriptional regulator that controls the P(N) promoter responsible for the anaerobic catabolism of benzoate in Azoarcus sp. CIB constitutes the prototype of a new subfamily of transcriptional regulators. Here, we provide some insights about the functional-structural relationships of the BzdR protein. Analytical ultracentrifugation studies revealed that BzdR is homodimeric in solution. An electron microscopy three-dimensional reconstruction of the BzdR dimer has been obtained, and the predicted structures of the respective N- and C-terminal domains of each BzdR monomer could be fitted into such a reconstruction. Gel retardation and ultracentrifugation experiments have shown that the binding of BzdR to its cognate promoter is cooperative. Different biochemical approaches revealed that the effector molecule benzoyl-CoA induces conformational changes in BzdR without affecting its oligomeric state. The BzdR-dependent inhibition of the P(N) promoter and its activation in the presence of benzoyl-CoA have been established by in vitro transcription assays. The monomeric BzdR4 and BzdR5 mutant regulators revealed that dimerization of BzdR is essential for DNA binding. Remarkably, a BzdRΔL protein lacking the linker region connecting the N- and C-terminal domains of BzdR is also dimeric and behaves as a super-repressor of the P(N) promoter. These data suggest that the linker region of BzdR is not essential for protein dimerization, but rather it is required to transfer the conformational changes induced by the benzoyl-CoA to the DNA binding domain leading to the release of the repressor. A model of action of the BzdR regulator has been proposed.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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14
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Site-saturation mutagenesis of formate dehydrogenase from Candida bodinii creating effective NADP+-dependent FDH enzymes. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Zhu X, Tan X. Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0082-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Andreadeli A, Flemetakis E, Axarli I, Dimou M, Udvardi MK, Katinakis P, Labrou NE. Cloning and characterization of Lotus japonicus formate dehydrogenase: a possible correlation with hypoxia. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:976-84. [PMID: 19281876 DOI: 10.1016/j.bbapap.2009.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 02/12/2009] [Accepted: 02/13/2009] [Indexed: 10/21/2022]
Abstract
Formate dehydrogenases (FDHs, EC 1.2.1.2) comprise a group of enzymes found in both prokaryotes and eukaryotes that catalyse the oxidation of formate to CO(2). FDH1 from the model legume Lotus japonicus (LjFDH1) was cloned and expressed in E. coli BL21(DE3) as soluble active protein. The enzyme was purified using affinity chromatography on Cibacron blue 3GA-Sepharose. The enzymatic properties of the recombinant enzyme were investigated and the kinetic parameters (K(m), k(cat)) for a number of substrates were determined. Molecular modelling studies were also employed to create a model of LjFDH1, based on the known structure of the Pseudomonas sp. 101 enzyme. The molecular model was used to help interpret biochemical data concerning substrate specificity and catalytic mechanism of the enzyme. The temporal expression pattern of LjFDH1 gene was studied by real-time RT-PCR in various plant organs and during the development of nitrogen-fixing nodules. Furthermore, the spatial transcript accumulation during nodule development and in young seedpods was determined by in situ RNA-RNA hybridization. These results considered together indicate a possible role of formate oxidation by LjFDH1 in plant tissues characterized by relative hypoxia.
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Affiliation(s)
- A Andreadeli
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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17
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Bolivar JM, Wilson L, Ferrarotti SA, Fernandez-Lafuente R, Guisan JM, Mateo C. Evaluation of different immobilization strategies to prepare an industrial biocatalyst of formate dehydrogenase from Candida boidinii. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.05.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Bolivar JM, Wilson L, Ferrarotti SA, Fernandez-Lafuente R, Guisan JM, Mateo C. Stabilization of a formate dehydrogenase by covalent immobilization on highly activated glyoxyl-agarose supports. Biomacromolecules 2006; 7:669-73. [PMID: 16529396 DOI: 10.1021/bm050947z] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate dehydrogenase (FDH) is a stable enzyme that may be readily inactivated by the interaction with hydrophobic interfaces (e.g., due to strong stirring). This may be avoided by immobilizing the enzyme on a porous support by any technique. Thus, even if the enzyme is going to be used in an ultra-membrane reactor, the immobilization presents some advantages. Immobilization on supports activated with bromocianogen, polyethylenimine, glutaraldehyde, etc., did not promote any stabilization of the enzyme under thermal inactivation. However, the immobilization of FDH on highly activated glyoxyl agarose has permitted increasing the enzyme stability against any distorting agent: pH, T, organic solvent, etc. The time of support-enzyme reaction, the temperature of immobilization, and the activation of the support need to be optimized to get the optimal stability-activity properties. Optimized biocatalyst retained 50% of the offered activity and became 50 times more stable at high temperature and neutral pH. Moreover, the quaternary structure of this dimeric enzyme becomes stabilized by immobilization under optimized conditions. Thus, at acidic pH (conditions where the subunit dissociation is the first step in the enzyme inactivation), the immobilization of both subunits of the enzyme on glyoxyl-agarose has allowed the enzyme to be stabilized by hundreds of times. Moreover, the optimal temperature of the enzyme has been increased (even by 10 degrees C at pH 4.5). Very interestingly, the activity with NAD(+)-dextran was around 60% of that observed with free cofactor.
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Affiliation(s)
- Juan M Bolivar
- Departamento de Biocatalisis, Instituto de Catalisis-CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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Kan E, Deshusses MA. Cometabolic degradation of TCE vapors in a foamed emulsion bioreactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2006; 40:1022-8. [PMID: 16509352 DOI: 10.1021/es0510055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Effective cometabolic biodegradation of trichloroethylene (TCE) vapors in a novel gas-phase bioreactor called the foamed emulsion bioreactor (FEBR) was demonstrated. Toluene vapors were used as the primary growth substrate for Burkholderia cepacia G4 which cometabolically biodegraded TCE. Batch operation of the reactor with respect to the liquid feed showed a drastic decrease of TCE and toluene removal over time, consistent with a loss of metabolic activity caused by the exposure to TCE metabolites. Sustained TCE removal could be achieved when continuous feeding of mineral medium was implemented, which supported cell growth and compensated for the deactivation of cells. The FEBR exhibited its highest TCE removal efficiencies (82-96%) and elimination capacities (up to 28 gTCE m(-3) h(-1)) when TCE and toluene vapors were fed sequentially to circumvent the competitive inhibition by toluene. The TCE elimination capacity was 2-1000 times higher than reported in other gas-phase biotreatment reports. During the experiments, 85-101% of the degraded TCE chlorine was recovered as chloride. Overall, the results suggestthatthe FEBR can be a very effective system to treat TCE vapors cometabolically.
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Affiliation(s)
- Eunsung Kan
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
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20
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Martins BM, Macedo-Ribeiro S, Bresser J, Buckel W, Messerschmidt A. Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans. FEBS J 2005; 272:269-81. [PMID: 15634349 DOI: 10.1111/j.1432-1033.2004.04417.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyses the reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate and belongs to the d-2-hydroxyacid NAD(+)-dependent dehydrogenase (d-2-hydroxyacid dehydrogenase) protein family. Its crystal structure was determined by phase combination to 1.98 A resolution. Structure-function relationships obtained by the comparison of HGDH with other members of the d-2-hydroxyacid dehydrogenase family give a chemically satisfying view of the substrate stereoselectivity and catalytic requirements for the hydride transfer reaction. A model for substrate recognition and turnover is discussed. The HGDH active site architecture is structurally optimized to recognize and bind the negatively charged substrate 2-oxoglutarate. The structural position of the side chain of Arg52, and its counterparts in other family members, strongly correlates with substrate specificity towards substitutions at the C3 atom (linear or branched substrates). Arg235 interacts with the substrate's alpha-carboxylate and carbonyl groups, having a dual role in both substrate binding and activation, and the gamma-carboxylate group can dock at an arginine cluster. The proton-relay system built up by Glu264 and His297 permits His297 to act as acid-base catalyst and the 4Re-hydrogen from NADH is transferred as hydride to the carbonyl group Si-face leading to the formation of the correct enantiomer (R)-2-hydroxyglutarate.
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21
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Yamamoto H, Mitsuhashi K, Kimoto N, Kobayashi Y, Esaki N. Robust NADH-regenerator: improved alpha-haloketone-resistant formate dehydrogenase. Appl Microbiol Biotechnol 2004; 67:33-9. [PMID: 15338080 DOI: 10.1007/s00253-004-1728-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Revised: 07/18/2004] [Accepted: 06/23/2004] [Indexed: 11/30/2022]
Abstract
Formate dehydrogenases (FDH) are useful for the regeneration of NADH, which is required for asymmetric reduction by several dehydrogenases and reductases. FDHs have relatively low activity and are labile, especially to alpha-haloketones, thus FDH cannot be applied to the industrial manufacture of optically active alpha-haloalcohols. To stabilize a FDH from Mycobacterium vaccae (McFDH) against the alpha-haloketone ethyl 4-chloroacetoacetate (ECAA), a set of cysteine-mutant enzymes was constructed. Sensitivity to ECAA of mutant C6S was similar to that of the wild-type enzyme, and mutants C249S and C355S showed little activity. In contrast, mutant C256S exhibited remarkable tolerance to ECAA. Surprisingly, mutant C146S was activated by several organic compounds such as ethyl acetate. An optimized mutant, C6A/C146S/C256V (McFDH-26), was obtained by combining several effective mutations. Ethyl (S)-4-chloro-3-hydroxybutanoate [(S)-ECHB] was synthesized from ECAA to 49.9 g/l with an optical purity of more than 99% e.e. using recombinant Escherichia coli cells coexpressing McFDH-26 and a carbonyl reductase (KaCR1) from Kluyveromyces aestuarii.
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Affiliation(s)
- H Yamamoto
- Life Science Development Center, CPI Company, Tsukuba Research Center, Daicel Chemical Industries, 27 Miyukigaoka, Tsukuba 305-0841, Japan.
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22
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Bell JK, Grant GA, Banaszak LJ. Multiconformational States in Phosphoglycerate Dehydrogenase†,‡. Biochemistry 2004; 43:3450-8. [PMID: 15035616 DOI: 10.1021/bi035462e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphoglycerate dehydrogenase (PGDH) catalyzes the first step in the serine biosynthetic pathway. In lower plants and bacteria, the PGDH reaction is regulated by the end-product of the pathway, serine. The regulation occurs through a V(max) mechanism with serine binding and inhibition occurring in a cooperative manner. The three-dimensional structure of the serine inhibited enzyme, determined by previous work, showed a tetrameric enzyme with 222 symmetry and an unusual overall toroidal appearance. To characterize the allosteric, cooperative effects of serine, we identified W139G PGDH as an enzymatically active mutant responsive to serine but not in a cooperative manner. The position of W139 near a subunit interface and the active site cleft suggested that this residue is a key player in relaying allosteric effects. The 2.09 A crystal structure of W139G-PGDH, determined in the absence of serine, revealed major quaternary and tertiary structural changes. Contrary to the wildtype enzyme where residues encompassing residue 139 formed extensive intersubunit contacts, the corresponding residues in the mutant were conformationally flexible. Within each of the three-domain subunits, one domain has rotated approximately 42 degrees relative to the other two. The resulting quaternary structure is now in a novel conformation creating new subunit-to-subunit contacts and illustrates the unusual flexibility in this V(max) regulated enzyme. Although changes at the regulatory domain interface have implications in other enzymes containing a similar regulatory or ACT domain, the serine binding site in W139G PGDH is essentially unchanged from the wildtype enzyme. The structural and previous biochemical characterization of W139G PGDH suggests that the allosteric regulation of PGDH is mediated not only by changes occurring at the ACT domain interface but also by conformational changes at the interface encompassing residue W139.
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Affiliation(s)
- Jessica K Bell
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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23
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Bykova NV, Stensballe A, Egsgaard H, Jensen ON, Moller IM. Phosphorylation of formate dehydrogenase in potato tuber mitochondria. J Biol Chem 2003; 278:26021-30. [PMID: 12714601 DOI: 10.1074/jbc.m300245200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two highly phosphorylated proteins were detected after two-dimensional (blue native/SDS-PAGE) gel electrophoretic separation of the matrix fraction isolated from potato tuber mitochondria. These two phosphoproteins were identified by mass spectrometry as formate dehydrogenase (FDH) and the E1alpha-subunit of pyruvate dehydrogenase (PDH). Isoelectric focusing/SDS-PAGE two-dimensional gels separated FDH and PDH and resolved several different phosphorylated forms of FDH. By using combinations of matrix-assisted laser desorption/ionization mass spectrometry and electrospray ionization tandem mass spectrometry, several phosphorylation sites were identified for the first time in FDH and PDH. FDH was phosphorylated on Thr76 and Thr333, whereas PDH was phosphorylated on Ser294. Both Thr76 and Thr333 in FDH were accessible to protein kinases, as demonstrated by protein structure homology modeling. The extent of phosphorylation of both FDH and PDH was strongly decreased by NAD+, formate, and pyruvate, indicating that reversible phosphorylation of FDH and PDHs was regulated in a similar fashion. At low oxygen concentrations inside the intact potato tubers, FDH activity was strongly increased relative to cytochrome c oxidase activity pointing to a possible involvement of FDH in hypoxic metabolism. Computational sequence analysis indicated that a conserved local sequence motif of pyruvate formate-lyase is found in the Arabidopsis thaliana genome, and this enzyme might be the source of formate for FDH in plants.
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Affiliation(s)
- Natalia V Bykova
- Plant Research Department, Risø National Laboratory, P. O. Box 49, DK-4000 Roskilde, Denmark
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24
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Razeto A, Kochhar S, Hottinger H, Dauter M, Wilson KS, Lamzin VS. Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus. J Mol Biol 2002; 318:109-19. [PMID: 12054772 DOI: 10.1016/s0022-2836(02)00086-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NAD-dependent Lactobacillus bulgaricus D-Lactate dehydrogenase (D-LDHb) catalyses the reversible conversion of pyruvate into D-lactate. Crystals of D-LDHb complexed with NADH were grown and X-ray data collected to 2.2 A. The structure of D-LDHb was solved by molecular replacement using the dimeric Lactobacillus helveticus D-LDH as a model and was refined to an R-factor of 20.7%. The two subunits of the enzyme display strong asymmetry due to different crystal environments. The opening angles of the two catalytic domains with respect to the core coenzyme binding domains differ by 16 degrees. Subunit A is in an "open" conformation typical for a dehydrogenase apo enzyme and subunit B is "closed". The NADH-binding site in subunit A is only 30% occupied, while in subunit B it is fully occupied and there is a sulphate ion in the substrate-binding pocket. A pyruvate molecule has been modelled in the active site and its orientation is in agreement with existing kinetic and structural data. On domain closure, a cluster of hydrophobic residues packs tightly around the methyl group of the modelled pyruvate molecule. At least three residues from this cluster govern the substrate specificity. Substrate binding itself contributes to the stabilisation of domain closure and activation of the enzyme. In pyruvate reduction, D-LDH can adapt another protonated residue, a lysine residue, to accomplish the role of the acid catalyst His296. Required lowering of the lysine pK(a) value is explained on the basis of the H296K mutant structure.
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Affiliation(s)
- Adelia Razeto
- European Molecular Biology Laboratory Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.
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25
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Galkin AG, Kutsenko AS, Bajulina NP, Esipova NG, Lamzin VS, Mesentsev AV, Shelukho DV, Tikhonova TV, Tishkov VI, Ustinnikova TB, Popov VO. Site-directed mutagenesis of the essential arginine of the formate dehydrogenase active centre. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1594:136-49. [PMID: 11825616 DOI: 10.1016/s0167-4838(01)00297-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Sequence alignment shows that residue Arg 284 (according to the numbering of the residues in formate dehydrogenase, FDH, from the methylotrophic bacterium Pseudomonas sp. 101) is conserved in NAD-dependent FDHs and D-specific 2-hydroxyacid dehydrogenases. Mutation of Arg 284 to glutamine and alanine results in a change of the catalytic, thermodynamic and spectral properties of FDH. In comparison to wild-type, the affinity of the mutants for the substrate (K(formate)m) or the transition state analogue (K(azide)i) decreases and correlates with the ability of the side chain of residue 284 to form H-bonds. In contrast, the affinity for the coenzyme (K(NAD)d or K(NAD)m) is either not affected or increases and correlates inversely with the partial positive charge of the side chain. The temperature dependence of circular dichroism (CD) spectra of the wild-type FDH and its Ala mutant has been studied over the 5-90 degrees C temperature range. Both proteins reveal regions of enhanced conformational mobility at the predenaturing temperatures (40-55 degrees C) associated with a change of enzyme kinetic parameters and a co-operative transition around 55-70 degrees C which is followed by the loss of enzyme activity. CD spectra of the wild-type and mutant proteins were deconvoluted and contributions from various types of secondary structure estimated. It is shown that the co-operative transition at 55-70 degrees C in the FDH protein globule is triggered by a loss of alpha-helical secondary structure. The results confirm the conclusion, from the crystal structures, that Arg 284 is directly involved in substrate binding. In addition this residue seems to exert a major structural role by supporting the catalytic conformation of the enzyme active centre.
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Affiliation(s)
- Andrey G Galkin
- Department of Chemical Enzymology, M.V. Lomonosov Moscow State University, Leninskie Gori, 119899 Moscow, Russia
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26
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Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A 2001; 98:9883-8. [PMID: 11481432 PMCID: PMC55547 DOI: 10.1073/pnas.161294798] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.
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Affiliation(s)
- M J Barnett
- Department of Biological Sciences, and Howard Hughes Medical Institute, Stanford University, CA 94305, USA
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27
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Labrou NE, Rigden DJ. Active-site characterization of Candida boidinii formate dehydrogenase. Biochem J 2001; 354:455-63. [PMID: 11171126 PMCID: PMC1221675 DOI: 10.1042/0264-6021:3540455] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NAD+-dependent formate dehydrogenase (FDH) from Candida boidinii was cloned and expressed to a high level in Escherichia coli (20% of soluble E. coli protein). Molecular modelling studies were used to create a three-dimensional model of C. boidinii FDH, based on a known structure of the Pseudomonas sp. 101 enzyme. This model was used for investigating the catalytic mechanism by site-directed mutagenesis. Eleven forms of C. boidinii FDH were characterized by steady-state kinetic analysis: the wild type as well as 10 mutants involving single (Phe-69-Ala, Asn-119-His, Ile-175-Ala, Gln-197-Leu, Arg-258-Ala, Gln-287-Glu and His-311-Gln) and double amino acid substitutions (Asn-119-His/His-311-Gln, Gln-287-Glu/His-311-Gln and Gln-287-Glu/Pro-288-Thr). The kinetic results of the mutant enzymes provide the first experimental support that hydrophobic patches, formed by Phe-69 and Ile-175, destabilize substrates and stabilize products. Also, the key role of Arg-258 in stabilization of the negative charge on the migrating hydride was established. Asn-119, besides being an anchor group for formate, also may comprise one of the hinge regions around which the two domains shift on binding of NAD+. The more unexpected results, obtained for the His-311-Gln and Gln-287-Glu/His-311-Gln mutants, combined with molecular modelling, suggest that steric as well as electrostatic properties of His-311 are important for enzyme function. An important structural role has also been attributed to cis-Pro-288. This residue may provide the key residues Gln-287 and His-311 with the proper orientation for productive binding of formate.
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Affiliation(s)
- N E Labrou
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece.
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28
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Labrou NE, Rigden DJ, Clonis YD. Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6657-64. [PMID: 11054119 DOI: 10.1046/j.1432-1327.2000.01761.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The 2',3'-dialdehyde derivative of ADP (oADP) has been shown to be an affinity label for the NAD+ binding site of recombinant Candida boidinii formate dehydrogenase (FDH). Inactivation of FDH by oADP at pH 7.6 followed biphasic pseudo first-order saturation kinetics. The rate of inactivation exhibited a nonlinear dependence on the concentration of oADP, which can be described by reversible binding of reagent to the enzyme (Kd = 0.46 mM for the fast phase, 0.45 mM for the slow phase) prior to the irreversible reaction, with maximum rate constants of 0.012 and 0.007 min-1 for the fast and slow phases, respectively. Inactivation of formate dehydrogenase by oADP resulted in the formation of an enzyme-oADP product, a process that was reversed after dialysis or after treatment with 2-mercaptoethanol (> 90% reactivation). The reactivation of the enzyme by 2-mercaptoethanol was prevented if the enzyme-oADP complex was previously reduced by NaBH4, suggesting that the reaction product was a stable Schiff's base. Protection from inactivation was afforded by nucleotides (NAD+, NADH and ADP) demonstrating the specificity of the reaction. When the enzyme was completely inactivated, approximately 1 mol of [14C]oADP per mol of subunit was incorporated. Cleavage of [14C]oADP-modified enzyme with trypsin and subsequent separation of peptides by RP-HPLC gave only one radioactive peak. Amino-acid sequencing of the radioactive tryptic peptide revealed the target site of oADP reaction to be Lys360. These results indicate that oADP inactivates FDH by specific reaction at the nucleotide binding site, with negative cooperativity between subunits accounting for the appearance of two phases of inactivation. Molecular modelling studies were used to create a model of C. boidinii FDH, based on the known structure of the Pseudomonas enzyme, using the MODELLER 4 program. The model confirmed that Lys360 is positioned at the NAD+-binding site. Site-directed mutagenesis was used in dissecting the structure and functional role of Lys360. The mutant Lys360-->Ala enzyme exhibited unchanged kcat and Km values for formate but showed reduced affinity for NAD+. The molecular model was used to help interpret these biochemical data concerning the Lys360-->Ala enzyme. The data are discussed in terms of engineering coenzyme specificity.
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Affiliation(s)
- N E Labrou
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, Greece
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29
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Torres RA, Schiøtt B, Bruice TC. Molecular Dynamics Simulations of Ground and Transition States for the Hydride Transfer from Formate to NAD+ in the Active Site of Formate Dehydrogenase. J Am Chem Soc 1999. [DOI: 10.1021/ja9912731] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rhonda A. Torres
- Contribution from the Department of Chemistry, University of California, Santa Barbara, California 93106
| | - Birgit Schiøtt
- Contribution from the Department of Chemistry, University of California, Santa Barbara, California 93106
| | - Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California, Santa Barbara, California 93106
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30
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Xu Y, Bhargava G, Wu H, Loeber G, Tong L. Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme: a new class of oxidative decarboxylases. Structure 1999. [DOI: 10.1016/s0969-2126(99)80115-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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31
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Neuhauser W, Steininger M, Haltrich D, Kulbe KD, Nidetzky B. A pH-controlled fed-batch process can overcome inhibition by formate in NADH-dependent enzymatic reductions using formate dehydrogenase-catalyzed coenzyme regeneration. Biotechnol Bioeng 1998; 60:277-82. [PMID: 10099429 DOI: 10.1002/(sici)1097-0290(19981105)60:3<277::aid-bit2>3.0.co;2-e] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The NAD-dependent, formate dehydrogenase-catalyzed oxidation of formate anion into CO2 is known as the method for the regeneration of NADH in reductive enzymatic syntheses. Inhibition by formate and inactivation by alkaline pH-shift that occurs when oxidation of formate is carried out at pH approximately 7.0 may, however, hamper the efficient application of this NADH recycling reaction. Here, we have devised a fed-batch process using pH-controlled feeding of formic acid that can overcome enzyme inhibition and inactivation. The reaction pH is thus kept constant by addition of acid, and formate dehydrogenase is supplied continuously with substrate as required, but the concentration of formate is maintained at a constant, non- or weakly inhibitory level throughout the enzymatic conversion, thus enabling a particular NADH-dependent dehydrogenase to operate stably and at high reaction rates. For xylitol production from xylose using yeast xylose reductase (Ki,Formate 182 mM), a fed-batch conversion of 0.5M xylose yielded productivities of 2.8 g (L h)-1 that are three-fold improved when contrasted to a conventional batch reaction that employed equal initial concentrations of xylose and formate.
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Affiliation(s)
- W Neuhauser
- Division of Biochemical Engineering, Universität für Bodenkultur Wien (BOKU), Muthgasse 18, A-1190 Wien, Austria
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32
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Schiøtt B, Zheng YJ, Bruice TC. Theoretical Investigation of the Hydride Transfer from Formate to NAD+ and the Implications for the Catalytic Mechanism of Formate Dehydrogenase. J Am Chem Soc 1998. [DOI: 10.1021/ja9807338] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Birgit Schiøtt
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Ya-Jun Zheng
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
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33
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Turner MA, Yuan CS, Borchardt RT, Hershfield MS, Smith GD, Howell PL. Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. NATURE STRUCTURAL BIOLOGY 1998; 5:369-76. [PMID: 9586999 DOI: 10.1038/nsb0598-369] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
S-Adenosylhomocysteine (AdoHcy) hydrolase regulates all adenosylmethionine-(AdoMet) dependent transmethylations by hydrolyzing the potent feedback inhibitor AdoHcy to homocysteine and adenosine. The crystallographic structure determination of a selenomethionyl-incorporated AdoHcy hydrolase inhibitor complex was accomplished using single wavelength anomalous diffraction data and the direct methods program, Snb v2.0, which produced the positions of all 30 crystallographically distinct selenium atoms. The mode of enzyme-cofactor binding is unique, requiring interactions from two protein monomers. An unusual dual role for a catalytic water molecule in the active site is revealed in the complex with the adenosine analog 2'-hydroxy, 3'-ketocyclopent-4'-enyladenine.
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Affiliation(s)
- M A Turner
- Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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34
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Suzuki K, Itai R, Suzuki K, Nakanishi H, Nishizawa NK, Yoshimura E, Mori S. Formate dehydrogenase, an enzyme of anaerobic metabolism, is induced by iron deficiency in barley roots. PLANT PHYSIOLOGY 1998; 116:725-32. [PMID: 9489019 PMCID: PMC35132 DOI: 10.1104/pp.116.2.725] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/1997] [Accepted: 11/14/1997] [Indexed: 05/20/2023]
Abstract
To identify the proteins induced by Fe deficiency, we have compared the proteins of Fe-sufficient and Fe-deficient barley (Hordeum vulgare L.) roots by two-dimensional polyacrylamide gel electrophoresis. Peptide sequence analysis of induced proteins revealed that formate dehydrogenase (FDH), adenine phosphoribosyltransferase, and the lds3 gene product (for Fe deficiency-specific) increased in Fe-deficient roots. FDH enzyme activity was detected in Fe-deficient roots but not in Fe-sufficient roots. A cDNA encoding FDH (Fdh) was cloned and sequenced. Fdh expression was induced by Fe deficiency. Fdh was also expressed under anaerobic stress and its expression was more rapid than that induced by Fe deficiency. Thus, the expression of Fdh observed in Fe-deficient barley roots appeared to be a secondary effect caused by oxygen deficiency in Fe-deficient plants.
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Affiliation(s)
- K Suzuki
- Department of Applied Biological Chemistry, University of Tokyo, Japan
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35
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Dengler U, Niefind K, Kiess M, Schomburg D. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. J Mol Biol 1997; 267:640-60. [PMID: 9126843 DOI: 10.1006/jmbi.1996.0864] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei is a homodimer with 333 amino acids and a molecular mass of 37 kDa per subunit. The enzyme belongs to the protein family of NAD+-dependent D-2-hydroxycarboxylate dehydrogenases and within this family to the subgroup of D-lactate dehydrogenases (D-LDHs). Compared with other D-LDHs D-HicDH is characterized by a very low specificity regarding size and chemical constitution of the accepted D-2-hydroxycarboxylates. Hexagonal crystals of recombinant D-HicDH in the presence of NAD+ and 2-oxoisocaproate (4-methyl-2-oxopentanoate) were grown with ammonium sulphate as precipitating agent. The structure of these crystals was solved by molecular replacement and refined to a final R-factor of 19.6% for all measured X-ray reflections in the resolution range (infinity to 1.86 A). Both NAD+ and 2-oxoisocaproate were identified in the electron density map; binding of the latter in the active site, however, competes with a sulphate ion, which is also defined by electron density. Additionally the final model contains 182 water molecules and a second sulphate ion. The binding of both an in vitro substrate and the natural cosubstrate in the active site provides substantial insight into the catalytic mechanism and allows us to assess previously published active site models for this enzyme family, in particular the two most controversial points, the role of the conserved Arg234 and substrate binding. Furthermore the overall topology and details of the D-HicDH structure are described, discussed against the background of homologous structures and compared with one closely and one distantly related protein.
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Affiliation(s)
- U Dengler
- Gesellschaft fur Biotechnologische Forschung (GBF), Abteilung Molekulare Strukturforschung, Braunschweig, Germany
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36
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Bernard N, Johnsen K, Gelpi JL, Alvarez JA, Ferain T, Garmyn D, Hols P, Cortes A, Clarke AR, Holbrook JJ, Delcour J. D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus. II. Mutagenic analysis of catalytically important residues. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:213-9. [PMID: 9063466 DOI: 10.1111/j.1432-1033.1997.00213.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Five residues involved in catalysis and coenzyme binding have been identified in D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus by using biochemical and genetical methods. Enzyme inactivation with diethylpyrocarbonate indicated that a single histidine residue was involved in catalysis. Since H296 is the only conserved histidine in the whole family of NAD-dependent D-2-hydroxyacid dehydrogenases, we constructed the H296Q and H296S mutants and showed that their catalytic efficiencies were reduced 10(5)-fold compared with the wild-type enzyme. This low residual activity was shown to be insensitive to diethylpyrocarbonate. Taken together these data demonstrate that H296 is responsible for proton exchange in the redox reaction. Two acidic residues (D259 and E264) were candidates for maintaining H296 in the protonated state and their roles were examined by mutagenesis. The D259N and E264Q mutant enzymes both showed similar and large reductions in their Kcat/K(m) ratios (200-800-fold, depending on pH), indicating that either D259 or E264 (or both) could partner H296. The conserved R235 residue was a candidate for binding the alpha-carboxyl group of the substrate and it was changed to lysine. The R235K mutant showed a 104-fold reduced Kcat/K(m) due to both an increased K(m) and a reduced Kcat for 2-oxo-4-methylvalerate. Thus R235 plays a role in binding the substrate carboxylate similar to R171 in the L-lactate dehydrogenases. Finally, we constructed the H205Q mutant to test the role of this partially conserved histidine residue (in 10/13 enzymes of the family). This mutant enzyme displayed a 7.7-fold increased Kcat and a doubled catalytic efficiency at pH 5, was as sensitive to diethylpyrocarbonate as the wild-type but showed a sevenfold increased K(m) for NADH and a 100-fold increase in Kd for NADH together with 10-30-fold lower substrate inhibition. The transient kinetic behaviour of the H205Q mutant is as predicted from our previous study on the enzymatic mechanism of D-2-hydroxy-4-methylvalerate dehydrogenase which showed that coenzyme binding is highly pH dependent and indicated that release of the oxidised coenzyme is a significant component of the rate-limiting processes in catalysis at pH 6.5.
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Affiliation(s)
- N Bernard
- Unité de Génétique, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Mesentsev AV, Lamzin VS, Tishkov VI, Ustinnikova TB, Popov VO. Effect of pH on kinetic parameters of NAD+-dependent formate dehydrogenase. Biochem J 1997; 321 ( Pt 2):475-80. [PMID: 9020883 PMCID: PMC1218093 DOI: 10.1042/bj3210475] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To define in detail the molecular mechanism of NAD+-dependent formate dehydrogenase, the pH dependences of various kinetic and spectroscopic parameters have been studied: Vmax, Km (NAD+), Km (formate), inhibition constants for structural analogues of substrate (NO3-) and product (CNS-, CNO-, N3-), CD and fluorescence properties. The value of Vmax, rate-limiting hydride transfer, is nearly constant throughout the entire pH range of enzyme stability (6.0-11.2) but decreases below 6. The K(m) values for both substrates remain constant within the pH range 6-10. At pH values below 6 (for the coenzyme) and above 10 (for both substrate and coenzyme) the Km values increase. In the acidic range this change is attributed to the ionization of two carboxy groups (pK approx. 5.5-6.0) located at the NAD+-binding site of the enzyme active centre. The pH transition in the basic region (pK 10.5 +/- 0.2) has a conformational origin and affects the enzyme's affinity for substrates and anion inhibitors. A similar transition has been observed for formate dehydrogenases from yeast Candida boidinii and Hansenula polymorpha. The results complement the conclusions about the catalytic mechanism deduced from the crystal structure of the enzyme.
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Affiliation(s)
- A V Mesentsev
- A. N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Moscow
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38
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Abstract
All natural proteins are composed of L-amino acids and are inherently chiral. The properties of both L- and chemically synthesized D-amino acids are identical except in optically asymmetric interactions. Structural studies of D-I racemic mixtures of crystallographic interest are discussed. The review also gives some recent examples of stereospecificity: how L-proteins deal with L- or D-substrates and how enzymes can function as racemases. Two particular examples of stereoselectivity are then discussed.
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Affiliation(s)
- V S Lamzin
- European Molecular Biology Laboratory, Hamburg, Germany
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Abstract
The nicotinamide adenine dinucleotide (NAD)-binding domains of dehydrogenases, containing a conserved double beta-alpha-beta-alpha-beta motif, are common structural feature of many enzymes that bind NAD, nicotinamide adenine dinucleotide phosphate (NADP) and related cofactors. Features of this folding pattern that create a natural binding site for such molecules have been described. The domain continues to appear in many structures, in the form of a common core with different peripheral additions or variations. Other structures that bind NAD and related molecules use entirely different topologies, although, in many, a phosphate group appears at the N terminus of an alpha helix. Ferredoxin reductase seems to show convergent evolution, containing a single beta-alpha-beta motif that is similar both in its structure and in its interactions with the ligand to a region in dehydrogenases.
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Affiliation(s)
- A M Lesk
- University of Cambridge Clinical School, UK
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Garmyn D, Ferain T, Bernard N, Hols P, Delplace B, Delcour J. Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis. J Bacteriol 1995; 177:3427-37. [PMID: 7539419 PMCID: PMC177045 DOI: 10.1128/jb.177.12.3427-3437.1995] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The gene encoding D-lactate dehydrogenase was isolated on a 2.9-kb insert from a library of Pediococcus acidilactici DNA by complementation for growth under anaerobiosis of an Escherichia coli lactate dehydrogenase and pyruvate-formate lyase double mutant. The nucleotide sequence of ldhD encodes a protein of 331 amino acids (predicted molecular mass of 37,210 Da) which shows similarity to the family of D-2-hydroxyacid dehydrogenases. The enzyme encoded by the cloned fragment is equally active on pyruvate and hydroxypyruvate, indicating that the enzyme has both D-lactate and D-glycerate dehydrogenase activities. Three other open reading frames were found in the 2.9-kb insert, one of which (rpsB) is highly similar to bacterial genes coding for ribosomal protein S2. Northern (RNA) blotting analyses indicated the presence of a 2-kb dicistronic transcript of ldhD (a metabolic gene) and rpsB (a putative ribosomal protein gene) together with a 1-kb monocistronic rpsB mRNA. These transcripts are abundant in the early phase of exponential growth but steadily fade away to disappear in the stationary phase. Primer extension analysis identified two distinct promoters driving either cotranscription of ldhD and rpsB or transcription of rpsB alone.
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Affiliation(s)
- D Garmyn
- Laboratoire de Génétique Moléculaire, Université Catholique, Louvain-la-Neuve, Belgium
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41
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Vinals C, De Bolle X, Depiereux E, Feytmans E. Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure. Proteins 1995; 21:307-18. [PMID: 7567953 DOI: 10.1002/prot.340210405] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A three-dimensional structure of the NAD-dependent D-lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge-based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D-LDH subunit shows, as for the formate dehydrogenase, an alpha/beta structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His-296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg-235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe-299, a candidate for stabilizing the methyl group of the substrate.
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Affiliation(s)
- C Vinals
- Facultés Universitaires Notre Dame de la Paix, Namur, Belgium
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Fjellström O, Olausson T, Hu X, Källebring B, Ahmad S, Bragg PD, Rydström J. Three-dimensional structure prediction of the NAD binding site of proton-pumping transhydrogenase from Escherichia coli. Proteins 1995; 21:91-104. [PMID: 7777492 DOI: 10.1002/prot.340210203] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A three-dimensional structure of the NAD site of Escherichia coli transhydrogenase has been predicted. The model is based on analysis of conserved residues among the transhydrogenases from five different sources, homologies with enzymes using NAD as cofactors or substrates, hydrophilicity profiles, and secondary structure predictions. The present model supports the hypothesis that there is one binding site, located relatively close to the N-terminus of the alpha-subunit. The proposed structure spans residues alpha 145 to alpha 287, and it includes five beta-strands and five alpha-helices oriented in a typical open twisted alpha/beta conformation. The amino acid sequence following the GXGXXG dinucleotide binding consensus sequence (residues alpha 172 to alpha 177) correlates exactly to a typical fingerprint region for ADP binding beta alpha beta folds in dinucleotide binding enzymes. In the model, aspartic acid alpha 195 forms hydrogen bonds to one or both hydroxyl groups on the adenosine ribose sugar moiety. Threonine alpha 196 and alanine alpha 256, located at the end of beta B and beta D, respectively, create a hydrophobic sandwich with the adenine part of NAD buried inside. The nicotinamide part is located in a hydrophobic cleft between alpha A and beta E. Mutagenesis work has been carried out in order to test the predicted model and to determine whether residues within this domain are important for proton pumping directly. All data support the predicted structure, and no residue crucial for proton pumping was detected. Since no three-dimensional structure of transhydrogenase has been solved, a well based tertiary structure prediction is of great value for further experimental design in trying to elucidate the mechanism of the energy-linked proton pump.
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Affiliation(s)
- O Fjellström
- Department of Biochemistry and Biophysics, Göteborg University, Sweden
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43
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Affiliation(s)
- V O Popov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Moscow
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Lamzin VS, Dauter Z, Wilson KS. Dehydrogenation through the looking-glass. NATURE STRUCTURAL BIOLOGY 1994; 1:281-2. [PMID: 7664032 DOI: 10.1038/nsb0594-281] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Goldberg JD, Yoshida T, Brick P. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. J Mol Biol 1994; 236:1123-40. [PMID: 8120891 DOI: 10.1016/0022-2836(94)90016-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
D-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of hydroxypyruvate to D-glycerate. GDH is a member of a family of NAD-dependent dehydrogenases that is characterized by a specificity for the D-isomer of the hydroxyacid substrate. The crystal structure of the apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined by the method of isomorphous replacement and refined at 2.4 A resolution using a restrained least-squares method. The crystallographic R-factor is 19.4% for all 24,553 measured reflections between 10.0 and 2.4 A resolution. The GDH molecule is a symmetrical dimer composed of subunits of molecular mass 38,000, and shares significant structural homology with another NAD-dependent enzyme, formate dehydrogenase. The GDH subunit consists of two structurally similar domains that are approximately related to each other by 2-fold symmetry. The domains are separated by a deep cleft that forms the putative NAD and substrate binding sites. One of the domains has been identified as the NAD-binding domain based on its close structural similarity to the NAD-binding domains of other NAD-dependent dehydrogenases. The topology of the second domain is different from that found in the various catalytic domains of other dehydrogenases. A model of a ternary complex of GDH has been built in which putative catalytic residues are identified based on sequence homology between the D-isomer specific dehydrogenases. A structural comparison between GDH and L-lactate dehydrogenase indicates a convergence of active site residues and geometries for these two enzymes. The reactions catalyzed are chemically equivalent but of opposing stereospecificity. A hypothesis is presented to explain how the two enzymes may exploit the same coenzyme stereochemistry and a similar spatial arrangement of catalytic residues to carry out reactions that proceed to opposite enantiomers.
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Affiliation(s)
- J D Goldberg
- Blackett Laboratory, Imperial College, London, England
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Chow CM, RajBhandary UL. Developmental regulation of the gene for formate dehydrogenase in Neurospora crassa. J Bacteriol 1993; 175:3703-9. [PMID: 8509325 PMCID: PMC204785 DOI: 10.1128/jb.175.12.3703-3709.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have isolated and characterized a gene, fdh, from Neurospora crassa which is developmentally regulated and which produces formate dehydrogenase activity when expressed in Escherichia coli. The gene is closely linked (less than 0.6 kb apart) to the leu-5 gene encoding mitochondrial leucyl-tRNA synthetase; the two genes are transcribed convergently from opposite strands. The expression patterns of these genes differ: fdh mRNA is found only during conidiation and early germination and is not detectable during mycelial growth, while leu-5 mRNA appears during germination and mycelial growth. The structure of the fdh gene was determined from the sequence of cDNA and genomic DNA clones and from mRNA mapping studies. The gene encodes a 375-amino-acid-long protein with sequence similarity to NAD-dependent dehydrogenases of the E. coli 3-phosphoglycerate dehydrogenase (serA gene product) subfamily. In particular, there is striking sequence similarity (52% identity) to formate dehydrogenase from Pseudomonas sp. strain 101. All of the residues thought to interact with NAD in the crystal structure of the Pseudomonas enzyme are conserved in the N. crassa enzyme. We have further shown that expression of the N. crassa gene in E. coli leads to the production of formate dehydrogenase activity, indicating that the N. crassa gene specifies a functional polypeptide.
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Affiliation(s)
- C M Chow
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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