Molecular modeling of formate dehydrogenase: the formation of the Michaelis complex

Nilov, Dmitry K.; Shabalin, I.G.; Popov, Vladimir O.; Švedas, Vytas K.

doi:10.1080/07391102.2012.677768

Cited by 19 publications

(15 citation statements)

References 29 publications

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“…In methylotrophic organisms, hydroxypyruvate reductase (DHGY_HYPME) plays a central role in carbon assimilation, converting hydroxypyruvate to glycerate as a key step in the serine cycle [63]. hydroxypyruvate (13), glyoxylate (12), phenylpyruvate (3), pyruvate (2), 4-hydroxyphenylpyruvate (2), hydroxyphenylpyruvate, oxaloacetate, 2-keto-D-gluconate, 2-hydroxyisocaproate, D-mandalate, 2-keto-L-gulonate, phenylglyoxylate, phosphonate, 3,4-dihydroxyphenylpyruvate, benzylformate, 2-keto-D-gluconic acidUsually possess better affinity to NADPH than NADH (GRHPR_HUMAN [38], HPPR_PLESU [62], GHRB_ECOLI [63]), but some enzymes work better with NADH (HPR1_ARATH [68]).GHRCglyoxylate/hydroxypyruvate reductases CAn enzyme from a methylotroph M. extorquens was shown to reduce hydroxypyruvate and glyoxylate, and catalyze reverse reaction with glycerate but not glycolate [19]. Bacteria and archaeaIt plays a central role in assimilation of carbon in methylotrophic organisms as it converts hydroxypyruvate to glycerate as a key step in the serine cycle, may also play an important role in C2 reactions by interconverting glyoxylate and glycolate [19].…”

Section: Resultsmentioning

confidence: 99%

“…VanH from Enterococcus faecium was shown to work best with pyruvate and 2-ketobutyrate [66], whereas relatively diverged Chlamydomonas reinhardtii D-LDH reduces pyruvate in chloroplasts and works as a tetramer [67]. Bacteria and lower eukaryotes (protists, fungi, green alga)The Bacilli enzymes are postulated to reduce pyruvate, the final product of glycolysis, to lactate [68]. VanH from E. faecium is involved in vancomycin resistance [66].…”

Section: Resultsmentioning

confidence: 99%

“…Chlamydomonas reinhardtii D-LDH reduces pyruvate in fermentation pathways in chloroplasts [67]. pyruvate (8), 2-ketobutyrate (7), phenylpyruvate (7), 2-ketovalerate (4), 2-ketoisocaproate (4), 2-ketocaproate (4), lactate (3), 2-ketoisovalerate (3), hydroxypyruvate (2), glyoxylate (2), 2-keto-3-methylbutyrate, 2-keto-4-methylmercaptobutyrate, mercaptopyruvate, 2-ketooctanoate, 2-oobutanoate, 4-hydroxyphenylpyruvate, oxaloacetate, 2-ketovalerate, 2-ketohexanoate, bromopyruvate, 2-keto-3-methylvalerateLDHD enzymes utilizes NADH as a cofactor [65, 67, 68]. PDXBerythronate-4-phosphate dehydrogenases E. coli PdxB oxidizes 4-phospho-D-erythronate to 2-keto-3-hydroxy-4-phosphobutanoate [69] and uses various 2-keto acids as co-substrates [27].…”

Section: Resultsmentioning

confidence: 99%

“…A wealth of structural data [21, 30, 35] and computational studies [67, 68] is available for the FDH subfamily, making it one of the most studied 2HADH subfamilies. As reflected by the high sequence similarity among its members (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

et al. 2018

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BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1309-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

et al. 2018

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“…Nilov et al 263 investigated the formation of the enzymesubstrate complex of formate dehydrogenase by applying classical, steered and hybrid QM/MM dynamic simulations. In their study, QM was defined as the region containing the formate molecule and nicotinamide-ribose fragment of NAD+ molecule, whereas the MM region contained the rest of the coenzyme, the protein, and the solvent.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

RM1 Semiempirical Model: Chemistry, Pharmaceutical Research, Molecular Biology and Materials Science

Lima¹,

Rocha²,

Freire³

et al. 2018

J. Braz. Chem. Soc.

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In this review, we show improvements to the semiempirical quantum chemical method RM1 and present a wide range of its applications as reported by researchers of various areas, such as theoretical, organic, physical, analytical, and inorganic chemistry, as well as their interfaces with medicinal chemistry, biology, and materials science. Success of RM1 is seemingly due to its ability to predict structural, energetic, electronic and wave function dependent properties of the investigated systems, coupled with its low computational demand required to perform calculations when compared to ab initio and density functional methods. Moreover, RM1 is widely available in several computational chemistry softwares, such as MOPAC, GAMESS, Amber, Spartan, HyperChem, and AMPAC. This review describes various case studies that perhaps can be of interest to researchers who might need a more solid basis from which to expand the frontier of applicability of RM1 to even more complex problems on larger systems.

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Carbon Dioxide Utilisation—The Formate Route

Maia

Moura

2020

Enzymes for Solving Humankind's Problems

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The relentless rise of atmospheric CO2 is causing large and unpredictable impacts on the Earth climate, due to the CO2 significant greenhouse effect, besides being responsible for the ocean acidification, with consequent huge impacts in our daily lives and in all forms of life. To stop spiral of destruction, we must actively reduce the CO2 emissions and develop new and more efficient “CO2 sinks”. We should be focused on the opportunities provided by exploiting this novel and huge carbon feedstock to produce de novo fuels and added-value compounds. The conversion of CO2 into formate offers key advantages for carbon recycling, and formate dehydrogenase (FDH) enzymes are at the centre of intense research, due to the “green” advantages the bioconversion can offer, namely substrate and product selectivity and specificity, in reactions run at ambient temperature and pressure and neutral pH. In this chapter, we describe the remarkable recent progress towards efficient and selective FDH-catalysed CO2 reduction to formate. We focus on the enzymes, discussing their structure and mechanism of action. Selected promising studies and successful proof of concepts of FDH-dependent CO2 reduction to formate and beyond are discussed, to highlight the power of FDHs and the challenges this CO2 bioconversion still faces.

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Molecular modeling of formate dehydrogenase: the formation of the Michaelis complex

Cited by 19 publications

References 29 publications

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase

RM1 Semiempirical Model: Chemistry, Pharmaceutical Research, Molecular Biology and Materials Science

Carbon Dioxide Utilisation—The Formate Route

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