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Rudolf K Thauer - One of the best experts on this subject based on the ideXlab platform.
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doi:10.1155/2011/973848 Review Article More Than 200 Genes Required for Methane Formation from H2 and CO2 and Energy Conservation Are Present in
2013Co-Authors: Methanothermobacter Marburgensis, Annekristin Kaster, Heiko Liesegang, Antje Wollherr, Henning Seedorf, Meike Goenrich, Gerhard Gottschalk, Methanothermobacter Thermautotrophicus, Rudolf K ThauerAbstract:Copyright © 2011 Anne-Kristin Kaster et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, Coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified
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more than 200 genes required for methane formation from h and co and energy conservation are present in methanothermobacter marburgensis and methanothermobacter thermautotrophicus
Archaea, 2011Co-Authors: Annekristin Kaster, Heiko Liesegang, Antje Wollherr, Henning Seedorf, Meike Goenrich, Gerhard Gottschalk, Rudolf K ThauerAbstract:The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, Coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified.
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More Than 200 Genes Required for Methane Formation from H2 and CO2 and Energy Conservation Are Present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus
Hindawi Limited, 2011Co-Authors: Annekristin Kaster, Heiko Liesegang, Antje Wollherr, Henning Seedorf, Meike Goenrich, Gerhard Gottschalk, Rudolf K ThauerAbstract:The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, Coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified
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the structure of formylmethanofuran tetrahydromethanopterin formyltransferase in complex with its Coenzymes
Journal of Molecular Biology, 2006Co-Authors: Priyamvada Acharya, Ulrich Ermler, Rudolf K Thauer, Eberhard Warkentin, Seigo ShimaAbstract:Formylmethanofuran:tetrahydromethanopterin formyltransferase is an essential enzyme in the one-carbon metabolism of methanogenic and sulfate-reducing archaea and of methylotrophic bacteria. The enzyme, which is devoid of a prosthetic group, catalyzes the reversible formyl transfer between the two substrates coenzyme methanofuran and coenzyme tetrahydromethanopterin (H 4 MPT) in a ternary complex catalytic mechanism. The structure of the formyltransferase without its Coenzymes has been determined earlier. We report here the structure of the enzyme in complex with both Coenzymes at a resolution of 2.0 A. Methanofuran, characterized for the first time in an enzyme structure, is embedded in an elongated cleft at the homodimer interface and fixed by multiple hydrophobic interactions. In contrast, tetrahydromethanopterin is only weakly bound in a shallow and wide cleft that provides two binding sites. It is assumed that the binding of the bulky Coenzymes induces conformational changes of the polypeptide in the range of 3 A that close the H 4 MPT binding cleft and position the reactive groups of both substrates optimally for the reaction. The key residue for substrate binding and catalysis is the strictly conserved Glu245. Glu245, embedded in a hydrophobic region and completely buried upon tetrahydromethanopterin binding, is presumably protonated prior to the reaction and is thus able to stabilize the tetrahedral oxyanion intermediate generated by the nucleophilic attack of the N 5 atom of tetrahydromethanopterin onto the formyl carbon atom of formylmethanofuran.
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crystal structure of methyl coenzyme m reductase the key enzyme of biological methane formation
Science, 1997Co-Authors: Ulrich Ermler, Marcel Goubeaud, Wolfgang Grabarse, Seigo Shima, Rudolf K ThauerAbstract:Methyl–coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an α 2 β 2 γ 2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum , determined at 1.45 angstrom resolution for the inactive enzyme state MCR ox1-silent , reveals that two molecules of the nickel porphinoid coenzyme F 430 are embedded between the subunits α, α′, β, and γ and α′, α, β′, and γ′, forming two identical active sites. Each site is accessible for the substrate methyl–coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCR silent ) containing the heterodisulfide of Coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.
Juan Ferrer - One of the best experts on this subject based on the ideXlab platform.
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A new D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity from Haloferax mediterranei, sequence analysis and heterologous overexpression
Biochimica et Biophysica Acta (BBA) - General Subjects, 2006Co-Authors: J. Domenech, Juan FerrerAbstract:Abstract A gene encoding a new d -2-hydroxyacid dehydrogenase (E.C. 1.1.1.) from the halophilic Archaeon Haloferax mediterranei has been sequenced, cloned and expressed in Escherichia coli cells with the inducible expression plasmid pET3a. The nucleotide sequence analysis showed an open reading frame of 927 bp which encodes a 308 amino acid protein. Multiple amino acid sequence alignments of the D-2-hydroxyacid dehydrogenase from H. mediterranei showed high homology with D-2-hydroxyacid dehydrogenases from different organisms and other enzymes of this family. Analysis of the amino acid sequence showed catalytic residues conserved in hydroxyacid dehydrogenases with d -stereospecificity. In the reductive reaction, the enzyme showed broad substrate specificity, although α-ketoisoleucine was the most favourable of all α-ketocarboxylic acids tested. Kinetic data revealed that this new D-2-hydroxyacid dehydrogenase from H. mediterranei exhibits dual coenzyme-specificity, using both NADPH and NADH as Coenzymes. To date, all D-2-hydroxyacid dehydrogenases have been found to be NADH-dependent. Here, we report the first example of a D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity.
Bernhard Krautler - One of the best experts on this subject based on the ideXlab platform.
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biochemistry of b12 cofactors in human metabolism
Sub-cellular biochemistry, 2012Co-Authors: Bernhard KrautlerAbstract:Vitamin B12, the “antipernicious anaemia factor”, is a crystallisable cobalt-complex, which belongs to a group of unique “complete” corrinoids, named cobalamins (Cbl). In humans, instead of the “vitamin”, two organometallic B12-forms are Coenzymes in two metabolically important enzymes: Methyl-cobalamin, the cofactor of methionine synthase, and coenzyme B12 (adenosyl-cobalamin), the cofactor of methylmalonyl-CoA mutase. The cytoplasmatic methionine synthase catalyzes the transfer of a methyl group from N-methyl-tetrahydrofolate to homocysteine to yield methionine and to liberate tetrahydrofolate. In the mitochondrial methylmalonyl-CoA mutase a radical process transforms methylmalonyl-CoA (a remains e.g. from uneven numbered fatty acids) into succinyl-CoA, for further metabolic use. In addition, in the human mitochondria an adenosyl-transferase incorporates the organometallic group of coenzyme B12. In all these enzymes, the bound B12-derivatives engage (or are formed) in exceptional organometallic enzymatic reactions. This chapter recapitulates the physiological chemistry of vitamin B12, relevant in the context of the metabolic transformation of B12-derivatives into the relevant coenzyme forms and their use in B12-dependent enzymes.
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1:Organometallic Chemistry of B12 Coenzymes
Metal-Carbon Bonds in Enzymes and Cofactors, 2009Co-Authors: Bernhard KrautlerAbstract:When coenzyme B12 was identified as organometallic derivative of vitamin B12, metal-carbon bonds were revealed to be relevant in life processes. Vitamin B12, the “antipernicious anaemia factor” required for human health, was isolated earlier as a crystallizable cyano-Co(III)-complex. B12 cofactors and other cobalt corrinoids play important roles not only in humans, but in the metabolism of archaea and other microorganisms, in particular. Indeed, the microorganisms are the only natural sources of the B12 derivatives. For other B12-requiring organisms the corrinoids are thus “vitamins”. However, vitamin B12 also needs to be converted into organometallic B12-forms, which are the typical Coenzymes in metabolically important enzymes. One of these, methionine synthase, catalyzes the transfer of a methyl group and its corrinoid cofactor is methylcobalamin. Another one, methylmalonyl-CoA mutase uses a reversible radical process, and coenzyme B12 (adenosylcobalamin) as its cofactor, to transform methylmalonyl-CoA into succinyl-CoA. In such enzymes, the bound B12 derivatives engage (or are formed) in exceptional organometallic enzymatic reactions, which depend upon the organometallic reactivity of the B12 cofactors. Clearly, organometallic B12 derivatives hold an important position in life and have thus attracted particular interest from the medical sciences, biology, and chemistry. This chapter outlines the unique structures of B12 derivatives and recapitulates their redox properties and their organometallic chemistry, relevant in the context of the metabolic transformation of B12 derivatives into the relevant coenzyme forms and for their use in B12-dependent enzymes.
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organometallic chemistry of b 12 Coenzymes
Metal ions in life sciences, 2009Co-Authors: Bernhard KrautlerAbstract:Abstract When coenzyme B(12) was identified as organometallic derivative of vitamin B(12), metal-carbon bonds were revealed to be relevant in life processes. Vitamin B(12), the "antipernicious anaemia factor" required for human health, was isolated earlier as a crystallizable cyano-Co(III)-complex. B(12) cofactors and other cobalt corrinoids play important roles not only in humans, but in the metabolism of archaea and other microorganisms, in particular. Indeed, the microorganisms are the only natural sources of the B(12) derivatives. For other B(12)-requiring organisms the corrinoids are thus "vitamins". However, vitamin B(12) also needs to be converted into organometallic B(12)-forms, which are the typical Coenzymes in metabolically important enzymes. One of these, methionine synthase, catalyzes the transfer of a methyl group and its corrinoid cofactor is methylcobalamin. Another one, methylmalonyl-CoA mutase uses a reversible radical process, and coenzyme B(12) (adenosylcobalamin) as its cofactor, to transform methylmalonyl-CoA into succinyl-CoA. In such enzymes, the bound B(12) derivatives engage (or are formed) in exceptional organometallic enzymatic reactions, which depend upon the organometallic reactivity of the B(12) cofactors. Clearly, organometallic B(12) derivatives hold an important position in life and have thus attracted particular interest from the medical sciences, biology, and chemistry. This chapter outlines the unique structures of B(12) derivatives and recapitulates their redox properties and their organometallic chemistry, relevant in the context of the metabolic transformation of B(12) derivatives into the relevant coenzyme forms and for their use in B(12)-dependent enzymes.
Volker M Arlt - One of the best experts on this subject based on the ideXlab platform.
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cytochrome b5 plays a dual role in the reaction cycle of cytochrome p450 3a4 during oxidation of the anticancer drug ellipticine
Monatshefte Fur Chemie, 2017Co-Authors: Marie Stiborová, Tomas Eckschlager, Radek Indra, Eva Frei, Heinz H Schmeiser, Volker M Arlt, Zbyněk Heger, Vojtěch Adam, Kateřina Kopeckova, Vaclav MartinekAbstract:Ellipticine is an anticancer agent that forms covalent DNA adducts after enzymatic activation by cytochrome P450 (CYP) enzymes, mainly by CYP3A4. This process is one of the most important ellipticine DNA-damaging mechanisms for its antitumor action. Here, we investigated the efficiencies of human hepatic microsomes and human recombinant CYP3A4 expressed with its reductase, NADPH:CYP oxidoreductase (POR), NADH:cytochrome b 5 reductase and/or cytochrome b 5 in Supersomes™ to oxidize this drug. We also evaluated the effectiveness of Coenzymes of two of the microsomal reductases, NADPH as a coenzyme of POR, and NADH as a coenzyme of NADH:cytochrome b 5 reductase, to mediate ellipticine oxidation in these enzyme systems. Using HPLC analysis we detected up to five ellipticine metabolites, which were formed by human hepatic microsomes and human CYP3A4 in the presence of NADPH or NADH. Among ellipticine metabolites, 9-hydroxy-, 12-hydroxy-, and 13-hydroxyellipticine were formed by hepatic microsomes as the major metabolites, while 7-hydroxyellipticine and the ellipticine N 2-oxide were the minor ones. Human CYP3A4 in Supersomes™ generated only three metabolic products, 9-hydroxy-, 12-hydroxy-, and 13-hydroxyellipticine. Using the 32P-postlabeling method two ellipticine-derived DNA adducts were generated by microsomes and the CYP3A4-Supersome system, both in the presence of NADPH and NADH. These adducts were derived from the reaction of 13-hydroxy- and 12-hydroxyellipticine with deoxyguanosine in DNA. In the presence of NADPH or NADH, cytochrome b 5 stimulated the CYP3A4-mediated oxidation of ellipticine, but the stimulation effect differed for individual ellipticine metabolites. This heme protein also stimulated the formation of both ellipticine-DNA adducts. The results demonstrate that cytochrome b 5 plays a dual role in the CYP3A4-catalyzed oxidation of ellipticine: (1) cytochrome b 5 mediates CYP3A4 catalytic activities by donating the first and second electron to this enzyme in its catalytic cycle, indicating that NADH:cytochrome b 5 reductase can substitute NADPH-dependent POR in this enzymatic reaction and (2) cytochrome b 5 can act as an allosteric modifier of the CYP3A4 oxygenase.
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nadh cytochrome b5 reductase and cytochrome b5 can act as sole electron donors to human cytochrome p450 1a1 mediated oxidation and dna adduct formation by benzo a pyrene
Chemical Research in Toxicology, 2016Co-Authors: Marie Stiborová, Radek Indra, Michaela Moserova, Eva Frei, Heinz H Schmeiser, Klaus Kopka, David H Philips, Volker M ArltAbstract:Benzo[a]pyrene (BaP) is a human carcinogen that covalently binds to DNA after activation by cytochrome P450 (P450). Here, we investigated whether NADH:cytochrome b5 reductase (CBR) in the presence of cytochrome b5 can act as sole electron donor to human P450 1A1 during BaP oxidation and replace the canonical NADPH:cytochrome P450 reductase (POR) system. We also studied the efficiencies of the Coenzymes of these reductases, NADPH as a coenzyme of POR, and NADH as a coenzyme of CBR, to mediate BaP oxidation. Two systems containing human P450 1A1 were utilized: human recombinant P450 1A1 expressed with POR, CBR, epoxide hydrolase, and cytochrome b5 in Supersomes and human recombinant P450 1A1 reconstituted with POR and/or with CBR and cytochrome b5 in liposomes. BaP-9,10-dihydrodiol, BaP-7,8-dihydrodiol, BaP-1,6-dione, BaP-3,6-dione, BaP-9-ol, BaP-3-ol, a metabolite of unknown structure, and two BaP-DNA adducts were generated by the P450 1A1-Supersomes system, both in the presence of NADPH and in the presenc...
Amir R Khan - One of the best experts on this subject based on the ideXlab platform.
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structure of nadp dependent glutamate dehydrogenase from escherichia coli reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases
FEBS Journal, 2013Co-Authors: Michael A Sharkey, Paul C. Engel, Tânia F Oliveira, Amir R KhanAbstract:Glutamate dehydrogenases (GDHs; EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate, using NAD(+) and/or NADP(+) as a cofactor. Subunits of homo-hexameric bacterial enzymes comprise a substrate-binding domain I followed by a nucleotide-binding domain II. The reaction occurs in a catalytic cleft between the two domains. Although conserved residues in the nucleotide-binding domains of various dehydrogenases have been linked to cofactor preferences, the structural basis for specificity in the GDH family remains poorly understood. Here, the refined crystal structure of Escherichia coli GDH in the absence of reactants is described at 2.5-A resolution. Modelling of NADP(+) in domain II reveals the potential contribution of positively charged residues from a neighbouring α-helical hairpin to phosphate recognition. In addition, a serine that follows the P7 aspartate is presumed to form a hydrogen bond with the 2'-phosphate. Mutagenesis and kinetic analysis confirms the importance of these residues in NADP(+) recognition. Surprisingly, one of the positively charged residues is conserved in all sequences of NAD(+)-dependent enzymes, but the conformations adopted by the corresponding regions in proteins whose structure has been solved preclude their contribution to the coordination of the 2'-ribose phosphate of NADP(+). These studies clarify the sequence-structure relationships in bacterial GDHs, revealing that identical residues may specify different coenzyme preferences, depending on the structural context. Primary sequence alone is therefore not a reliable guide for predicting coenzyme specificity. We also consider how it is possible for a single sequence to accommodate both Coenzymes in the dual-specificity GDHs of animals.