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Pesquisa : D08.811.520.241.300.650 [Categoria DeCS]
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[PMID]:28183913
[Au] Autor:Levin BJ; Huang YY; Peck SC; Wei Y; Martínez-Del Campo A; Marks JA; Franzosa EA; Huttenhower C; Balskus EP
[Ad] Endereço:Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
[Ti] Título:A prominent glycyl radical enzyme in human gut microbiomes metabolizes -4-hydroxy-l-proline.
[So] Source:Science;355(6325), 2017 02 10.
[Is] ISSN:1095-9203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate -4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.
[Mh] Termos MeSH primário: Microbioma Gastrointestinal/genética
Trato Gastrointestinal/microbiologia
Hidroxiprolina/metabolismo
Prolina Oxidase/química
Prolina Oxidase/genética
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Anaerobiose
Seres Humanos
Metagenoma
Prolina Oxidase/metabolismo
Propanodiol Desidratase/química
Propanodiol Desidratase/genética
Processamento de Proteína Pós-Traducional
Alinhamento de Sequência
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
EC 1.5.3.- (Proline Oxidase); EC 4.2.1.28 (Propanediol Dehydratase); RMB44WO89X (Hydroxyproline)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170211
[St] Status:MEDLINE


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[PMID]:27252380
[Au] Autor:LaMattina JW; Keul ND; Reitzer P; Kapoor S; Galzerani F; Koch DJ; Gouvea IE; Lanzilotta WN
[Ad] Endereço:From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602 and.
[Ti] Título:1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY.
[So] Source:J Biol Chem;291(30):15515-26, 2016 07 22.
[Is] ISSN:1083-351X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Glycyl radical enzymes (GREs) represent a diverse superfamily of enzymes that utilize a radical mechanism to catalyze difficult, but often essential, chemical reactions. In this work we present the first biochemical and structural data for a GRE-type diol dehydratase from the organism Roseburia inulinivorans (RiDD). Despite high sequence (48% identity) and structural similarity to the GRE-type glycerol dehydratase from Clostridium butyricum, we demonstrate that the RiDD is in fact a diol dehydratase. In addition, the RiDD will utilize both (S)-1,2-propanediol and (R)-1,2-propanediol as a substrate, with an observed preference for the S enantiomer. Based on the new structural information we developed and successfully tested a hypothesis that explains the functional differences we observe.
[Mh] Termos MeSH primário: Proteínas de Bactérias/química
Clostridiales/enzimologia
Propanodiol Desidratase/química
Propilenoglicol/química
[Mh] Termos MeSH secundário: Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Clostridiales/genética
Propanodiol Desidratase/genética
Propanodiol Desidratase/metabolismo
Propilenoglicol/metabolismo
Especificidade por Substrato/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 6DC9Q167V3 (Propylene Glycol); EC 4.2.1.28 (Propanediol Dehydratase)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160603
[St] Status:MEDLINE
[do] DOI:10.1074/jbc.M116.721142


  3 / 146 MEDLINE  
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[PMID]:27072298
[Au] Autor:Matsubara M; Urano N; Yamada S; Narutaki A; Fujii M; Kataoka M
[Ad] Endereço:Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
[Ti] Título:Fermentative production of 1-propanol from d-glucose, l-rhamnose and glycerol using recombinant Escherichia coli.
[So] Source:J Biosci Bioeng;122(4):421-6, 2016 Oct.
[Is] ISSN:1347-4421
[Cp] País de publicação:Japan
[La] Idioma:eng
[Ab] Resumo:Fermentative production of 1-propanol, which is one of the promising precursors of polypropylene production, from d-glucose, l-rhamnose and glycerol using metabolically engineered Escherichia coli was examined. To confer the ability to produce 1-propanol from 1,2-propanediol (1,2-PD) in recombinant E. coli, a part of the pdu regulon including the diol dehydratase and the propanol dehydrogenase genes together with the adenosylcobalamin (AdoCbl) regeneration enzyme genes of Klebsiella pneumoniae was cloned, and an expression vector for these genes (pRSF_pduCDEGHOQS) was constructed. Recombinant E. coli harboring pRSF_pduCDEGHOQS with 1,2-PD synthetic pathway (pKK_mde) genes, which was constructed in our previous report (Urano et al., Appl. Microbiol. Biotechnol., 99, 2001-2008, 2015), produced 16.1 mM of 1-propanol from d-glucose with a molar yield of 0.36 mol/mol after 72 h cultivation. 29.9 mM of 1-propanol was formed from l-rhamnose with a molar yield of 0.81 mol/mol using E. coli carrying only pRSF_pduCDEGHOQS. In addition, 1-propanol production from glycerol was achieved by addition of the ATP-dependent dihydroxyacetone kinase gene to E. coli harboring pKK_mde and pRSF_pduCDEGOQS. In all cases, 1-propanol production was achieved by adding only a small amount of AdoCbl.
[Mh] Termos MeSH primário: 1-Propanol/metabolismo
Escherichia coli/metabolismo
Fermentação
Glucose/metabolismo
Glicerol/metabolismo
Engenharia Metabólica
Ramnose/metabolismo
[Mh] Termos MeSH secundário: Cobamidas/biossíntese
Cobamidas/metabolismo
Cobamidas/farmacologia
Escherichia coli/efeitos dos fármacos
Escherichia coli/genética
Fermentação/efeitos dos fármacos
Genes Bacterianos
Klebsiella pneumoniae/enzimologia
Klebsiella pneumoniae/genética
Fosfotransferases (Aceptor do Grupo Álcool)/genética
Fosfotransferases (Aceptor do Grupo Álcool)/metabolismo
Propanodiol Desidratase/genética
Propanodiol Desidratase/metabolismo
Propilenoglicóis/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cobamides); 0 (Propylene Glycols); 5965N8W85T (1,3-propanediol); 96F264O9SV (1-Propanol); EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)); EC 2.7.1.29 (glycerone kinase); EC 4.2.1.28 (Propanediol Dehydratase); F0R1QK73KB (cobamamide); IY9XDZ35W2 (Glucose); PDC6A3C0OX (Glycerol); QN34XC755A (Rhamnose)
[Em] Mês de entrada:1704
[Cu] Atualização por classe:170817
[Lr] Data última revisão:
170817
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160414
[St] Status:MEDLINE


  4 / 146 MEDLINE  
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[PMID]:26704729
[Au] Autor:Toraya T; Tanokuchi A; Yamasaki A; Nakamura T; Ogura K; Tobimatsu T
[Ad] Endereço:Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
[Ti] Título:Diol Dehydratase-Reactivase Is Essential for Recycling of Coenzyme B12 in Diol Dehydratase.
[So] Source:Biochemistry;55(1):69-78, 2016 Jan 12.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Holoenzymes of adenosylcobalamin-dependent diol and glycerol dehydratases undergo mechanism-based inactivation by glycerol and O2 inactivation in the absence of substrate, which accompanies irreversible cleavage of the coenzyme Co-C bond. The inactivated holodiol dehydratase and the inactive enzyme·cyanocobalamin complex were (re)activated by incubation with NADH, ATP, and Mg(2+) (or Mn(2+)) in crude extracts of Klebsiella oxytoca, suggesting the presence of a reactivating system in the extract. The reducing system with NADH could be replaced by FMNH2. When inactivated holoenzyme or the enzyme·cyanocobalamin complex, a model of inactivated holoenzyme, was incubated with purified recombinant diol dehydratase-reactivase (DD-R) and an ATP:cob(I)alamin adenosyltransferase in the presence of FMNH2, ATP, and Mg(2+), diol dehydratase activity was restored. Among the three adenosyltransferases (PduO, EutT, and CobA) of this bacterium, PduO and CobA were much more efficient for the reactivation than EutT, although PduO showed the lowest adenosyltransfease activity toward free cob(I)alamin. These results suggest that (1) diol dehydratase activity is maintained through coenzyme recycling by a reactivating system for diol dehydratase composed of DD-R, PduO adenosyltransferase, and a reducing system, (2) the releasing factor DD-R is essential for the recycling of adenosycobalamin, a tightly bound, prosthetic group-type coenzyme, and (3) PduO is a specific adenosylating enzyme for the DD reactivation, whereas CobA and EutT exert their effects through free synthesized coenzyme. Although FMNH2 was mainly used as a reductant in this study, a natural reducing system might consist of PduS cobalamin reductase and NADH.
[Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo
Cobamidas/metabolismo
Ativação Enzimática
Klebsiella oxytoca/metabolismo
Propanodiol Desidratase/metabolismo
[Mh] Termos MeSH secundário: Trifosfato de Adenosina/metabolismo
Alquil e Aril Transferases/metabolismo
Mononucleotídeo de Flavina/metabolismo
Hidroquinonas/metabolismo
Klebsiella oxytoca/enzimologia
Magnésio/metabolismo
NAD/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Cobamides); 0 (Hydroquinones); 0 (flavin mononucleotide hydroquinone); 0U46U6E8UK (NAD); 7N464URE7E (Flavin Mononucleotide); 8L70Q75FXE (Adenosine Triphosphate); EC 2.5.- (Alkyl and Aryl Transferases); EC 2.5.1.17 (cob(I)alamin adenosyltransferase); EC 4.2.1.28 (Propanediol Dehydratase); F0R1QK73KB (cobamamide); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1605
[Cu] Atualização por classe:161126
[Lr] Data última revisão:
161126
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151226
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.5b01023


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[PMID]:26465746
[Au] Autor:Chen Z; Sun H; Huang J; Wu Y; Liu D
[Ad] Endereço:Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China.
[Ti] Título:Metabolic Engineering of Klebsiella pneumoniae for the Production of 2-Butanone from Glucose.
[So] Source:PLoS One;10(10):e0140508, 2015.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:2-Butanone is an important commodity chemical of wide application in different areas. In this study, Klebsiella pneumoniae was engineered to directly produce 2-butanone from glucose by extending its native 2, 3-butanediol synthesis pathway. To identify the potential enzyme for the efficient conversion of 2, 3-butanediol to 2-butanone, we screened different glycerol dehydratases and diol dehydratases. By introducing the diol dehydratase from Lactobacillus brevis and deleting the ldhA gene encoding lactate dehydrogenase, the engineered K. pneumoniae was able to accumulate 246 mg/L of 2-butanone in shake flask. With further optimization of culture condition, the titer of 2-butanone was increased to 450 mg/L. This study lays the basis for developing an efficient biological process for 2-butanone production.
[Mh] Termos MeSH primário: Butanonas/metabolismo
Glucose/metabolismo
Klebsiella pneumoniae/genética
Klebsiella pneumoniae/metabolismo
Engenharia Metabólica
[Mh] Termos MeSH secundário: Vias Biossintéticas
Cobamidas/metabolismo
Desidratação
Ativação Enzimática
Fermentação
Deleção de Genes
Expressão Gênica
Hidroliases/genética
Hidroliases/metabolismo
Cinética
Engenharia Metabólica/métodos
Propanodiol Desidratase/genética
Propanodiol Desidratase/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Butanones); 0 (Cobamides); 6PT9KLV9IO (methylethyl ketone); EC 4.2.1.- (Hydro-Lyases); EC 4.2.1.28 (Propanediol Dehydratase); EC 4.2.1.30 (glycerol dehydratase); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1606
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151015
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0140508


  6 / 146 MEDLINE  
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[PMID]:25490349
[Au] Autor:Jain R; Sun X; Yuan Q; Yan Y
[Ti] Título:Systematically engineering Escherichia coli for enhanced production of 1,2-propanediol and 1-propanol.
[So] Source:ACS Synth Biol;4(6):746-56, 2015 Jun 19.
[Is] ISSN:2161-5063
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The biological production of high value commodity 1,2-propanediol has been established by engineering the glycolysis pathway. However, the simultaneous achievement of high titer and high yield has not been reported yet, as all efforts in increasing the titer have resulted in low yields. In this work, we overcome this limitation by employing an optimal minimal set of enzymes, channeling the carbon flux into the 1,2-propanediol pathway, increasing NADH availability, and improving the anaerobic growth of the engineered Escherichia coli strain by developing a cell adaptation method. These efforts lead to 1,2-propanediol production at a titer of 5.13 g/L with a yield of 0.48 g/g glucose in 20 mL shake flask studies. On this basis, we pursue the enhancement of 1-propanol production from the 1,2-propanediol platform. By constructing a fusion diol dehydratase and developing a dual strain process, we achieve a 1-propanol titer of 2.91 g/L in 20 mL shake flask studies. To summarize, we report the production of 1,2-propanediol at enhanced titer and enhanced yield simultaneously in E. coli for the first time. Furthermore, we establish an efficient system for the production of biofuel 1-propanol biologically.
[Mh] Termos MeSH primário: 1-Propanol/metabolismo
Escherichia coli/metabolismo
Engenharia Metabólica
Propilenoglicol/metabolismo
[Mh] Termos MeSH secundário: Biocombustíveis
Carbono/metabolismo
Enzimas/genética
Enzimas/metabolismo
Escherichia coli/genética
Escherichia coli/crescimento & desenvolvimento
Glucose/metabolismo
NAD/metabolismo
Plasmídeos/genética
Plasmídeos/metabolismo
Propanodiol Desidratase/genética
Propanodiol Desidratase/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Biofuels); 0 (Enzymes); 0U46U6E8UK (NAD); 6DC9Q167V3 (Propylene Glycol); 7440-44-0 (Carbon); 96F264O9SV (1-Propanol); EC 4.2.1.28 (Propanediol Dehydratase); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1603
[Cu] Atualização por classe:150619
[Lr] Data última revisão:
150619
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:141210
[St] Status:MEDLINE
[do] DOI:10.1021/sb500345t


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[PMID]:25054226
[Au] Autor:Ghiaci P; Norbeck J; Larsson C
[Ad] Endereço:Department of Chemical and Biological Engineering, System and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden.
[Ti] Título:2-Butanol and butanone production in Saccharomyces cerevisiae through combination of a B12 dependent dehydratase and a secondary alcohol dehydrogenase using a TEV-based expression system.
[So] Source:PLoS One;9(7):e102774, 2014.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:2-Butanol and its chemical precursor butanone (methyl ethyl ketone--MEK) are chemicals with potential uses as biofuels and biocommodity chemicals. In order to produce 2-butanol, we have demonstrated the utility of using a TEV-protease based expression system to achieve equimolar expression of the individual subunits of the two protein complexes involved in the B12-dependent dehydratase step (from the pdu-operon of Lactobacillus reuteri), which catalyze the conversion of meso-2,3-butanediol to butanone. We have furthermore identified a NADH dependent secondary alcohol dehydrogenase (Sadh from Gordonia sp.) able to catalyze the subsequent conversion of butanone to 2-butanol. A final concentration of 4±0.2 mg/L 2-butanol and 2±0.1 mg/L of butanone was found. A key factor for the production of 2-butanol was the availability of NADH, which was achieved by growing cells lacking the GPD1 and GPD2 isogenes under anaerobic conditions.
[Mh] Termos MeSH primário: Oxirredutases do Álcool/metabolismo
Proteínas de Bactérias/metabolismo
Butanóis/metabolismo
Butanonas/metabolismo
Propanodiol Desidratase/metabolismo
Saccharomyces cerevisiae/metabolismo
[Mh] Termos MeSH secundário: Oxirredutases do Álcool/genética
Proteínas de Bactérias/genética
Sequência de Bases
Vias Biossintéticas
Western Blotting
Endopeptidases/genética
Endopeptidases/metabolismo
Expressão Gênica
Engenharia Genética/métodos
Gordonia (Bactéria)/enzimologia
Gordonia (Bactéria)/genética
Microbiologia Industrial/métodos
Lactobacillus reuteri/enzimologia
Lactobacillus reuteri/genética
Dados de Sequência Molecular
Óperon/genética
Propanodiol Desidratase/genética
Reprodutibilidade dos Testes
Saccharomyces cerevisiae/genética
Vitamina B 12/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Butanols); 0 (Butanones); 0TUL3ENK62 (2-butanol); EC 1.1.- (Alcohol Oxidoreductases); EC 1.1.1.71 (alcohol dehydrogenase (NAD(P)+)); EC 3.4.- (Endopeptidases); EC 3.4.- (TEV protease); EC 4.2.1.28 (Propanediol Dehydratase); P6YC3EG204 (Vitamin B 12)
[Em] Mês de entrada:1504
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140724
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0102774


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[PMID]:24078133
[Au] Autor:Wei X; Meng X; Chen Y; Wei Y; Du L; Huang R
[Ti] Título:Cloning, expression, and characterization of coenzyme-B12-dependent diol dehydratase from Lactobacillus diolivorans.
[So] Source:Biotechnol Lett;36(1):159-65, 2014 Jan.
[Is] ISSN:1573-6776
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The three gldCDE genes from Lactobacillus diolivorans, that encode the three subunits of the glycerol dehydratase, were cloned and the proteins were co-expressed in soluble form in Escherichia coli with added sorbitol and betaine hydrochloride. The purified enzyme exists as a heterohexamer (α2ß2γ2) structure with a native molecular mass of 210 kDa. It requires coenzyme B12 for catalytic activity and is subject to suicide inactivation by glycerol during catalysis. The enzyme had maximum activity at pH 8.6 and 37 °C. The apparent K m values for coenzyme B12, 1,2-ethanediol, 1,2-propanediol, and glycerol were 1.5 µM, 10.5 mM, 1.3 mM, and 5.8 mM, respectively. Together, these results indicated that the three genes gldCDE encoding the proteins make up a coenzyme B12-dependent diol dehydratase and not a glycerol dehydratase.
[Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo
Lactobacillus/enzimologia
Propanodiol Desidratase/metabolismo
Proteínas Recombinantes/metabolismo
[Mh] Termos MeSH secundário: Proteínas de Bactérias/química
Proteínas de Bactérias/genética
Clonagem Molecular
Cobamidas
Glicerol/metabolismo
Lactobacillus/genética
Oxigênio/metabolismo
Propanodiol Desidratase/química
Propanodiol Desidratase/genética
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Cobamides); 0 (Recombinant Proteins); EC 4.2.1.28 (Propanediol Dehydratase); F0R1QK73KB (cobamamide); PDC6A3C0OX (Glycerol); S88TT14065 (Oxygen)
[Em] Mês de entrada:1409
[Cu] Atualização por classe:161125
[Lr] Data última revisão:
161125
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:131001
[St] Status:MEDLINE


  9 / 146 MEDLINE  
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[PMID]:24229359
[Au] Autor:Mori K; Obayashi K; Hosokawa Y; Yamamoto A; Yano M; Yoshinaga T; Toraya T
[Ad] Endereço:Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University , Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
[Ti] Título:Essential roles of nucleotide-switch and metal-coordinating residues for chaperone function of diol dehydratase-reactivase.
[So] Source:Biochemistry;52(48):8677-86, 2013 Dec 03.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Diol dehydratase-reactivase (DD-R) is a molecular chaperone that reactivates inactivated holodiol dehydratase (DD) by cofactor exchange. Its ADP-bound and ATP-bound forms are high-affinity and low-affinity forms for DD, respectively. Among DD-Rs mutated at the nucleotide-binding site, neither the Dα8N nor Dα413N mutant was effective as a reactivase. Although Dα413N showed ATPase activity, it did not mediate cyanocobalamin (CN-Cbl) release from the DD·CN-Cbl complex in the presence of ATP or ADP and formed a tight complex with apoDD even in the presence of ATP, suggesting the involvement of Aspα413 in the nucleotide switch. In contrast, Dα8N showed very low ATPase activity and did not mediate CN-Cbl release from the complex in the presence of ATP, but it did cause about 50% release in the presence of ADP. The complex formation of this mutant with DD was partially reversed by ATP, suggesting that Aspα8 is involved in the ATPase activity but only partially in the nucleotide switch. Among DD-Rs mutated at the Mg(2+)-binding site, only Eß31Q was about 30% as active as wild-type DD-R and formed a tight complex with apoDD, indicating that the DD-R ß subunit is not absolutely required for reactivation. If subunit swapping occurs between the DD-R ß and DD ß subunits, Gluß97 of DD would coordinate to Mg(2+). The complex of Eß97Q DD with CN-Cbl was not activated by wild-type DD-R. No complex was formed between this mutant and wild-type DD-R, indicating that the coordination of Gluß97 to Mg(2+) is essential for subunit swapping and therefore for (re)activation.
[Mh] Termos MeSH primário: Chaperonas Moleculares/química
Nucleotídeos/metabolismo
Propanodiol Desidratase/química
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Proteínas de Bactérias/química
Proteínas de Bactérias/fisiologia
Sítios de Ligação
Reativadores Enzimáticos/química
Seres Humanos
Cinética
Klebsiella oxytoca/enzimologia
Metais/química
Modelos Moleculares
Dados de Sequência Molecular
Ligação Proteica
Domínios e Motivos de Interação entre Proteínas/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Enzyme Reactivators); 0 (Metals); 0 (Molecular Chaperones); 0 (Nucleotides); EC 4.2.1.28 (Propanediol Dehydratase)
[Em] Mês de entrada:1403
[Cu] Atualização por classe:131203
[Lr] Data última revisão:
131203
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:131116
[St] Status:MEDLINE
[do] DOI:10.1021/bi401290j


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[PMID]:23123722
[Au] Autor:Doitomi K; Kamachi T; Yoshizawa K
[Ad] Endereço:Institute for Materials Chemistry and Engneering, Kyushu University, Fukuoka, Japan.
[Ti] Título:[Computational mutation analysis of enzymatic reaction].
[So] Source:Yakugaku Zasshi;132(11):1297-305, 2012.
[Is] ISSN:1347-5231
[Cp] País de publicação:Japan
[La] Idioma:jpn
[Ab] Resumo:Density functional theory (DFT) calculations are established as a useful research tool to investigate the structures and reactivity of biological systems; however, their high computational costs still restrict their applicability to systems of several tens up to a few hundred atoms. Recently, a combined quantum mechanical/molecular mechanical (QM/MM) approach has become an important method to study enzymatic reactions. In the past several years, we have investigated B12-dependent diol dehydratase using QM/MM calculations. The enzyme catalyzes chemically difficult reactions by utilizing the high reactivity of free radicals. In this paper, we explain our QM/MM calculations for the structure and reactivity of diol dehydratase and report key findings with respect to the catalytic roles of the active-site amino acid residues, computational mutational analysis of the active-site amino acid residues, assignment of the central metal ion, and function of the central metal ion. Our QM/MM calculations can correctly describe the structures and activation barriers of intermediate and transition states in the protein environment. Moreover, predicted relative activities of mutants are consistent with experimentally observed reactivity. These results will encourage the application of QM/MM research to the mechanistic study of enzymatic reactions, functional analysis of active-site residues, and rational design of enzymes with new catalytic functions.
[Mh] Termos MeSH primário: Biologia Computacional/métodos
Mutação
Propanodiol Desidratase/química
Propanodiol Desidratase/genética
Teoria Quântica
Vitamina B 12
[Mh] Termos MeSH secundário: Aminoácidos/química
Aminoácidos/genética
Sítios de Ligação/genética
Biocatálise
Estrutura Molecular
Compostos Organometálicos/química
[Pt] Tipo de publicação:ENGLISH ABSTRACT; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0 (Organometallic Compounds); EC 4.2.1.28 (Propanediol Dehydratase); P6YC3EG204 (Vitamin B 12)
[Em] Mês de entrada:1404
[Cu] Atualização por classe:121105
[Lr] Data última revisão:
121105
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:121106
[St] Status:MEDLINE



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