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[PMID]:26908349
[Au] Autor:Ju Z; Cao JZ; Gu H
[Ad] Endereço:School of Control Science and Engineering, Dalian University of Technology, #2 Ling-gong Road, Dalian 116024, People׳s Republic of China. Electronic address: juzhe1120@hotmail.com.
[Ti] Título:Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳s general PseAAC.
[So] Source:J Theor Biol;397:145-50, 2016 May 21.
[Is] ISSN:1095-8541
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:As a new type of post-translational modification, lysine phosphoglycerylation plays a key role in regulating glycolytic process and metabolism in cells. Due to the traditional experimental methods are time-consuming and labor-intensive, it is important to develop computational methods to identify the potential phosphoglycerylation sites. However, the prediction performance of the existing phosphoglycerylation site predictor is not satisfactory. In this study, a novel predictor named CKSAAP_PhoglySite is developed to predict phosphoglycerylation sites by using composition of k-spaced amino acid pairs and fuzzy support vector machine. On the one hand, after many aspects of assessments, we find the composition of k-spaced amino acid pairs is more suitable for representing the protein sequence around the phosphoglycerylation sites than other encoding schemes. On the other hand, the proposed fuzzy support vector machine algorithm can effectively handle the imbalanced and noisy problem in phosphoglycerylation sites training dataset. Experimental results indicate that CKSAAP_PhoglySite outperforms the existing phosphoglycerylation site predictor Phogly-PseAAC significantly. A matlab software package for CKSAAP_PhoglySite can be freely downloaded from https://github.com/juzhe1120/Matlab_Software/blob/master/CKSAAP_PhoglySite_Matlab_Software.zip.
[Mh] Termos MeSH primário: Algoritmos
Aminoácidos/metabolismo
Biologia Computacional/métodos
Lógica Fuzzy
Lisina/metabolismo
Máquina de Vetores de Suporte
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Aminoácidos/genética
Sítios de Ligação/genética
Ácidos Difosfoglicéricos/metabolismo
Lisina/genética
Processamento de Proteína Pós-Traducional
Reprodutibilidade dos Testes
Software
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Amino Acids); 0 (Diphosphoglyceric Acids); 1981-49-3 (glycerate 1,3-biphosphate); K3Z4F929H6 (Lysine)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170104
[Lr] Data última revisão:
170104
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160225
[St] Status:MEDLINE


  2 / 2560 MEDLINE  
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[PMID]:24862258
[Au] Autor:Sciacovelli M; Gaude E; Hilvo M; Frezza C
[Ad] Endereço:Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom.
[Ti] Título:The metabolic alterations of cancer cells.
[So] Source:Methods Enzymol;542:1-23, 2014.
[Is] ISSN:1557-7988
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Cancer cells exhibit profound metabolic alterations, allowing them to fulfill the metabolic needs that come with increased proliferation and additional facets of malignancy. Such a metabolic transformation is orchestrated by the genetic changes that drive tumorigenesis, that is, the activation of oncogenes and/or the loss of oncosuppressor genes, and further shaped by environmental cues, such as oxygen concentration and nutrient availability. Understanding this metabolic rewiring is essential to elucidate the fundamental mechanisms of tumorigenesis as well as to find novel, therapeutically exploitable liabilities of malignant cells. Here, we describe key features of the metabolic transformation of cancer cells, which frequently include the switch to aerobic glycolysis, a profound mitochondrial reprogramming, and the deregulation of lipid metabolism, highlighting the notion that these pathways are not independent but rather cooperate to sustain proliferation. Finally, we hypothesize that only those genetic defects that effectively support anabolism are selected in the course of tumor progression, implying that cancer-associated mutations may undergo a metabolically convergent evolution.
[Mh] Termos MeSH primário: Glicólise
Mitocôndrias/metabolismo
Neoplasias/metabolismo
[Mh] Termos MeSH secundário: Transformação Celular Neoplásica
Ácidos Difosfoglicéricos/metabolismo
Ácidos Graxos/biossíntese
Seres Humanos
Isocitrato Desidrogenase/genética
Isocitrato Desidrogenase/metabolismo
Metabolismo dos Lipídeos
Mutação
Neoplasias/genética
Oncogenes
Fosfofrutoquinase-1/metabolismo
Fosfofrutoquinase-2/metabolismo
Fosfoglicerato Desidrogenase/metabolismo
Fosfoglicerato Mutase/metabolismo
Piruvato Quinase/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Diphosphoglyceric Acids); 0 (Fatty Acids); 1981-49-3 (glycerate 1,3-biphosphate); EC 1.1.1.41 (Isocitrate Dehydrogenase); EC 1.1.1.95 (Phosphoglycerate Dehydrogenase); EC 2.7.1.105 (Phosphofructokinase-2); EC 2.7.1.11 (Phosphofructokinase-1); EC 2.7.1.40 (Pyruvate Kinase); EC 5.4.2.11 (Phosphoglycerate Mutase)
[Em] Mês de entrada:1505
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140528
[St] Status:MEDLINE


  3 / 2560 MEDLINE  
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[PMID]:24593686
[Au] Autor:Reddy GK; Wendisch VF
[Ti] Título:Characterization of 3-phosphoglycerate kinase from Corynebacterium glutamicum and its impact on amino acid production.
[So] Source:BMC Microbiol;14:54, 2014 Mar 04.
[Is] ISSN:1471-2180
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Corynebacterium glutamicum cg1790/pgk encodes an enzyme active as a 3-phosphoglycerate kinase (PGK) (EC 2.7.2.3) catalyzing phosphoryl transfer from 1,3-biphosphoglycerate (bPG) to ADP to yield 3-phosphoglycerate (3-PG) and ATP in substrate chain phosphorylation. RESULTS: C. glutamicum 3-phosphoglycerate kinase was purified to homogeneity from the soluble fraction of recombinant E. coli. PGK(His) was found to be active as a homodimer with molecular weight of 104 kDa. The enzyme preferred conditions of pH 7.0 to 7.4 and required Mg²âº for its activity. PGK(His) is thermo labile and it has shown maximal activity at 50-65°C. The maximal activity of PGK(His) was estimated to be 220 and 150 U mg-1 with KM values of 0.26 and 0.11 mM for 3-phosphoglycerate and ATP, respectively. A 3-phosphoglycerate kinase negative C. glutamicum strain ∆pgk was constructed and shown to lack the ability to grow under glycolytic or gluconeogenic conditions unless PGK was expressed from a plasmid to restore growth. When pgk was overexpressed in L-arginine and L-ornithine production strains the production increased by 8% and by 17.5%, respectively. CONCLUSION: Unlike many bacterial PGKs, C. glutamicum PGK is active as a homodimer. PGK is essential for growth of C. glutamicum with carbon sources requiring glycolysis and gluconeogenesis. Competitive inhibition by ADP reveals the critical role of PGK in gluconeogenesis by energy charge. Pgk overexpression improved the productivity in L-arginine and L-ornithine production strains.
[Mh] Termos MeSH primário: Aminoácidos/metabolismo
Corynebacterium glutamicum/enzimologia
Fosfoglicerato Quinase/genética
Fosfoglicerato Quinase/metabolismo
[Mh] Termos MeSH secundário: Difosfato de Adenosina/metabolismo
Coenzimas/metabolismo
Corynebacterium glutamicum/genética
Corynebacterium glutamicum/crescimento & desenvolvimento
Corynebacterium glutamicum/metabolismo
Ácidos Difosfoglicéricos/metabolismo
Estabilidade Enzimática
Escherichia coli/genética
Deleção de Genes
Glicólise
Concentração de Íons de Hidrogênio
Cinética
Magnésio/metabolismo
Peso Molecular
Fosfoglicerato Quinase/química
Fosfoglicerato Quinase/isolamento & purificação
Multimerização Proteica
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/isolamento & purificação
Proteínas Recombinantes/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Amino Acids); 0 (Coenzymes); 0 (Diphosphoglyceric Acids); 0 (Recombinant Proteins); 1981-49-3 (glycerate 1,3-biphosphate); 61D2G4IYVH (Adenosine Diphosphate); EC 2.7.2.3 (Phosphoglycerate Kinase); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1409
[Cu] Atualização por classe:150515
[Lr] Data última revisão:
150515
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140306
[St] Status:MEDLINE
[do] DOI:10.1186/1471-2180-14-54


  4 / 2560 MEDLINE  
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[PMID]:24098433
[Au] Autor:Yang T; Rao Z; Zhang X; Xu M; Xu Z; Yang ST
[Ad] Endereço:The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province, China.
[Ti] Título:Improved production of 2,3-butanediol in Bacillus amyloliquefaciens by over-expression of glyceraldehyde-3-phosphate dehydrogenase and 2,3-butanediol dehydrogenase.
[So] Source:PLoS One;8(10):e76149, 2013.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Previously, a safe strain, Bacillus amyloliquefaciens B10-127 was identified as an excellent candidate for industrial-scale microbial fermentation of 2,3-butanediol (2,3-BD). However, B. amyloliquefaciens fermentation yields large quantities of acetoin, lactate and succinate as by-products, and the 2,3-BD yield remains prohibitively low for commercial production. METHODOLOGY/PRINCIPAL FINDINGS: In the 2,3-butanediol metabolic pathway, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of 3-phosphate glyceraldehyde to 1,3-bisphosphoglycerate, with concomitant reduction of NAD(+) to NADH. In the same pathway, 2,3-BD dehydrogenase (BDH) catalyzes the conversion of acetoin to 2,3-BD with concomitant oxidation of NADH to NAD(+). In this study, to improve 2,3-BD production, we first over-produced NAD(+)-dependent GAPDH and NADH-dependent BDH in B. amyloliquefaciens. Excess GAPDH reduced the fermentation time, increased the 2,3-BD yield by 12.7%, and decreased the acetoin titer by 44.3%. However, the process also enhanced lactate and succinate production. Excess BDH increased the 2,3-BD yield by 16.6% while decreasing acetoin, lactate and succinate production, but prolonged the fermentation time. When BDH and GAPDH were co-overproduced in B. amyloliquefaciens, the fermentation time was reduced. Furthermore, in the NADH-dependent pathways, the molar yield of 2,3-BD was increased by 22.7%, while those of acetoin, lactate and succinate were reduced by 80.8%, 33.3% and 39.5%, relative to the parent strain. In fed-batch fermentations, the 2,3-BD concentration was maximized at 132.9 g/l after 45 h, with a productivity of 2.95 g/l·h. CONCLUSIONS/SIGNIFICANCE: Co-overexpression of bdh and gapA genes proved an effective method for enhancing 2,3-BD production and inhibiting the accumulation of unwanted by-products (acetoin, lactate and succinate). To our knowledge, we have attained the highest 2,3-BD fermentation yield thus far reported for safe microorganisms.
[Mh] Termos MeSH primário: Oxirredutases do Álcool/genética
Bacillus/genética
Bacillus/metabolismo
Butileno Glicóis/metabolismo
Expressão Gênica
Gliceraldeído 3-Fosfato Desidrogenase (NADP+)/genética
[Mh] Termos MeSH secundário: Oxirredutases do Álcool/metabolismo
Técnicas de Cultura Celular por Lotes
Reatores Biológicos
Ácidos Difosfoglicéricos/metabolismo
Fermentação
Ordem dos Genes
Vetores Genéticos/genética
Glucose/metabolismo
Gliceraldeído 3-Fosfato Desidrogenase (NADP+)/metabolismo
Redes e Vias Metabólicas
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Butylene Glycols); 0 (Diphosphoglyceric Acids); 1981-49-3 (glycerate 1,3-biphosphate); 45427ZB5IJ (2,3-butylene glycol); EC 1.1.- (Alcohol Oxidoreductases); EC 1.1.1.4 (butanediol dehydrogenase); EC 1.2.1.9 (Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)); IY9XDZ35W2 (Glucose)
[Em] Mês de entrada:1407
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:131008
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0076149


  5 / 2560 MEDLINE  
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[PMID]:23908237
[Au] Autor:Moellering RE; Cravatt BF
[Ad] Endereço:The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA. rmoeller@scripps.edu
[Ti] Título:Functional lysine modification by an intrinsically reactive primary glycolytic metabolite.
[So] Source:Science;341(6145):549-53, 2013 Aug 02.
[Is] ISSN:1095-9203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The posttranslational modification of proteins and their regulation by metabolites represent conserved mechanisms in biology. At the confluence of these two processes, we report that the primary glycolytic intermediate 1,3-bisphosphoglycerate (1,3-BPG) reacts with select lysine residues in proteins to form 3-phosphoglyceryl-lysine (pgK). This reaction, which does not require enzyme catalysis, but rather exploits the electrophilicity of 1,3-BPG, was found by proteomic profiling to be enriched on diverse classes of proteins and prominently in or around the active sites of glycolytic enzymes. pgK modifications inhibit glycolytic enzymes and, in cells exposed to high glucose, accumulate on these enzymes to create a potential feedback mechanism that contributes to the buildup and redirection of glycolytic intermediates to alternate biosynthetic pathways.
[Mh] Termos MeSH primário: Ácidos Difosfoglicéricos/metabolismo
Glicerofosfatos/metabolismo
Glicólise
Lisina/análogos & derivados
Lisina/metabolismo
Processamento de Proteína Pós-Traducional
Proteínas/metabolismo
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Biomarcadores Tumorais/química
Biomarcadores Tumorais/metabolismo
Catálise
Linhagem Celular
Proteínas de Ligação a DNA/química
Proteínas de Ligação a DNA/metabolismo
Glucose/metabolismo
Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/química
Gliceraldeído-3-Fosfato Desidrogenase (Fosforiladora)/metabolismo
Seres Humanos
Camundongos
Dados de Sequência Molecular
Fosfopiruvato Hidratase/química
Fosfopiruvato Hidratase/metabolismo
Proteínas/química
Proteínas Supressoras de Tumor/química
Proteínas Supressoras de Tumor/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Biomarkers, Tumor); 0 (DNA-Binding Proteins); 0 (Diphosphoglyceric Acids); 0 (Glycerophosphates); 0 (Proteins); 0 (Tumor Suppressor Proteins); 1981-49-3 (glycerate 1,3-biphosphate); EC 1.2.1.12 (Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)); EC 4.2.1.11 (ENO1 protein, human); EC 4.2.1.11 (Phosphopyruvate Hydratase); IY9XDZ35W2 (Glucose); K3Z4F929H6 (Lysine)
[Em] Mês de entrada:1308
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130803
[St] Status:MEDLINE
[do] DOI:10.1126/science.1238327


  6 / 2560 MEDLINE  
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[PMID]:23865479
[Au] Autor:Kouril T; Esser D; Kort J; Westerhoff HV; Siebers B; Snoep JL
[Ad] Endereço:Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Germany.
[Ti] Título:Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus.
[So] Source:FEBS J;280(18):4666-80, 2013 Sep.
[Is] ISSN:1742-4658
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature instability of the pathway intermediates to carbon loss from the system. The reconstituted system, consisting of phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, triose phosphate isomerase and the fructose 1,6-bisphosphate aldolase/phosphatase, maintained a constant consumption rate of 3-phosphoglycerate and production of fructose 6-phosphate over a 1-h period. Cofactors ATP and NADPH were regenerated via pyruvate kinase and glucose dehydrogenase. A mathematical model was constructed on the basis of the kinetics of the purified enzymes and the measured half-life times of the pathway intermediates. The model quantitatively predicted the system fluxes and metabolite concentrations. Relative enzyme concentrations were chosen such that half the carbon in the system was lost due to degradation of the thermolabile intermediates dihydroxyacetone phosphate, glyceraldehyde 3-phosphate and 1,3-bisphosphoglycerate, indicating that intermediate instability at high temperature can significantly affect pathway efficiency.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Frutose-Bifosfato Aldolase/metabolismo
Gliceraldeído-3-Fosfato Desidrogenases/metabolismo
Modelos Estatísticos
Fosfoglicerato Quinase/metabolismo
Sulfolobus solfataricus/enzimologia
Triose-Fosfato Isomerase/metabolismo
[Mh] Termos MeSH secundário: Proteínas Arqueais/genética
Fosfato de Di-Hidroxiacetona/metabolismo
Ácidos Difosfoglicéricos/metabolismo
Estabilidade Enzimática
Escherichia coli/genética
Escherichia coli/metabolismo
Frutose-Bifosfato Aldolase/genética
Frutosefosfatos/biossíntese
Gluconeogênese/genética
Gliceraldeído 3-Fosfato/metabolismo
Gliceraldeído-3-Fosfato Desidrogenases/genética
Ácidos Glicéricos/metabolismo
Meia-Vida
Temperatura Alta
Cinética
Fosfoglicerato Quinase/genética
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Sulfolobus solfataricus/química
Sulfolobus solfataricus/genética
Termodinâmica
Triose-Fosfato Isomerase/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Diphosphoglyceric Acids); 0 (Fructosephosphates); 0 (Glyceric Acids); 0 (Recombinant Proteins); 142-10-9 (Glyceraldehyde 3-Phosphate); 1981-49-3 (glycerate 1,3-biphosphate); 57-04-5 (Dihydroxyacetone Phosphate); 6814-87-5 (fructose-6-phosphate); 820-11-1 (3-phosphoglycerate); EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases); EC 2.7.2.3 (Phosphoglycerate Kinase); EC 4.1.2.13 (Fructose-Bisphosphate Aldolase); EC 5.3.1.1 (Triose-Phosphate Isomerase)
[Em] Mês de entrada:1310
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:130720
[St] Status:MEDLINE
[do] DOI:10.1111/febs.12438


  7 / 2560 MEDLINE  
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[PMID]:22667589
[Au] Autor:Schofield J; Inder P; Kapral R
[Ad] Endereço:Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada. jmschofi@chem.utoronto.ca
[Ti] Título:Modeling of solvent flow effects in enzyme catalysis under physiological conditions.
[So] Source:J Chem Phys;136(20):205101, 2012 May 28.
[Is] ISSN:1089-7690
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.
[Mh] Termos MeSH primário: Biocatálise
Modelos Biológicos
Fosfoglicerato Quinase/metabolismo
[Mh] Termos MeSH secundário: Difosfato de Adenosina/metabolismo
Trifosfato de Adenosina/metabolismo
Simulação por Computador
Difusão
Ácidos Difosfoglicéricos/metabolismo
Ácidos Glicéricos/metabolismo
Cinética
Modelos Moleculares
Fosfoglicerato Quinase/química
Conformação Proteica
Solventes/metabolismo
Processos Estocásticos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Diphosphoglyceric Acids); 0 (Glyceric Acids); 0 (Solvents); 1981-49-3 (glycerate 1,3-biphosphate); 61D2G4IYVH (Adenosine Diphosphate); 820-11-1 (3-phosphoglycerate); 8L70Q75FXE (Adenosine Triphosphate); EC 2.7.2.3 (Phosphoglycerate Kinase)
[Em] Mês de entrada:1209
[Cu] Atualização por classe:131121
[Lr] Data última revisão:
131121
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:120607
[St] Status:MEDLINE
[do] DOI:10.1063/1.4719539


  8 / 2560 MEDLINE  
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[PMID]:21798238
[Au] Autor:Smith CD; Chattopadhyay D; Pal B
[Ad] Endereço:University of Alabama at Birmingham, Birmingham, AL 35294, USA.
[Ti] Título:Crystal structure of Plasmodium falciparum phosphoglycerate kinase: evidence for anion binding in the basic patch.
[So] Source:Biochem Biophys Res Commun;412(2):203-6, 2011 Aug 26.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:3-Phosphoglycerate kinase (EC 2.7.2.3) is a key enzyme in the glycolytic pathway and catalyzes an important phosphorylation step leading to the production of ATP. The crystal structure of Plasmodium falciparum phosphoglycerate kinase (PfPGK) in the open conformation is presented in two different groups, namely I222 and P6(1)22. The structure in I222 space group is solved using MAD and refined at 3Å whereas that in P6(1)22A is solved using MR and refined at 2.7Å. I222 form has three monomers in asymmetric unit whereas P6(1)22 form has two monomers in the asymmetric unit. In both crystal forms a sulphate ion is located at the active site where ATP binds, but no Mg(2+) ion is observed. For the first time another sulphate ion is found at the basic patch where the 3-phosphate of 1,3-biphosphoglycerate normally binds. This was found in both chains of P6(1)22 form but only in chain A of I222 form.
[Mh] Termos MeSH primário: Fosfoglicerato Quinase/química
Plasmodium falciparum/enzimologia
[Mh] Termos MeSH secundário: Ânions/química
Cristalografia por Raios X
Ácidos Difosfoglicéricos/química
Magnésio/química
Ligação Proteica
Conformação Proteica
Sulfatos/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Anions); 0 (Diphosphoglyceric Acids); 0 (Sulfates); 1981-49-3 (glycerate 1,3-biphosphate); EC 2.7.2.3 (Phosphoglycerate Kinase); I38ZP9992A (Magnesium)
[Em] Mês de entrada:1110
[Cu] Atualização por classe:131121
[Lr] Data última revisão:
131121
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:110730
[St] Status:MEDLINE
[do] DOI:10.1016/j.bbrc.2011.07.045


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[PMID]:21409597
[Au] Autor:Jia B; Linh le T; Lee S; Pham BP; Liu J; Pan H; Zhang S; Cheong GW
[Ad] Endereço:College of Plant Sciences, Jilin University, Changchun, 130-062, China.
[Ti] Título:Biochemical characterization of glyceraldehyde-3-phosphate dehydrogenase from Thermococcus kodakarensis KOD1.
[So] Source:Extremophiles;15(3):337-46, 2011 May.
[Is] ISSN:1433-4909
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an essential role in glycolysis by catalyzing the conversion of D-glyceraldehyde 3-phosphate (D-G3P) to 1,3-diphosphoglycerate using NAD(+) as a cofactor. In this report, the GAPDH gene from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (GAPDH-tk) was cloned and the protein was purified to homogeneity. GAPDH-tk exists as a homotetramer with a native molecular mass of 145 kDa; the subunit molecular mass was 37 kDa. GAPDH-tk is a thermostable protein with a half-life of 5 h at 80-90°C. The apparent K (m) values for NAD(+) and D-G3P were 77.8 ± 7.5 µM and 49.3 ± 3.0 µM, respectively, with V (max) values of 45.1 ± 0.8 U/mg and 59.6 ± 1.3 U/mg, respectively. Transmission electron microscopy (TEM) and image processing confirmed that GAPDH-tk has a tetrameric structure. Interestingly, GAPDH-tk migrates as high molecular mass forms (~232 kDa and ~669 kDa) in response to oxidative stress.
[Mh] Termos MeSH primário: Proteínas Arqueais/metabolismo
Gliceraldeído-3-Fosfato Desidrogenases/metabolismo
Thermococcus/enzimologia
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Proteínas Arqueais/química
Proteínas Arqueais/genética
Proteínas Arqueais/isolamento & purificação
Domínio Catalítico
Clonagem Molecular
Ácidos Difosfoglicéricos/metabolismo
Estabilidade Enzimática
Gliceraldeído 3-Fosfato/metabolismo
Gliceraldeído-3-Fosfato Desidrogenases/química
Gliceraldeído-3-Fosfato Desidrogenases/genética
Gliceraldeído-3-Fosfato Desidrogenases/isolamento & purificação
Meia-Vida
Temperatura Alta
Cinética
Microscopia Eletrônica de Transmissão
Dados de Sequência Molecular
Peso Molecular
Mutação
NAD/metabolismo
Estresse Oxidativo
Estrutura Quaternária de Proteína
Relação Estrutura-Atividade
Thermococcus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Archaeal Proteins); 0 (Diphosphoglyceric Acids); 0U46U6E8UK (NAD); 142-10-9 (Glyceraldehyde 3-Phosphate); 1981-49-3 (glycerate 1,3-biphosphate); EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases)
[Em] Mês de entrada:1108
[Cu] Atualização por classe:171013
[Lr] Data última revisão:
171013
[Sb] Subgrupo de revista:IM; S
[Da] Data de entrada para processamento:110317
[St] Status:MEDLINE
[do] DOI:10.1007/s00792-011-0365-4


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[PMID]:20436470
[Au] Autor:Campbell KL; Roberts JE; Watson LN; Stetefeld J; Sloan AM; Signore AV; Howatt JW; Tame JR; Rohland N; Shen TJ; Austin JJ; Hofreiter M; Ho C; Weber RE; Cooper A
[Ad] Endereço:Department of Biological Sciences, University of Manitoba, Winnipeg, Canada. campbelk@cc.umanitoba.ca
[Ti] Título:Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance.
[So] Source:Nat Genet;42(6):536-40, 2010 Jun.
[Is] ISSN:1546-1718
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We have genetically retrieved, resurrected and performed detailed structure-function analyses on authentic woolly mammoth hemoglobin to reveal for the first time both the evolutionary origins and the structural underpinnings of a key adaptive physiochemical trait in an extinct species. Hemoglobin binds and carries O(2); however, its ability to offload O(2) to respiring cells is hampered at low temperatures, as heme deoxygenation is inherently endothermic (that is, hemoglobin-O(2) affinity increases as temperature decreases). We identify amino acid substitutions with large phenotypic effect on the chimeric beta/delta-globin subunit of mammoth hemoglobin that provide a unique solution to this problem and thereby minimize energetically costly heat loss. This biochemical specialization may have been involved in the exploitation of high-latitude environments by this African-derived elephantid lineage during the Pleistocene period. This powerful new approach to directly analyze the genetic and structural basis of physiological adaptations in an extinct species adds an important new dimension to the study of natural selection.
[Mh] Termos MeSH primário: Adaptação Fisiológica/genética
Evolução Molecular
Hemoglobinas/genética
Mamutes/genética
[Mh] Termos MeSH secundário: Substituição de Aminoácidos
Animais
Temperatura Baixa
Ácidos Difosfoglicéricos/química
Elefantes/genética
Fósseis
Hemoglobinas/química
Modelos Moleculares
Dados de Sequência Molecular
Oxigênio/química
Pressão Parcial
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Diphosphoglyceric Acids); 0 (Hemoglobins); 9008-02-0 (deoxyhemoglobin); S88TT14065 (Oxygen)
[Em] Mês de entrada:1006
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:100504
[St] Status:MEDLINE
[do] DOI:10.1038/ng.574



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