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| − | * '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme <br/><br/>
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| − | {| align="right" border="1" cellpadding="2"
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| − | |style="background:#ABCDEF;" align="center"|'''Gene name'''
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| − | |''gapA''
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| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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| − | |style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
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| − | |style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
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| − | |style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
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| − | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
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| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
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| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[pgk]]''
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| − | |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gapA_nucleotide.txt Gene sequence (+200bp) ]'''
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| − | |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gapA_protein.txt Protein sequence]'''
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| − | |colspan="2" | '''Genetic context''' <br/> [[Image:gapA_context.gif]]
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| − | |}
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| − | __TOC__
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| − | <br/><br/>
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| − |
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| − | =The gene=
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| − |
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| − | === Basic information ===
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| − | * '''Coordinates:''' 3480732 - 3481736
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| − |
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| − | ===Phenotypes of a mutant ===
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| − | essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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| − | essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]
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| − |
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| − | === Database entries ===
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| − | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
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| − | * '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]
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| − |
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| − | === Additional information===
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| − |
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| − | =The protein=
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| − |
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| − | === Basic information/ Evolution ===
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| − | * '''Catalyzed reaction/ biological activity:''' glyceraldehyde-3-phosphate dehydrogenase, (NADH-dependent). Catalyzes the reaction from glyceraldehyde-3-phosphate to 1.3-bi-phosphoglycerate. This reaction is part of the glycolysis.
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| − | * '''Protein family:'''
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| − | * '''Paralogous protein(s):''' [[GapB]]
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| − |
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| − | === Extended information on the protein ===
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| − | * '''Kinetic information:''' K(M) for NAD: 5.7 mM, K(cat) for NAD: 70/sec (determined for GapA from ''Geobacillus stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]
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| − | * '''Domains:'''
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| − | * '''Modification:''' Phosphorylation (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
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| − | * '''Cofactor(s):'''
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| − | * '''Effectors of protein activity:'''
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| − | * '''Interactions:'''
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| − | ** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
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| − | ** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
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| − | * '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed], loosely membrane associated[http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
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| − |
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| − | === Database entries ===
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| − | * '''Structure:'''
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| − | ** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CMC 3CMC] (from ''Geobacillus stearothermophilus'')
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| − | ** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)
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| − | * '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P09124 P09124]
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| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940 KEGG]
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| − | * '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?1.2.1.12 1.2.1.12]
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| − |
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| − | === Additional information===
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| − | GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).
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| − |
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| − | =Expression and regulation=
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| − | * '''Operon:'''
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| − | ** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]''
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| − | ** ''[[cggR]]-[[gapA]]''
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| − | The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. The processing event requires the [[Rny]] protein.
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| − | * '''Sigma factor:''' [[SigA]]
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| − | * '''Regulation:''' [[CggR]] represses the operon in the absence of glycolytic sugars [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12622823 PubMed]
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| − | * '''Regulatory mechanism:''' repression
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| − | * '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]
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| − | * '''Additional information:''' GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).
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| − |
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| − | =Biological materials =
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| − | * '''Mutant:''' essential
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| − | * '''Expression vector:''' pGP90 (N-terminal Strep-tag, purification from ''B. subtilis'', in [[pGP380]]), pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)
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| − | * '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)
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| − | * '''GFP fusion:'''
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| − | * '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
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| − | * '''Antibody:''' available in [[Stülke]] lab
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| − | =Labs working on this gene/protein=
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| − | [[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
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| − | [[Stülke|Jörg Stülke]], University of Göttingen, Germany
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| − | [http://wwwuser.gwdg.de/~genmibio/stuelke.html homepage]
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| − | =Your additional remarks=
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| − | =References=
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| − | # Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
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| − | # Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. subm.
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| − | # Doan, T., and S. Aymerich. 2003. Regulation of the central glycolytic pathways in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol. Microbiol. 47: 1709-1721. [http://www.ncbi.nlm.nih.gov/sites/entrez/12622823 PubMed]
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| − | # Evguenieva-Hackenberg, E., Schiltz, E., and Klug, G. (2002) Dehydrogenases from all three domains of life cleave RNA. J Biol Chem 277, 46145-46150. [http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]
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| − | # Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., and Aymerich, S. (2000) Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 275, 14031-14037. [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]
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| − | # Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. [http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]
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| − | # Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
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| − | # Ludwig, H., Rebhan, N., Blencke, H.-M., Merzbacher, M. & Stülke, J. (2002). Control of the glycolytic ''gapA'' operon by the catabolite control protein A in ''Bacillus subtilis'': a novel mechanism of CcpA-mediated regulation. Mol Microbiol 45, 543-553.[http://www.ncbi.nlm.nih.gov/sites/entrez/12123463 PubMed]
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| − | # Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
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| − | # Meinken, C., Blencke, H. M., Ludwig, H., and Stülke, J. (2003) Expression of the glycolytic ''gapA'' operon in ''Bacillus subtilis'': differential synthesis of proteins encoded by the operon. Microbiology 149, 751-761. [http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]
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| − | # Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
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| − | # Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
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| − | # Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J., and Hecker, M. (1999) Role of CcpA in regulation of the central pathways of carbon catabolism in ''Bacillus subtilis''. J Bacteriol 181, 6996-7004.[http://www.ncbi.nlm.nih.gov/sites/entrez/10559165 PubMed]
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