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| − | * '''Description:''' catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression <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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| − | |''rocG''
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| − | |-
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| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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| − | |style="background:#ABCDEF;" align="center"| '''Essential''' || no
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| − | |style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)
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| − | |-
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| − | |style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of GltC
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| − | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
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| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
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| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
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| − | |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_nucleotide.txt Gene sequence (+200bp) corrected ]'''
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| − | |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_protein.txt Protein sequence]'''
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| − | |-
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| − | |colspan="2" | '''Genetic context''' <br/> [[Image:rocG_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:''' 3879765 - 3881036
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| − |
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| − | ===Phenotypes of a mutant ===
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| − | Poor growth on complex media such as LB. No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])
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| − |
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| − | === Database entries ===
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| − | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocG.html]
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| − | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]
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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:''' L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the [[GltC]] transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
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| − | * '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family
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| − | * '''Paralogous protein(s):''' [[GudB]]
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| − |
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| − | === Extended information on the protein ===
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| − | * '''Kinetic information:'''
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| − | * '''Domains:'''
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| − | * '''Modification:'''
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| − | * '''Cofactor(s):'''
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| − | * '''Effectors of protein activity:'''
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| − | * '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''gltAB'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
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| − | * '''Localization:'''
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| − |
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| − | === Database entries ===
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| − | * '''Structure:'''
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| − | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633]
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| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]
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| − | * '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2]
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| − |
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| − | === Additional information===
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| − | =Expression and regulation=
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| − | * '''Operon:''' ''rocG''
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| − | * '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
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| − | * '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])
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| − | * '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression
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| − | * '''Additional information:'''
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| − | Activation by RocR requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
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| − |
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| − | =Biological materials =
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| − | * '''Mutant:''' GP747 (spc), GP726 (aphA3), available in [[Stülke]] lab
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| − | * '''Expression vector:''' pGP902 (in [[pGP172]], N-terminal Strep-tag), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab
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| − | * '''lacZ fusion:'''
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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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| − |
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| − | =Labs working on this gene/protein=
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| − | [[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
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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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| − | # Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
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| − | # Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
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| − | # Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
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| − | # Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
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| − | # Ali, N. O., J. Jeusset, E. Larquet, E. le Cam, B. Belitsky, A. L. Sonenshein, T. Msadek, and M. Débarbouillé. 2003. Specificity of the interaction of RocR with the rocG-rocA intergenic region in Bacillus subtilis. Microbiology 149: 739-750. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
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| − | # Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
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| − | # Belitsky BR, Sonenshein, AL: An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA 1999, 96:10290-10295. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
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| − | # Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150224 PubMed]
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| − | # Belitsky BR, Sonenshein AL (2004) Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186:3399-3407 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150225 PubMed]
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| − | # Khan, M. I., K. Ito, H. Kim, H. Ashida, T. Ishikawa, H. Shibata, and Y. Sawa. 2005. Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis. Biosci. Biotechnol. Biochem. 69: 1861-1870. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16244435 PubMed]
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| − | # Stillman TJ, Baker PJ, Britton KL, Rice DW Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol 1993, 234:1131-1139. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8263917 PubMed]
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