Revision as of 15:26, 16 July 2009

Description: trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression

Gene name	rocG
Synonyms
Essential	no
Product	glutamate dehydrogenase (major)
Function	arginine utilization, controls the activity of GltC
Metabolic function and regulation of this protein in SubtiPathways: Ammonium/ glutamate
MW, pI	46.2 kDa, 6.28
Gene length, protein length	1272 bp, 424 amino acids
Immediate neighbours	yweA, rocA
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList

The gene

Basic information

Locus tag: BSU37790

Phenotypes of a mutant

Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants (gudB1)

Database entries

DBTBS entry: [1]

SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

Catalyzed reaction/ biological activity: L-glutamate + H₂O + NAD⁺ = 2-oxoglutarate + NH₃ + NADH (according to Swiss-Prot) L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the GltC transcription activator PubMed

Protein family: Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family

Paralogous protein(s): GudB

Extended information on the protein

Kinetic information:

Domains:

Modification:

Cofactor(s):

Effectors of protein activity:

Interactions: RocG-GltC, this interaction prevents transcription activation of the gltA-gltB operon by GltC PubMed

Localization:

Database entries

Structure:

Swiss prot entry: P39633

KEGG entry: [3]

E.C. number: 1.4.1.2 1.4.1.2]

Additional information

Expression and regulation

Operon: rocG

Sigma factor: SigL PubMed

Regulation: induced by arginine (RocR, AhrC), ornithine or proline, subject to carbon catabolite repression (CcpA)

Regulatory mechanism: RocR: transcription activation PubMed PubMed; AhrC: transcription activation ; CcpA: transcription repression

Additional information:

Activation by RocR requires binding of RocG to a downstream element PubMed

Biological materials

Mutant: GP747 (spc), GP726 (aphA3), GP810 (tet) available in Stülke lab

Expression vector:
- expression of native rocG in B. subtilis: pGP529 (in pBQ200), available in Stülke lab
- for purification of RocG carrying an N-terminal Strep-tag: pGP902 (in pGP172), a series of rocG variants is also available in pGP172, available in Stülke lab

lacZ fusion:

GFP fusion:

two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

Antibody: available in Stülke lab

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

Enzymatic activity of RocG

Shigeki Kada, Masahiro Yabusaki, Takayuki Kaga, Hitoshi Ashida, Ken-ichi Yoshida
Identification of two major ammonia-releasing reactions involved in secondary natto fermentation.
Biosci Biotechnol Biochem: 2008, 72(7);1869-76
[PubMed:18603778] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Katrin Gunka, Jens J Landmann, Jörg Stülke
Glutamate metabolism in Bacillus subtilis: gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system.
J Bacteriol: 2008, 190(10);3557-64
[PubMed:18326565] [WorldCat.org] [DOI] (I p)

Md Iqbal Hassan Khan, Kousuke Ito, Hyeung Kim, Hiroyuki Ashida, Takahiro Ishikawa, Hitoshi Shibata, Yoshihiro Sawa
Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis.
Biosci Biotechnol Biochem: 2005, 69(10);1861-70
[PubMed:16244435] [WorldCat.org] [DOI] (P p)

Iqbal Hassan Khan, Hyeung Kim, Hiroyuki Ashida, Takahiro Ishikawa, Hitoshi Shibata, Yoshihiro Sawa
Altering the substrate specificity of glutamate dehydrogenase from Bacillus subtilis by site-directed mutagenesis.
Biosci Biotechnol Biochem: 2005, 69(9);1802-5
[PubMed:16195607] [WorldCat.org] [DOI] (P p)

B R Belitsky, A L Sonenshein
Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.
J Bacteriol: 1998, 180(23);6298-305
[PubMed:9829940] [WorldCat.org] [DOI] (P p)

Function in the control of GltC activity

Christina Herzberg, Lope Andrés Flórez Weidinger, Bastian Dörrbecker, Sebastian Hübner, Jörg Stülke, Fabian M Commichau
SPINE: a method for the rapid detection and analysis of protein-protein interactions in vivo.
Proteomics: 2007, 7(22);4032-5
[PubMed:17994626] [WorldCat.org] [DOI] (P p)

Fabian M Commichau, Christina Herzberg, Philipp Tripal, Oliver Valerius, Jörg Stülke
A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC.
Mol Microbiol: 2007, 65(3);642-54
[PubMed:17608797] [WorldCat.org] [DOI] (P p)

Fabian M Commichau, Ingrid Wacker, Jan Schleider, Hans-Matti Blencke, Irene Reif, Philipp Tripal, Jörg Stülke
Characterization of Bacillus subtilis mutants with carbon source-independent glutamate biosynthesis.
J Mol Microbiol Biotechnol: 2007, 12(1-2);106-13
[PubMed:17183217] [WorldCat.org] [DOI] (P p)

Boris R Belitsky, Abraham L Sonenshein
Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase.
J Bacteriol: 2004, 186(11);3399-407
[PubMed:15150225] [WorldCat.org] [DOI] (P p)

Expression of rocG

Structural analysis of glutamate dehydrogenase

T J Stillman, P J Baker, K L Britton, D W Rice
Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
J Mol Biol: 1993, 234(4);1131-9
[PubMed:8263917] [WorldCat.org] [DOI] (P p)

@@ Line 1: / Line 1: @@
-Test again, again.
+* '''Description:''' trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression  <br/><br/>
+{| align="right" border="1" cellpadding="2"
+|-
+|style="background:#ABCDEF;" align="center"|'''Gene name'''
+|''rocG''
+|-
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|-
+|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+|-
+|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)
+|-
+|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of [[GltC]]
+|-
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''
+|-
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
+|-
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
+|-
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
+|-
+|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15806&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|-
+|colspan="2" | '''Genetic context''' <br/> [[Image:rocG_context.gif]]
+ <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
+|-
+|}
+__TOC__
+<br/><br/><br/><br/><br/><br/>
+=The gene=
+=== Basic information ===
+* '''Locus tag:''' BSU37790
+===Phenotypes of a mutant ===
+Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])
+=== Database entries ===
+* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocG.html]
+* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]
+=== Additional information===
+=The protein=
+=== Basic information/ Evolution ===
+* '''Catalyzed reaction/ biological activity:''' L-glutamate + H<sub>2</sub>O + NAD<sup>+</sup> = 2-oxoglutarate + NH<sub>3</sub> + NADH (according to Swiss-Prot) 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]
+* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family
+* '''Paralogous protein(s):''' [[GudB]]
+=== Extended information on the protein ===
+* '''Kinetic information:'''
+* '''Domains:'''
+* '''Modification:'''
+* '''Cofactor(s):'''
+* '''Effectors of protein activity:'''
+* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''[[gltA]]-[[gltB]]'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
+* '''Localization:'''
+=== Database entries ===
+* '''Structure:'''
+* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633 P39633]
+* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]
+* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2 1.4.1.2]  1.4.1.2]
+=== Additional information===
+=Expression and regulation=
+* '''Operon:''' ''rocG''
+* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
+* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])
+* '''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
+* '''Additional information:'''
+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]
+=Biological materials =
+* '''Mutant:''' GP747 (spc), GP726 (aphA3), GP810 (tet) available in [[Stülke]] lab
+* '''Expression vector:'''
+** expression of native ''rocG'' in ''B. subtilis'': pGP529 (in [[pBQ200]]), available in [[Stülke]] lab
+** for purification of RocG carrying an N-terminal Strep-tag: pGP902 (in [[pGP172]]), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab
+* '''lacZ fusion:'''
+* '''GFP fusion:'''
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+* '''Antibody:''' available in [[Stülke]] lab
+=Labs working on this gene/protein=
+[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
+[[Stülke|Jörg Stülke]], University of Göttingen, Germany
+[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
+=Your additional remarks=
+=References=
+'''Enzymatic activity of RocG'''
+<pubmed>18603778,,16244435 16195607 ,18326565, 9829940  </pubmed>
+'''Function in the control of [[GltC]] activity'''
+<pubmed>15150225,17994626 ,17608797 17183217   </pubmed>
+'''Expression of ''rocG'''''
+<pubmed>12634342,15150224 10468601 9829940  </pubmed>
+'''Structural analysis of glutamate dehydrogenase'''
+<pubmed>8263917 </pubmed>

Difference between revisions of "Sandbox"

Revision as of 15:26, 16 July 2009

Contents

The gene

Basic information

Phenotypes of a mutant

Database entries

Additional information

The protein

Basic information/ Evolution

Extended information on the protein

Database entries

Additional information

Expression and regulation

Biological materials

Labs working on this gene/protein

Your additional remarks

References

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