Difference between revisions of "Sandbox"

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* '''Description:''' protein component of ribonuclease P  <br/><br/>
+
* '''Description:''' 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''rnpA''
+
|''rocA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-76d ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || protein component of RNase P (substrate specificity)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || cleavage of precursor sequences <br/>from the 5' ends of pre-tRNAs
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine, ornithine and citrulline utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 10.804  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.58  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 348 bp, 116 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1545 bp, 515 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIIJ]]'', ''[[rpmH]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocB]]'', ''[[rocG]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16142&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15805&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rocA_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU41050
+
* '''Locus tag:''' BSU37780
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocABC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10063]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10622]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' (S)-1-pyrroline-5-carboxylate + NAD(P)<sup>+</sup> + 2 H<sub>2</sub>O = L-glutamate + NAD(P)H (according to Swiss-Prot)  
  
−
* '''Protein family:''' rnpA family (according to Swiss-Prot)
+
* '''Protein family:''' RocA subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on (Thr-2 OR Thr-4 OR Tyr-5) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RnpA]]-[[RpmH]],  RnpA-[[RnpB]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1A6F 1A6F], [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1A6F 1AF6]  [http://www.ncbi.nlm.nih.gov/sites/entrez/9563955 PubMed]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25814 P25814]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39634 P39634]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU41050]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37780]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.26.5 3.1.26.5]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.5.1.12 1.5.1.12]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[rocA]]-[[rocB]]-[[rocC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induction by arginine ([[RocR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed], [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Roland Hartmann]], Marburg University, Germany [http://www.pharmazie.uni-marburg.de/pharmchem/akhartmann/ag_hartmann.htm homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>11454206 9563955, </pubmed>
+
<pubmed>8113162 17218307, </pubmed>
−
# Hansen, A., Pfeiffer, T., Zuleeg, T., Limmer, S., Ciesiolka, J., Feltens, R. & Hartmann, R. K. (2001). Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzyme from ''Escherichia coli'' and ''Bacillus subtilis''. Mol Microbiol 41, 131-143. [http://www.ncbi.nlm.nih.gov/sites/entrez/11454206 PubMed]
+
# Calogero S, Gardan R, Glaser P, Schweizer J, Rapoport G, Debarbouille M. (1994) RocR, a novel regulatory protein controlling arginine utilization in ''Bacillus subtilis'', belongs to the NtrC/NifA family of transcriptional activators. ''J. Bacteriol.'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
−
# Stams T, Niranjanakumari S, Fierke CA, Christianson DW (1998) Ribonuclease P protein structure: evolutionary origins in the translational apparatus.''Science'' '''280:''' 752-755. [http://www.ncbi.nlm.nih.gov/sites/entrez/9563955 PubMed]
+
# 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]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:33, 8 June 2009

  • Description: 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase

Gene name rocA
Synonyms ipa-76d
Essential no
Product 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase
Function arginine, ornithine and citrulline utilization
MW, pI 56 kDa, 5.58
Gene length, protein length 1545 bp, 515 aa
Immediate neighbours rocB, rocG
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RocA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37780

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: (S)-1-pyrroline-5-carboxylate + NAD(P)+ + 2 H2O = L-glutamate + NAD(P)H (according to Swiss-Prot)
  • Protein family: RocA subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on (Thr-2 OR Thr-4 OR Tyr-5) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

S Calogero, R Gardan, P Glaser, J Schweizer, G Rapoport, M Debarbouille
RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators.
J Bacteriol: 1994, 176(5);1234-41
[PubMed:8113162] [WorldCat.org] [DOI] (P p)

  1. Calogero S, Gardan R, Glaser P, Schweizer J, Rapoport G, Debarbouille M. (1994) RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators. J. Bacteriol. volume: page-page. PubMed
  2. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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