RocD

• Description: ornithine transaminase
  
  

Gene name	rocD
Synonyms
Essential	no
Product	ornithine transaminase
Function	arginine, ornithine and citrulline utilization
Gene expression levels in SubtiExpress: rocD
Metabolic function and regulation of this protein in SubtiPathways: rocD
MW, pI	43 kDa, 4.894
Gene length, protein length	1203 bp, 401 aa
Immediate neighbours	rocE, rocR
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

utilization of amino acids

This gene is a member of the following regulons

AhrC regulon, CodY regulon, RocR regulon, SigL regulon, Spo0A regulon

The gene

Basic information

• Locus tag: BSU40340

Database entries

• BsubCyc: BSU40340

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid (according to Swiss-Prot)

• Protein family: OAT subfamily (according to Swiss-Prot)

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactor(s):

• Effectors of protein activity:

• Interactions:

• Localization:

Database entries

• BsubCyc: BSU40340

• Structure: 3RUY (from B. anthracis)

• UniProt: P38021

• KEGG entry: [3]

• E.C. number: 2.6.1.13

Expression and regulation

• Operon: rocD-rocE-rocF PubMed

• Expression browser: rocD PubMed

• Sigma factor: SigL PubMed

• Regulation:
  • induced by arginine (RocR, AhrC) PubMed
  • repressed under conditions that trigger sporulation (Spo0A) PubMed
  • repressed during growth in the presence of branched chain amino acids (CodY) PubMed

• Regulatory mechanism:
  • RocR, AhrC: transcription activation PubMed
  • Spo0A: transcription repression PubMed
  • CodY: transcription repression PubMed
• Additional information:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 337 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 113714 PubMed

Biological materials

• Mutant: GP656, aphA3, available in Jörg Stülke's lab

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

References

Adrienne Zaprasis, Tamara Hoffmann, Guido Wünsche, Lope A Flórez, Jörg Stülke, Erhard Bremer
Mutational activation of the RocR activator and of a cryptic rocDEF promoter bypass loss of the initial steps of proline biosynthesis in Bacillus subtilis.
Environ Microbiol: 2014, 16(3);701-17
[PubMed:23869754] [WorldCat.org] [DOI] (I p)

Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647] [WorldCat.org] [DOI] (P p)

Virginie Molle, Yoshiko Nakaura, Robert P Shivers, Hirotake Yamaguchi, Richard Losick, Yasutaro Fujita, Abraham L Sonenshein
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis.
J Bacteriol: 2003, 185(6);1911-22
[PubMed:12618455] [WorldCat.org] [DOI] (P p)

R Gardan, G Rapoport, M Débarbouillé
Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis.
J Mol Biol: 1995, 249(5);843-56
[PubMed:7540694] [WorldCat.org] [DOI] (P p)