rocR [2019-09-05 11:46:18]

transcriptional activator of arginine utilization operons

locus: BSU_40350

pI: 6.08

mw: 52.01 kDa

protein length: 461 aa

gene length: 1386 bp

function: transcriptional activator of arginine utilization operons

product: transcriptional activator

essential: no

synonyms

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.3|Amino acid/ nitrogen metabolism] → [category|SW 2.3.2|Utilization of amino acids] → [category|SW 2.3.2.4|Utilization of arginine/ ornithine]
• [category|SW 3|Information processing] → [category|SW 3.4|Regulation of gene expression] → [category|SW 3.4.2|Transcription factors and their control] → [category|SW 3.4.2.5|Transcription factors/ other]

Gene

Coordinates: 4,145,747 → 4,147,132

The protein

Catalyzed reaction/ biological activity

• transcription activation at [protein|1118A21CC581B0470EC6E7C178F2523CDCA70F93|SigL]-dependent promoters of [gene|69838717DC6BB27864D88C282BF5BC7CC558BFD7|rocABC], [gene|617FE9E40E8822D58B0446128585CB6CA05A50C6|rocDEF], and [gene|56CBEBCFEF5CFB4A0175498338C7AF2F45EAA3E3|rocG]

Protein family

• [protein|1118A21CC581B0470EC6E7C178F2523CDCA70F93| Sigma-54] interacting transcription activator
• [SW|Transcription factors activating transcription at SigL-dependent promoters]

[SW|Domains]

• [protein|1118A21CC581B0470EC6E7C178F2523CDCA70F93| Sigma-54] factor interaction domain (143–372)
• 2x nucleotid-binding domain (171–178),(233–242)
• HTH motif (434–453)
• [SW|PAS domain]

[SW|Cofactors]

• ornithine or citrulline are required for RocR-dependent transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709 PubMed]

Structure

• [PDB|1OJL] (from Salmonella typhimurium, corresponds to aa 143 ... 454, 41% identity) [pubmed|16005641]

additional information

• information on binding sites can be found in the [http://www.prodoric2.de/detail.php?acc=MX000062 PRODORIC2 database]

Expression and Regulation

Operons

• genes: [gene|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]
  description: [pubmed|22383849]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [PubMed|7540694], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|RocR]: autorepression, [Pubmed|2548995], in [regulon|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|RocR regulon]
  • [protein|D267AF38B0CF107042326E9B8F3DD3C9C85840E4|LexA]: autorepression, in [regulon|D267AF38B0CF107042326E9B8F3DD3C9C85840E4|LexA regulon]

  regulation

  • autoregulation by [protein|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|RocR] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids= 7540694 PubMed]

Biological materials

Mutant

• GP2312 (Δ[gene|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]::''tet'', available in [SW|Jörg Stülke]'s lab)
• QB5533 (aphA3), from [SW|Michel Debarbouille], available in [SW|Jörg Stülke]'s lab
• 1A911 ( ''rocR''::''kan''), [Pubmed|16585774], available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A911&Search=1A911 BGSC]
• BKE40350 (Δ[gene|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]::''erm'', available in the BGSC, in [SW|Fabian Commichau]'s, and in [SW|Jörg Stülke]'s lab) [pubmed|28189581]
• BKE40350 (Δ[gene|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE40350 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CACTGTATGAACCTCCCTCA, downstream forward: _UP4_CAATATCGGCTGAAGAAATT
• BKK40350 (Δ[gene|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK40350 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CACTGTATGAACCTCCCTCA, downstream forward: _UP4_CAATATCGGCTGAAGAAATT

labs

• [SW|Michel Debarbouille], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]

References

• 12634342,8113162,9194709,21965396,23869754,21906631,16005641