gabR [2017-12-19 09:11:24]

transcription activator of [gene|4E1FD02C6FE4103E3B4942BF5221C062CB8D0B9B|gabT]-[gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD], repressor of [gene|search|gabR ]([SW|MocR/ GabR family])

locus: BSU03890

pI: 6.71

mw: 55.00 kDa

protein length: 479 aa

gene length: 1437 bp

function: regulation of gamma-amino butyric acid utilization

product: transcription regulator

essential: no

synonyms: ycnF

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 2.3.2.10|Utilization of gamma-amino butyric acid]
• [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: 440,025 → 441,464

The protein

Catalyzed reaction/ biological activity

• transcription activation of the [gene|4E1FD02C6FE4103E3B4942BF5221C062CB8D0B9B|gabT]-[gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD] operon in the presence of GABA and PLP, transcription repression of [gene|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|gabR] [Pubmed|15223311]

Protein family

• [SW|MocR/ GabR family] [Pubmed|22020104]

Paralogous protein(s)

• [protein|05A23F4611674B0092262DEC309F7AD6B9B5BE30|YdeL], [protein|D0498CC264FFC4B4C0DECAEBBBB884DB1122A4B2|YhdI], there are 5 more members of the [SW|MocR/ GabR family ]in B. subtilis

[SW|Domains]

• N-terminal DNA-binding helix-turn-helix motif (corresponding to domains of the [SW|GntR family]) [Pubmed|24127574]
• C-terminal domain is homologous to PLP-binding large domain of aminotransferases [Pubmed|24127574]

[SW|Cofactors]

• gamma-aminobutyric acid, PLP [Pubmed|24127574]

Effectors of protein activity

• activation of ''[gene|4E1FD02C6FE4103E3B4942BF5221C062CB8D0B9B|gabT]-[gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD]'' expression is triggered by gamma-amino butyrate and pyridoxalphosphate [Pubmed|15223311]

Structure

• [PDB|4MGR] (the apo-protein) [Pubmed|24127574]
• [PDB|4N0B] (the complex with PLP) [Pubmed|24127574]

Expression and Regulation

Operons

• genes: [gene|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|gabR]
  description: [pubmed|22383849]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|12123465], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|GabR]: negative autoregulation, [Pubmed|12123465], in [regulon|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|GabR regulon]

Biological materials

Mutant

• MGNA-C014 (ycnF::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/2012 NBRP B. subtilis, Japan]
• BKE03890 (Δ[gene|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|gabR]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE03890 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTTGTAGTTTCTCCTTC, downstream forward: _UP4_AAAATCCCCGTTACAGGGGA
• BKK03890 (Δ[gene|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|gabR]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK03890 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTTGTAGTTTCTCCTTC, downstream forward: _UP4_AAAATCCCCGTTACAGGGGA

Labs working on this gene/protein

• [SW|Linc Sonenshein], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

References

• 11756427,15223311,12123465,24127574,22020104,25388514,25911692,27640111,26681693,28348215,28412355