gabD [2019-07-23 09:15:07]

succinate-semialdehyde dehydrogenase (NADP), general stress protein

locus: BSU_03910

pI: 4.76

mw: 50.10 kDa

protein length: 462 aa

gene length: 1389 bp

function: utilization of gamma-amino butyric acid

product: succinate-semialdehyde dehydrogenase (NADP)

essential: no

synonyms: ycnH

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 4|Lifestyles] → [category|SW 4.3|Coping with stress] → [category|SW 4.3.1|General stress proteins (controlled by SigB)]

Gene

Coordinates: 442,950 444,338

Phenotypes of a mutant

• growth defect in the presence of gamma-aminobutyrate [Pubmed|24127574]

The protein

Protein family

• [SW|aldehyde dehydrogenase family] (according to UniProt)

Paralogous protein(s)

• [protein|EF0AAAF5BAE8E1F54FCA296643F7B9E3CE257B1D|YfmT], [protein|F3341F205CB939498109D2A54DE842065C488DD5|AldX], [protein|F9CF067A2A8E3B2BACC6A51A0E87E84640349980|AldY], [protein|1ADC55F8E265AF86E29743C671CE1EA1BE7EB41E|GbsA], [protein|2042F691CB37B1BAFE2CF3906A9F7F47457C3995|PutC], [protein|5B66ADB81AB141982F187B1C5E3A9346AA064DE2|YcbD], [protein|67A72A0EABCD807C25D8EAC61C251142B45C174E|DhaS], [protein|69838717DC6BB27864D88C282BF5BC7CC558BFD7|RocA], [protein|762718A15E5256261D79DF60F9106AF0CE2D60C6|IolA], [protein|99F1FAF28FB4817D94E84BD5288FA33124558933|YwdH]

Structure

• [PDB|3RHH] (from from ''Bacillus halodurans'' C-125 complexed with NADP, 36% identity, 68% similarity)

Expression and Regulation

Operons

• genes: [gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD]
  description: [Pubmed|12123465]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|12123465], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]
  • [protein|580011DE5DC40EC9E7E0512791D328FAA010DCB8|SigB]: sigma factor, [Pubmed|15805528], in [regulon|580011DE5DC40EC9E7E0512791D328FAA010DCB8|SigB regulon]

  regulatory mechanism

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

  regulation

  • ''[protein|search|gabD]'': induced by stress ([protein|search|SigB]) [Pubmed|15805528]

• genes: [gene|4E1FD02C6FE4103E3B4942BF5221C062CB8D0B9B|gabT]-[gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD]
  description: [Pubmed|12123465]

  sigma factors

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

  regulatory mechanism

  • [protein|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|GabR]: activation, [Pubmed|32147931,12123465], in [regulon|C7C36FAC0CE72226960FC7E8E016B8EC77AF1036|GabR regulon]

  regulation

  • ''[protein|A0BEB92D54799956A4ADE106A1388E5710141069|GabD]'': induced by stress ([protein|580011DE5DC40EC9E7E0512791D328FAA010DCB8|SigB]) [Pubmed|15805528]

Biological materials

Mutant

• MGNA-C015 (ycnH::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/2013 NBRP B. subtilis, Japan]
• BKE03910 ([gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE03910 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTGAACATTCCTTTCT, downstream forward: _UP4_TAAAAGAATGCACGCTCCTG
• BKK03910 ([gene|A0BEB92D54799956A4ADE106A1388E5710141069|gabD]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK03910 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTGAACATTCCTTTCT, downstream forward: _UP4_TAAAAGAATGCACGCTCCTG

labs

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

References

• 15223311,12123465,11544224,15805528,28516784