yoaD

similar to phosphoglycerate dehydrogenase

locus: BSU_18560

pI: 5.62

mw: 38.47 kDa

protein length: 344 aa

gene length: 1035 bp

function: methionine biosynthesis

product: unknown

essential: no

synonyms

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.3|Amino acid/ nitrogen metabolism] → [category|SW 2.3.1|Biosynthesis/ acquisition of amino acids] → [category|SW 2.3.1.11|Biosynthesis/ acquisition of methionine/ S-adenosylmethionine/ based on similarity]

Gene

Coordinates: 2,024,042 2,025,076

The protein

Catalyzed reaction/ biological activity

• YoaD is likely to convert 3-phosphoglycerate to serine for use in methionine biosynthesis (based on [protein|search|S-box] regulation)

Protein family

• D-isomer specific 2-hydroxyacid dehydrogenase family (with [protein|B0145F4E13F004ECC773E8758B5844669F4C74D7|YvcT] and [protein|8AD1C7C761FF8B407A973381CA135C264B995CB7|SerA], according to UniProt)

Structure

• [PDB|1WWK] (phosphoglycerate dehydrogenase from Pyrococcus horikoshii, 35% identity)

Additional information

• The gene is annotated in KEGG as an ortholog of D-3-phosphoglycerate dehydrogenase EC 1.1.1.95. No EC annotation is available in Swiss-Prot. In MetaCyc the protein is marked as similar to phosphorglycerate dehydrogenase. No literature/experimental evidence supporting the annotation is available. [Pubmed|19935659]

Expression and Regulation

Operons

• genes: [gene|3769B79A180412C0FE98B3FC54BA49750BAFEDF6|yoaD]-[gene|182B8EFA41DAE695B008CBAA561F3730D11750B1|yoaC]-[gene|FF60633F2902E4CA58B34FF3DAFF85B0D4007622|yoaB]
  description: [Pubmed|10094622]

  regulatory mechanism

  • [regulon|S-box|S-box]: termination, the [SW|S-box] [SW|riboswitch] binds S-adenosylmethionine resulting in termination [Pubmed|10094622], in [regulon|S-box|S-box]

  regulation

  • induced by methionine starvation ([SW|S-box]) [Pubmed|10094622]
  • the [SW|S-box] RNA is degraded by [protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y] [pubmed|29794222]

Biological materials

Mutant

• MGNA-A835 (yoaD::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/835 NBRP B. subtilis, Japan]
• BKE18560 ([gene|3769B79A180412C0FE98B3FC54BA49750BAFEDF6|yoaD]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE18560 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATAAAAAAAATCTCTTTCC, downstream forward: _UP4_TAAGAAAGGAGGCTAACAGA
• BKK18560 ([gene|3769B79A180412C0FE98B3FC54BA49750BAFEDF6|yoaD]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK18560 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATAAAAAAAATCTCTTTCC, downstream forward: _UP4_TAAGAAAGGAGGCTAACAGA

References

• 19258532,10094622,12107147,18039762,29794222