yjmC [2019-06-27 15:26:09]

similar to ureidoglycolate dehydrogenase, may be involved in galacturonate utilization

locus: BSU12320

pI: 5.67

mw: 36.32 kDa

protein length: 337 aa

gene length: 1014 bp

function: unknown

product: unknown

essential: no

synonyms

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.2|Carbon metabolism] → [category|SW 2.2.2|Utilization of specific carbon sources] → [category|SW 2.2.2.15|Utilization of hexuronate]
• [category|SW 4|Lifestyles] → [category|SW 4.2|Sporulation] → [category|SW 4.2.1|Sporulation proteins] → [category|SW 4.2.1.4|Sporulation proteins/ other]

Gene

Coordinates: 1,303,423 1,304,436

The protein

Protein family

• LDH2/MDH2 oxidoreductase family (according to Swiss-Prot)

Structure

• [PDB|4H8A] (ureidoglycolate dehydrogenase from E. coli, 41% identity) [pubmed|23284870]

[SW|Localization]

• cytoplasm (according to Swiss-Prot)

Additional information

• The gene is annotated in KEGG as an ortholog of malate dehydrogenase EC 1.1.1.37. but it is marked as uncharacterized oxidoreductase (EC 1.1.1.-) in Swiss-Prot. In MetaCyc it is marked as similar to malate dehydrogenase. As the paper by Mekjian et al. [Pubmed|9882655] suggests this gene is more likely to be involved in the glucuronate pathway (for which EC 1.1.1.37 is not a member), no literature/experimental evidence supporting the annotation is available. [Pubmed|19935659]

Expression and Regulation

Operons

• genes: [gene|3AEA5D769B89E676C916FD8934D762B4C9A02AA2|yjmC]-[gene|CC55984E31C5698668CCCD4AC6E2210B2B41ACAB|yjmD]-[gene|A0A6D36BEC397345A1D17E6A7C34E1F612FD46C7|uxuA]-[gene|B886E504A767343042DE9BF4E23E6798D124A2CF|yjmF]-[gene|6D08E897DD697523FD0720704A25AD4472075B6C|exuT]-[gene|69B143987DCF73B5D080E3FD87A6CA2940E07DA8|exuR]-[gene|A1C64447E0074B06C9210CC51680273FAAE703FA|uxaB]-[gene|ED29D2DE48AADEA09C90F08B6021555C357946B4|uxaA]
  description: [Pubmed|9882655]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|9882655], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]
  • [protein|3CB24D493B3282278B7DC61CE3C793DFA815F9E2|SigE]: sigma factor, [Pubmed|15699190,9882655], in [regulon|3CB24D493B3282278B7DC61CE3C793DFA815F9E2|SigE regulon]

  regulatory mechanism

  • [protein|69B143987DCF73B5D080E3FD87A6CA2940E07DA8|ExuR]: repression, in the absence of inducer, in [regulon|69B143987DCF73B5D080E3FD87A6CA2940E07DA8|ExuR regulon]
  • [protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA]: repression, [pubmed|9882655] [pubmed|10666464], in [regulon|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA regulon]

  regulation

  • induced by galacturonate ([protein|search|ExuR]) [Pubmed|9882655]

• genes: [gene|5A0C29C7E218701727523885D01A48D02266B421|uxaC]-[gene|59CD3E4C24326542D9C85BB6FE64FBF49869EB55|yjmB]-[gene|3AEA5D769B89E676C916FD8934D762B4C9A02AA2|yjmC]-[gene|CC55984E31C5698668CCCD4AC6E2210B2B41ACAB|yjmD]-[gene|A0A6D36BEC397345A1D17E6A7C34E1F612FD46C7|uxuA]-[gene|B886E504A767343042DE9BF4E23E6798D124A2CF|yjmF]-[gene|6D08E897DD697523FD0720704A25AD4472075B6C|exuT]-[gene|69B143987DCF73B5D080E3FD87A6CA2940E07DA8|exuR]-[gene|A1C64447E0074B06C9210CC51680273FAAE703FA|uxaB]-[gene|ED29D2DE48AADEA09C90F08B6021555C357946B4|uxaA]
  description: [Pubmed|9882655]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|9882655], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|69B143987DCF73B5D080E3FD87A6CA2940E07DA8|ExuR]: repression, in the absence of inducer, in [regulon|69B143987DCF73B5D080E3FD87A6CA2940E07DA8|ExuR regulon]
  • [protein|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA]: repression, [pubmed|9882655] [pubmed|10666464], in [regulon|E39AFEB7B7F28969A35C4B51CC6E7819F71C79D9|CcpA regulon]

  regulation

  • induced by galacturonate ([protein|search|ExuR]) [Pubmed|9882655]

Biological materials

Mutant

• MGNA-A367 (yjmC::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/367 NBRP B. subtilis, Japan]
• BKE12320 ([gene|3AEA5D769B89E676C916FD8934D762B4C9A02AA2|yjmC]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE12320 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAAGCAAGTGCCTCCTTCCT, downstream forward: _UP4_TTCTTAAAAAGCAGGTGAGT
• BKK12320 ([gene|3AEA5D769B89E676C916FD8934D762B4C9A02AA2|yjmC]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK12320 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CAAGCAAGTGCCTCCTTCCT, downstream forward: _UP4_TTCTTAAAAAGCAGGTGAGT

References

• 9579062,9882655,10666464,19935659,27941785,23284870