ybdZ

unknown

locus: BSU_31959

pI: 4.48

mw: 7.90 kDa

protein length: 69 aa

gene length: 210 bp

function: unknown

product: unknown

essential: -

synonyms

Genomic Context

categories

• [category|SW 6|Groups of genes] → [category|SW 6.7|Proteins of unknown function]

Gene

Coordinates: 3,280,294 → 3,280,503

The protein

Structure

• [PDB|5U89] (from Geobacillus sp., 66% identity) [pubmed|28434915]

Expression and Regulation

Operons

• genes: [gene|42C8D303AABFA2A9706295A0F90B0B49F854B0BF|dhbA]-[gene|0D4D200095AD4F9B30179B9AF500306EDA61F5D1|dhbC]-[gene|B864EC6D21AD5E524AC13AE1BE41F5CD7FC399C5|dhbE]-[gene|1346D57F906EE5BD36F7FBFA1E4884EEBC8585FA|dhbB]-[gene|95B75CFF126AF0AD845E62B4036DD3B6DAC8C7FA|dhbF]-[gene|DD647083C2E6968AD26A41C9F4EFBA942D75207C|ybdZ]
  description: [Pubmed|8921902]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|8550523], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]
  • [protein|3DEAC421B4B173C6BBC700E57790751B7AFDF319|SigI]: sigma factor, [pubmed|29914988], in [regulon|3DEAC421B4B173C6BBC700E57790751B7AFDF319|SigI regulon]

  regulatory mechanism

  • [protein|F899F1EE27E6D503BCC06BC52E3C7FD80B8EF725|Fur]: repression, [pubmed|12354229], in [regulon|F899F1EE27E6D503BCC06BC52E3C7FD80B8EF725|Fur regulon]
  • [protein|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB]: repression, [Pubmed|20817675], in [regulon|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB regulon]
  • [protein|65E2F7197D46F5C884CC96018EE4F3EEE94FFA18|Kre]: repression, in [regulon|65E2F7197D46F5C884CC96018EE4F3EEE94FFA18|Kre regulon]

  regulation

  • induced by iron starvation (second wave to allow iron scavenging from the environment) ([protein|F899F1EE27E6D503BCC06BC52E3C7FD80B8EF725|Fur]) [Pubmed|29133393,12354229]
  • expression of the operon is strongly induced at the beginning of [SW|biofilm formation] [pubmed|31113899]

  additional information

  • the ''[gene|42C8D303AABFA2A9706295A0F90B0B49F854B0BF|dhbA]-[gene|0D4D200095AD4F9B30179B9AF500306EDA61F5D1|dhbC]-[gene|B864EC6D21AD5E524AC13AE1BE41F5CD7FC399C5|dhbE]-[gene|1346D57F906EE5BD36F7FBFA1E4884EEBC8585FA|dhbB]-[gene|95B75CFF126AF0AD845E62B4036DD3B6DAC8C7FA|dhbF]'' operon is strongly unregulated in a ''[SW|kre]'' mutant [Pubmed|26110430]

Biological materials

Mutant

• BKE31959 (Δ[gene|DD647083C2E6968AD26A41C9F4EFBA942D75207C|ybdZ]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE31959 BGSC], [Pubmed|28189581], upstream reverse: _UP1_ATTTGCCATTCTATTTCTCC, downstream forward: _UP4_TAATCTTATCAAAAAGAGAC
• BKK31959 (Δ[gene|DD647083C2E6968AD26A41C9F4EFBA942D75207C|ybdZ]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK31959 BGSC], [Pubmed|28189581], upstream reverse: _UP1_ATTTGCCATTCTATTTCTCC, downstream forward: _UP4_TAATCTTATCAAAAAGAGAC

References

Research papers

• 28434915