sirB [2019-07-01 10:18:43]

sirohydrochlorin ferrochelatase

locus: BSU15620

pI: 6.06

mw: 28.69 kDa

protein length: 261 aa

gene length: 786 bp

function: siroheme biosynthesis, sulfite reduction

product: sirohydrochlorin ferrochelatase

essential: no

synonyms: ylnE

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.2|Biosynthesis of cofactors] → [category|SW 2.6.2.6|Biosynthesis of heme/ siroheme]

Gene

Coordinates: 1,634,837 1,635,622

The protein

Catalyzed reaction/ biological activity

• insertion of Fe2+ into the substrate sirohydrochlorin (SHC) in siroheme biosynthesis [pubmed|30778451]

Protein family

• SirB subfamily (according to Swiss-Prot)

Structure

• Apo-form: [PDB|5ZT8] [pubmed|30778451]
• Co²⁺ bound: [PDB|5ZT7] ([pubmed|30778451]), [PDB|6JV6]
• Ni²⁺ bound: [PDB|5ZT9]
• Fe³⁺ bound: [PDB|5ZTA]

Expression and Regulation

Operons

• genes: [gene|51EB09C122A7166D662AE72842A44EC5FBA03134|cysH]-[gene|58A5A7F12664EC38AC21E24C1AD89671D7E648CF|cysP]-[gene|6CF2A9A517B641C44C0B46EF242BC5E668EA846B|sat]-[gene|3C71659E4868744A9301C26608EABF7B98217DCF|cysC]-[gene|92831D5A8E07A18BA6C6978123769D00D685BB45|ylnD]-[gene|9349C4646A56F933041EBE750F1BE86BAE7A60D9|sirB]-[gene|8BAB9B12D9D58A45446DC6CB7F48869089800FD3|ylnF]
  description: [Pubmed|11004190]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|11004190], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|50930C56C27D22715620A350220E3C56ADB41020|CymR]: repression, in [regulon|50930C56C27D22715620A350220E3C56ADB41020|CymR regulon]
  • [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-B369 (ylnE::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/1368 NBRP B. subtilis, Japan]
• BKE15620 ([gene|9349C4646A56F933041EBE750F1BE86BAE7A60D9|sirB]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE15620 BGSC], [Pubmed|28189581], upstream reverse: _UP1_ATATAAAATTGCTTGTTTCA, downstream forward: _UP4_CAATTTGATTTTGATGGAGG
• BKK15620 ([gene|9349C4646A56F933041EBE750F1BE86BAE7A60D9|sirB]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK15620 BGSC], [Pubmed|28189581], upstream reverse: _UP1_ATATAAAATTGCTTGTTTCA, downstream forward: _UP4_CAATTTGATTTTGATGGAGG

References

• 16267287,11004190,12107147,18039762,30778451