ribD [2019-07-04 13:30:44]

5-amino-6-(5-phosphoribosylamino)uracil reductase

locus: BSU23280

pI: 6.08

mw: 39.15 kDa

protein length: 361 aa

gene length: 1086 bp

function: riboflavin biosynthesis

product: 5-amino-6-(5-phosphoribosylamino)uracil reductase

essential: no

ec: 3.5.4.26

synonyms: ribG

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.2|Biosynthesis of cofactors] → [category|SW 2.6.2.2|Biosynthesis/ acquisition of riboflavin/ FAD]

Gene

Coordinates: 2,430,258 2,431,343

The protein

Catalyzed reaction/ biological activity

• 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine H₂O = 5-amino-6-(5-phosphoribosylamino)uracil NH₃ (according to Swiss-Prot)

Protein family

• [SW|Cytidine and deoxycytidylate deaminase family] (according to UniProt)

Structure

• [PDB|3EX8] [Pubmed|18986985]

Expression and Regulation

Operons

• genes: [gene|3DFCF7C5FE15C9A3E9E7E4B0DA8E926B85DBD180|ribD]-[gene|4E18BD4B084094EE4FBC8FE2AC95B14581D20C0F|ribE]-[gene|F07B7062C850106A95C15978E36DA500F8B089D6|ribA]-[gene|2A5DCBFAB51996F0DDEC964D5D178274AF86CE69|ribH]-[gene|8146A052E4E7844F781E7169C264EC927DEB7387|ribT]
  description: [Pubmed|8159171]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|8159171], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [regulon|FMN-box|FMN-box]: transcription termination, via [SW|FMN-box] in the presence of FMN or FMNH₂, this is counter-acted upon binding of [protein|3D32B6C1DC9CAC615B02E14EA846648C3B0E61D6|RibR], in [regulon|FMN-box|FMN-box]

  regulation

  • expressed in the absence of FMN ([SW|FMN-box]) [Pubmed|15808508]
  • binding of FMN to the [SW|FMN-box] RNA is facilitated by [protein|43CFA3477B4EEB4CE0B2DF63ED2B5EDB171E79C7|NusG]-mediated transcription pausing [pubmed|32817529]
  • the [SW|FMN-box] RNA is degraded by [protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y] [pubmed|29794222]

Biological materials

Mutant

• BKE23280 ([gene|3DFCF7C5FE15C9A3E9E7E4B0DA8E926B85DBD180|ribD]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE23280 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTGTTTCCCTCCCCTCT, downstream forward: _UP4_CCGACAAAGGAATAGGATGG
• BKK23280 ([gene|3DFCF7C5FE15C9A3E9E7E4B0DA8E926B85DBD180|ribD]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK23280 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATTTGTTTCCCTCCCCTCT, downstream forward: _UP4_CCGACAAAGGAATAGGATGG

References

• 12456892,15808508,18986985,8159171,7934830,23270261,26494285,29794222,29864427