ribD

168

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

locus: BSU_23280

Molecular weight: 39.15 kDa

pI: 6.08

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: ribD, ribG

List of homologs in different organisms, belongs to COG1985 (Galperin et al., 2021)

Gene

Coordinates: 2,430,258  2,431,343

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The protein

Catalyzed reaction/ biological activity

• 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H⁺ + H₂O --> 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH₄⁺ (according to UniProt)
• 5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP⁺ --> 5-amino-6-(5-phospho-D-ribosylamino)uracil + H⁺ + NADPH (according to UniProt)

Protein family

• N-terminal part: [wiki|Cytidine and deoxycytidylate deaminase family] (according to UniProt)
• C-terminal part: HTP reductase family (single member, according to UniProt)

[wiki|Domains]

• [wiki|CMP/dCMP-type deaminase domain] (aa 1–122) (according to UniProt)

Structure

• [PDB|3EX8] [Pubmed|18986985]
• [AF|P17618]

[wiki|Localization]

• cytoplasm [pubmed|34474681]

Expression and Regulation

Operons

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

  description: [Pubmed|8159171]

  regulation

  • expressed in the absence of FMN ([wiki|FMN-box]) [Pubmed|15808508]
  • binding of [protein|3D32B6C1DC9CAC615B02E14EA846648C3B0E61D6|ribR] to the [wiki|FMN-box] riboswitch can enforce expression even in the presence of FMN [pubmed|26494285]
  • the [wiki|FMN-box] RNA is degraded by [protein|872CCB5A49C9000BD95E4B0472556D5F60F7D7A4|RNase Y] [pubmed|29794222]

  regulatory mechanism

  • FMN-box: RNA switch, via [wiki|FMN-box] in the presence of FMN or FMNH₂, this is counter-acted upon binding of [protein|3D32B6C1DC9CAC615B02E14EA846648C3B0E61D6|ribR], in [regulon|other_regulator:FMN-box|FMN-box]
  • [protein|3D32B6C1DC9CAC615B02E14EA846648C3B0E61D6|ribR]: antitermination, [pubmed|26494285], in [regulon|protein:3D32B6C1DC9CAC615B02E14EA846648C3B0E61D6|ribR regulon]

  sigma factors

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

Biological materials

Mutant

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

References

• 12456892,15808508,18986985,8159171,7934830,23270261,26494285,29794222,29864427,32817529,34474681