ribD [2020-09-09 16:05:17]

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

Locus: BSU_23280

Isoelectric point: 6.08

Molecular weight: 39.15 kDa

Protein length: 361 aa

Gene length: 1086 bp

Function: riboflavin biosynthesis

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

Essential: no

E.C.: 3.5.4.26

Synonyms: ribG

Genomic Context

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Categories containing this gene/protein

• Metabolism → Additional metabolic pathways → Biosynthesis of cofactors → 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 + 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: Cytidine and deoxycytidylate deaminase family (according to UniProt)
• C-terminal part: HTP reductase family (single member, according to UniProt)

Domains

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

Structure

• 3EX8 PubMed

Expression and Regulation

Operons

• Genes: ribD-ribE-ribA-ribH-ribT
  Description: PubMed

  Sigma factors

  • SigA: sigma factor, PubMed, in SigA regulon

  Regulatory mechanism

  • FMN-box: transcription termination, via FMN-box in the presence of FMN or FMNH₂, this is counter-acted upon binding of RibR, in FMN-box

  Regulation

  • expressed in the absence of FMN (FMN-box) PubMed
  • binding of FMN to the FMN-box RNA is facilitated by NusG-mediated transcription pausing PubMed
  • the FMN-box RNA is degraded by RNase Y PubMed

Biological materials

Mutant

• BKE23280 (ribD::erm trpC2) available at BGSC, PubMed, upstream reverse: _UP1_CATTTGTTTCCCTCCCCTCT, downstream forward: _UP4_CCGACAAAGGAATAGGATGG
• BKK23280 (ribD::kan trpC2) available at BGSC, PubMed, upstream reverse: _UP1_CATTTGTTTCCCTCCCCTCT, downstream forward: _UP4_CCGACAAAGGAATAGGATGG

References

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