Homologous Superfamily

DHBP synthase RibB-like alpha/beta domain superfamily (IPR017945)

Short name: DHBP_synth_RibB-like_a/b_dom

Overlapping entries

Description

This superfamily represents a structural domain consisting of segregated alpha and beta regions in 3-layers. Homologous domains with this structure are found in:

  • 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC:4.1.99.12) (DHBP synthase) (RibB)
  • A family of eukaryotic and prokaryotic hypothetical proteins that includes YrdC and YciO from Escherichia coli and MTH1692 from the archaea Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum)

DHBP synthase RibB catalyses the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate, the latter serving as the biosynthetic precursor for the xylene ring of riboflavin [PMID: 9211332]. In Photobacterium leiognathi, the riboflavin synthesis genes ribB (DHBP synthase), ribE (riboflavin synthase), ribH (lumazone synthase) and ribA (GTP cyclohydrolase II) all reside in the lux operon [PMID: 11396941]. RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin (IPR000926). No sequences with significant homology to DHBP synthase are found in the metazoa.

The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation [PMID: 12211024]. YrdC from Escherichia coli preferentially binds to double-stranded RNA and DNA. YrdC is predicted to be an rRNA maturation factor, as deletions in its gene lead to immature ribosomal 30S subunits and, consequently, fewer translating ribosomes [PMID: 15716138]. Therefore, YrdC may function by keeping an rRNA structure needed for proper processing of 16S rRNA, especially at lower temperatures. Threonylcarbamoyl-AMP synthase (Sua5) is an example of a multi-domain protein that contains an N-terminal YrdC-like domain and a C-terminal Sua5 domain. Sua5 was identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a translation initiation defect in the cytochrome c gene and is required for formation of a threonylcarbamoyl group on adenosine at position 37 in tRNAs [PMID: 18004774,PMID: 19287007]. HypF is involved in the synthesis of the active site of [NiFe]-hydrogenases [PMID: 12377778].

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
SUPERFAMILY