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Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with one Manganese, and a glycerol

Source organism: Pyricularia grisea
Biochemical function: metal ion binding
Biological process: riboflavin biosynthetic process
Cellular component: cytosol

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EC 4.1.99.12: 3,4-dihydroxy-2-butanone-4-phosphate synthase

Reaction catalysed:
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
Systematic name:
D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)
Alternative Name(s):
  • DHBP synthase
  • L-3,4-dihydroxybutan-2-one-4-phosphate synthase

GO terms

Sequence family

Pfam Protein family (Pfam)
PF00926
Domain description: 3,4-dihydroxy-2-butanone 4-phosphate synthase
Occurring in:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase
The deposited structure of PDB entry 1k4o contains 1 copy of Pfam domain PF00926 (3,4-dihydroxy-2-butanone 4-phosphate synthase) in 3,4-dihydroxy-2-butanone 4-phosphate synthase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR000422
Domain description: 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB
Occurring in:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase
IPR017945
Domain description: DHBP synthase RibB-like alpha/beta domain superfamily
Occurring in:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase

Structure domain

CATH CATH domain
3.90.870.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: DHBP synthase
Homology: DHBP synthase
Occurring in:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase
The deposited structure of PDB entry 1k4o contains 1 copy of CATH domain 3.90.870.10 (DHBP synthase) in 3,4-dihydroxy-2-butanone 4-phosphate synthase. Showing 1 copy in chain A.
SCOP SCOP annotation
64372
Class: Alpha and beta proteins (a+b)
Fold: YrdC/RibB
Superfamily: YrdC/RibB
Occurring in:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase
The deposited structure of PDB entry 1k4o contains 1 copy of SCOP domain 64372 (3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB) in 3,4-dihydroxy-2-butanone 4-phosphate synthase. Showing 1 copy in chain A.

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