› 1k4o

X-ray diffraction
1.1Å resolution

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

Released:
DOI: 10.2210/pdb1k4o/pdb
PDB entry 1k4o coloured by chain, front view.
PDB entry 1k4o coloured by chain, side view.
PDB entry 1k4o coloured by chain, top view.
Source organism: Pyricularia grisea
Primary publication:
Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase.
Liao DI, Zheng YJ, Viitanen PV, Jordan DB
Biochemistry 41 1795-806 (2002)
PMID: 11827524

Function and Biology Details

Reaction catalysed: 
D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186271 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3,4-dihydroxy-2-butanone 4-phosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 25.04 KDa
Source organism: Pyricularia grisea
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8TG90 (Residues: 1-233; Coverage: 100%)
Gene names: MGG_01049, RIB3
Sequence domains: 3,4-dihydroxy-2-butanone 4-phosphate synthase
Structure domains: DHBP synthase

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand MN 1 x MN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P21212
Unit cell:
a: 53.613Å b: 88.069Å c: 43.851Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.177 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Elucidating biosynthetic pathways for vitamins and cofactors.
Webb et al. (2007)
1 more