› 7uf4

X-ray diffraction
2.2Å resolution

RibB from Vibrio cholera bound with intermediate 1 of the reaction cycle and D-ribulose-5-phosphate (D-Ru5P)

Released:
DOI: 10.2210/pdb7uf4/pdb
PDB entry 7uf4 coloured by chain, front view.
PDB entry 7uf4 coloured by chain, side view.
PDB entry 7uf4 coloured by chain, top view.
Source organism: Vibrio cholerae
Primary publication:
Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis.
Kenjić N, Meneely KM, Wherritt DJ, Denler MC, Jackson TA, Moran GR, Lamb AL
OpenAccess logo J Am Chem Soc (2022)
PMID: 35802469

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191917 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3,4-dihydroxy-2-butanone 4-phosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 218 amino acids
Theoretical weight: 23.59 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KKP2 (Residues: 1-218; Coverage: 100%)
Gene names: VC_A1060, ribB
Sequence domains: 3,4-dihydroxy-2-butanone 4-phosphate synthase

Ligands and Environments

4 bound ligands:
Ligand N46 1 x N46
Ligand 5RP 1 x 5RP
Ligand MN 2 x MN
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2221
Unit cell:
a: 60.337Å b: 78.558Å c: 90.535Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.169 0.224
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Inhibitors of riboflavin biosynthetic pathway enzymes as potential antibacterial drugs.
Islam et al. (2023)
1 other article

1 mention without citation

Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis.
Kenjić et al. (2022)