› 2f59

X-ray diffraction
2.3Å resolution

Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1) complexed with inhibitor 5-Nitro-6-(D-Ribitylamino)-2,4(1H,3H) Pyrimidinedione

Released:
DOI: 10.2210/pdb2f59/pdb
PDB entry 2f59 coloured by chain, front view.
PDB entry 2f59 coloured by chain, side view.
PDB entry 2f59 coloured by chain, top view.
Source organism: Brucella abortus
Primary publication:
Structural and kinetic properties of lumazine synthase isoenzymes in the order Rhizobiales.
Klinke S, Zylberman V, Bonomi HR, Haase I, Guimarães BG, Braden BC, Bacher A, Fischer M, Goldbaum FA
J Mol Biol 373 664-80 (2007)
PMID: 17854827

Function and Biology Details

Reaction catalysed: 
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H(2)O + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo pentamer (preferred)
homo decamer
Assembly name:
PDBe Complex ID:
PDB-CPX-176519 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6,7-dimethyl-8-ribityllumazine synthase 1 Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 157 amino acids
Theoretical weight: 16.81 KDa
Source organism: Brucella abortus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q57DY1 (Residues: 1-157; Coverage: 100%)
Gene names: BruAb1_0785, ribH, ribH-1, ribH1
Sequence domains: 6,7-dimethyl-8-ribityllumazine synthase
Structure domains: Lumazine/riboflavin synthase

Ligands and Environments

2 bound ligands:
Ligand CA 6 x CA
Ligand INI 5 x INI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE D03B-MX1
Spacegroup: P3221
Unit cell:
a: 95.317Å b: 95.317Å c: 171.743Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.217 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers.
Abbas et al. (2011)
3 more

1 mention without citation

Unusual arginine formations in protein function and assembly: rings, strings, and stacks.
Neves et al. (2012)