› 2a58

X-ray diffraction
2.8Å resolution

Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe mutant W27Y with bound riboflavin

Released:
DOI: 10.2210/pdb2a58/pdb
PDB entry 2a58 coloured by chain, front view.
PDB entry 2a58 coloured by chain, side view.
PDB entry 2a58 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
Structural basis of charge transfer complex formation by riboflavin bound to 6,7-dimethyl-8-ribityllumazine synthase.
Koch M, Breithaupt C, GerhardtHaase S, Weber S, Cushman M, Huber R, Bacher A, Fischer M
Eur J Biochem 271 3208-14 (2004)
PMID: 15265040

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-194103 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6,7-dimethyl-8-ribityllumazine synthase Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 159 amino acids
Theoretical weight: 17.18 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UUB1 (Residues: 1-159; Coverage: 100%)
Gene names: SPBC409.13, rib4
Sequence domains: 6,7-dimethyl-8-ribityllumazine synthase
Structure domains: Lumazine/riboflavin synthase

Ligands and Environments

2 bound ligands:
Ligand PO4 5 x PO4
Ligand RBF 5 x RBF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2221
Unit cell:
a: 111.64Å b: 145.13Å c: 129.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.222
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

1 mention without citation

Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier.
Kumar et al. (2022)