› 1kyy

X-ray diffraction
2.4Å resolution

Lumazine Synthase from S.pombe bound to nitropyrimidinedione

Released:
DOI: 10.2210/pdb1kyy/pdb
PDB entry 1kyy coloured by chain, front view.
PDB entry 1kyy coloured by chain, side view.
PDB entry 1kyy coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.
Gerhardt S, Haase I, Steinbacher S, Kaiser JT, Cushman M, Bacher A, Huber R, Fischer M
J Mol Biol 318 1317-29 (2002)
PMID: 12083520

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 domain:

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: 17.21 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 INI 5 x INI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2221
Unit cell:
a: 111.261Å b: 145.044Å c: 127.86Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.183 0.206
Expression system: Escherichia coli

Quick links

Citations

10 review citations

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

2 mentions without citation

Second career of a biosynthetic enzyme: Lumazine synthase as a virus-like nanoparticle in vaccine development.
Ladenstein et al. (2020)
1 more