› 1nqw

X-ray diffraction
2.2Å resolution

Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid

Released:
DOI: 10.2210/pdb1nqw/pdb
PDB entry 1nqw coloured by chain, front view.
PDB entry 1nqw coloured by chain, side view.
PDB entry 1nqw coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus.
Zhang X, Meining W, Cushman M, Haase I, Fischer M, Bacher A, Ladenstein R
J Mol Biol 328 167-82 (2003)
PMID: 12684006

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

Assembly composition:
homo 60-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130334 (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: 154 amino acids
Theoretical weight: 16.73 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O66529 (Residues: 1-154; Coverage: 100%)
Gene names: aq_132, ribH
Sequence domains: 6,7-dimethyl-8-ribityllumazine synthase
Structure domains: Lumazine/riboflavin synthase

Ligands and Environments

1 bound ligand:
Ligand 5YL 5 x 5YL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: I23
Unit cell:
a: 180.096Å b: 180.096Å c: 180.096Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.161 0.177
Expression system: Escherichia coli

Quick links

Citations

7 review citations

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

3 mentions without citation

Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.
Yang et al. (2009)
2 more