1NQU: Crystal Structure Of Lumazine Synthase From Aquifex Aeolicus In Complex With Inhibitor: 6,7-dioxo-5h-8-ribitylaminolumazine

6,7-Dimethyl-8-ribityllumazine is the biosynthetic precursor of riboflavin, which, as a coenzyme, plays a vital role in the electron transfer process for energy production in all cellular organisms. The enzymes involved in lumazine biosynthesis have been studied in considerable detail. However, the conclusive mechanism of the reaction catalyzed by lumazine synthase has remained unclear. Here, we report four crystal structures of the enzyme from the hyperthermophilic bacterium Aquifex aeolicus in complex with different inhibitor compounds. The structures were refined at resolutions of 1.72 A, 1.85 A, 2.05 A and 2.2 A, respectively. The inhibitors have been designed in order to mimic the substrate, the putative reaction intermediates and the final product. Structural comparisons of the native enzyme and the inhibitor complexes as well as the kinetic data of single-site mutants of lumazine synthase from Bacillus subtilis showed that several highly conserved residues at the active site, namely Phe22, His88, Arg127, Lys135 and Glu138 are most likely involved in catalysis. A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, inorganic phosphate elimination, formation of the Schiff base and cyclization is proposed.
PDB ID: 1NQUDownload
MMDB ID: 26008
PDB Deposition Date: 2003/1/23
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 1.75  Å
Source Organism:
Similar Structures:
Biological Unit for 1NQU: 60-meric; determined by author and by software (PISA,PQS)
Molecular Components in 1NQU
Label Count Molecule
Proteins (60 molecules)
6,7-dimethyl-8-ribityllumazine Synthase(Gene symbol: ribH)
Molecule annotation
Chemicals (120 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB