2VI5 image
Deposition Date 2007-11-27
Release Date 2008-04-08
Last Version Date 2023-12-13
Entry Detail
PDB ID:
2VI5
Keywords:
Title:
LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dione-5-yl-propionamide
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.29
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
Chain IDs:A, B, C, D, E, F, G, H, I, J
Chain Length:160
Number of Molecules:10
Biological Source:MYCOBACTERIUM TUBERCULOSIS
Primary Citation
A New Series of N-[2,4-Dioxo-6-D-Ribitylamino-1,2, 3,4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives as Inhibitors of Lumazine Syntase and Riboflavin Synthase: Design, Synthesis, Biochemical Evaluation, Crystallography and Mechanistic Implications.
J.Org.Chem. 73 2715 ? (2008)
PMID: 18331058 DOI: 10.1021/JO702631A

Abstact

The penultimate step in the biosynthesis of riboflavin is catalyzed by lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the lumazine synthase-catalyzed reaction were synthesized and evaluated as lumazine synthase inhibitors. All three intermediate analogues were inhibitors of Mycobacterium tuberculosis lumazine synthase, Bacillus subtilis lumazine synthase, and Schizosaccharomyces pombe lumazine synthase, while one of them proved to be an extremely potent inhibitor of Escherichia coli riboflavin synthase with a Ki of 1.3 nM. The crystal structure of M. tuberculosis lumazine synthase in complex with one of the inhibitors provides a model of the conformation of the intermediate occurring immediately after phosphate elimination, supporting a mechanism in which phosphate elimination occurs before a conformational change of the Schiff base intermediate toward a cyclic structure.

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