2GQ2 image
Deposition Date 2006-04-19
Release Date 2006-06-27
Last Version Date 2024-11-20
Entry Detail
PDB ID:
2GQ2
Keywords:
Title:
Mycobacterium tuberculosis ThyX-NADP complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Thymidylate synthase thyX
Mutations:I65M / L175M double mutant
Chain IDs:A, B, C, D
Chain Length:258
Number of Molecules:4
Biological Source:Mycobacterium tuberculosis H37Rv
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET SELENOMETHIONINE
Primary Citation
NADP+ expels both the co-factor and a substrate analog from the Mycobacterium tuberculosis ThyX active site: opportunities for anti-bacterial drug design.
J.Mol.Biol. 360 1 6 (2006)
PMID: 16730023 DOI: 10.1016/j.jmb.2006.04.061

Abstact

The novel flavin-dependent thymidylate synthase, ThyX, is absent in humans but several pathogenic bacteria depend exclusively on ThyX activity to synthesize thymidylate. Reduction of the enzyme-bound FAD by NADPH is suggested to be the critical first step in ThyX catalysis. We soaked Mycobacterium tuberculosis ThyX-FAD-BrdUMP ternary complex crystals in a solution containing NADP+ to gain structural insights into the reductive step of the catalytic cycle. Surprisingly, the NADP+ displaced both FAD and BrdUMP from the active site. In the resultant ThyX-NADP+ binary complex, the AMP moiety is bound in a deep pocket similar to that of the same moiety of FAD in the ternary complex, while the nicotinamide part of NADP+ is engaged in a limited number of contacts with ThyX. The additional 2'-phosphate group attached to the AMP ribose of NADP+ could be accommodated with minor rearrangement of water molecules. The newly introduced 2'-phosphate groups are engaged in water-mediated interactions across the non-crystallographic 2-fold axis of the ThyX tetramer, suggesting possibilities for design of high-affinity bivalent inhibitors of this intriguing enzyme.

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Primary Citation of related structures