1ZPR

E. COLI THYMIDYLATE SYNTHASE MUTANT E58Q IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)

Summary for 1ZPR

• Entry DOI: 10.2210/pdb1zpr/pdb
• Descriptor: THYMIDYLATE SYNTHASE, 2'-DEOXYURIDINE 5'-MONOPHOSPHATE, 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID, ... (4 entities in total)
• Functional Keywords: transferase, active site mutant, reaction intermediate
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A884
• Total number of polymer chains: 2
• Total formula weight: 62688.66

Authors

Sage, C.R.,Stout, T.J.,Rutenber, E.E.,Stroud, R.M. (deposition date: 1996-10-15, release date: 1997-07-07, Last modification date: 2021-11-03)

Primary citation

Sage, C.R.,Rutenber, E.E.,Stout, T.J.,Stroud, R.M.
An essential role for water in an enzyme reaction mechanism: the crystal structure of the thymidylate synthase mutant E58Q.
Biochemistry, 35:16270-16281, 1996

PubMed Abstract: A water-mediated hydrogen bond network coordinated by glutamate 60(58) appears to play an important role in the thymidylate synthase (TS) reaction mechanism. We have addressed the role of glutamate 60(58) in the TS reaction by cocrystalizing the Escherichia coli TS mutant E60(58)Q with dUMP and the cofactor analog CB3717 and have determined the X-ray crystal structure to 2.5 A resolution with a final R factor of 15.2% (Rfree = 24.0%). Using difference Fourier analysis, we analyzed directly the changes that occur between wild-type and mutant structures. The structure of the mutant enzyme suggests that E60(58) is not required to properly position the ligands in the active site and that the coordinated hydrogen bond network has been disrupted in the mutant, providing an atomic resolution explanation for the impairment of the TS reaction by the E60(58)Q mutant and confirming the proposal that E60(58) coordinates this conserved hydrogen bond network. The structure also provides insight into the role of specific waters in the active site which have been suggested to be important in the TS reaction. Finally, the structure shows a unique conformation for the cofactor analog, CB3717, which has implications for structure-based drug design and sheds light on the controversy surrounding the previously observed enzymatic nonidentity between the chemically identical monomers of the TS dimer.

PubMed: 8973201
DOI: 10.1021/bi961269r

Experimental method

X-RAY DIFFRACTION (2.5 Å)