5TMP

COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR AZTP5A

Summary for 5TMP

• Entry DOI: 10.2210/pdb5tmp/pdb
• Descriptor: PROTEIN (THYMIDYLATE KINASE), P1-(5'-ADENOSYL)P5-(5'-(3'AZIDO-3'-DEOXYTHYMIDYL))PENTAPHOSPHATE (3 entities in total)
• Functional Keywords: atp:dtmp phosphotransferase, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 24739.49

Authors

Lavie, A.,Ostermann, N.,Schlichting, I. (deposition date: 1998-09-01, release date: 1998-11-25, Last modification date: 2023-12-27)

Primary citation

Lavie, A.,Ostermann, N.,Brundiers, R.,Goody, R.S.,Reinstein, J.,Konrad, M.,Schlichting, I.
Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.
Proc.Natl.Acad.Sci.USA, 95:14045-14050, 1998

PubMed Abstract: The crystal structures of Escherichia coli thymidylate kinase (TmpK) in complex with P1-(5'-adenosyl)-P5-(5'-thymidyl)pentaphosphate and P1-(5'-adenosyl)P5-[5'-(3'-azido-3'-deoxythymidine)] pentaphosphate have been solved to 2.0-A and 2.2-A resolution, respectively. The overall structure of the bacterial TmpK is very similar to that of yeast TmpK. In contrast to the human and yeast TmpKs, which phosphorylate 3'-azido-3'-deoxythymidine 5'-monophosphate (AZT-MP) at a 200-fold reduced turnover number (kcat) in comparison to the physiological substrate dTMP, reduction of kcat is only 2-fold for the bacterial enzyme. The different kinetic properties toward AZT-MP between the eukaryotic TmpKs and E. coli TmpK can be rationalized by the different ways in which these enzymes stabilize the presumed transition state and the different manner in which a carboxylic acid side chain in the P loop interacts with the deoxyribose of the monophosphate. Yeast TmpK interacts with the 3'-hydroxyl of dTMP through Asp-14 of the P loop in a bidentate manner: binding of AZT-MP results in a shift of the P loop to accommodate the larger substituent. In E. coli TmpK, the corresponding residue is Glu-12, and it interacts in a side-on fashion with the 3'-hydroxyl of dTMP. This different mode of interaction between the P loop carboxylic acid with the 3' substituent of the monophosphate deoxyribose allows the accommodation of an azido group in the case of the E. coli enzyme without significant P loop movement. In addition, although the yeast enzyme uses Arg-15 (a glycine in E. coli) to stabilize the transition state, E. coli seems to use Arg-153 from a region termed Lid instead. Thus, the binding of AZT-MP to the yeast TmpK results in the shift of a catalytic residue, which is not the case for the bacterial kinase.

PubMed: 9826650
DOI: 10.1073/pnas.95.24.14045

Experimental method

X-RAY DIFFRACTION (1.98 Å)