Steve Ealick's Research Group


Human Deoxycytidine Kinase


PDB file:

2A7Q, human dCK + clofarabine + ADP

*2QRN, dCK/dCMP/UDP/Mg complex

*2QRO, dCK/dAMP/UDP/Mg complex

Description:

Clofarabine is the first new drug for pediatric leukemia to be approved in more than a decade. To exhibit the cytotoxic activity, clofarabine must be phosphorylated to clofarabine triphosphate. During this process, the initial phosphorylation to the monophosphate by deoxycytidine kinase (dCK) is the rate-limiting step and plays a crucial role in the activation of the prodrug. dCK phosphorylates clofarabine with a much higher efficiency than the physiological substrate dCA. The comparison of our structure of human dCK complexed with clorfarabine and ADP with other structures of dCK in complex with pyrimidine nucleoside analogs reveals the key interactions that contribute to the high catalytic efficiency for clofarabine. This study provides a structural basis for developing more effective drugs and for protein engineering in the application of prodrug activation via gene therapy. The structure was solved by molecular replacement using the published structure (pdb 1P61) as the search model.

This dCK/clofarabine/ADP complex is the first reported structure of dCK bound to a purine nucleoside analog. The overall fold of each subunit is an αβα three-layer sandwich.

 

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Human dCK is a homodimer with 260 residues per subunit.

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The active site of dCK is located along the C-terminal edge of the central β-sheet and covered by the lid. Clofarabine is almost completely buried in a pocket inside the enzyme and is shielded from the solvent. A schematic drawing of the deoxynucleoside binding site reveals key hydrogen bonds and van der Waals interactions.

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Reference:

Zhang Y, Secrist JA III, and Ealick SE. The crystal structure of human deoxycytidine kinase in complex with clofarabine reveals key interactions for prodrug activation. Acta Crystallogr. D. 62:133-139 (2006).

*Soriano EV, Clark VC, and Ealick SE. Structures of Human Deoxycitidine Kinase Product Complexes. Acta Crystallogr. D. 63:1201-1207 (2007).



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