2ZI7 image
Entry Detail
PDB ID:
2ZI7
Keywords:
Title:
C4S dCK variant of dCK in complex with D-dG+UDP
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2008-02-13
Release Date:
2008-07-08
Method Details:
Experimental Method:
Resolution:
1.97 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Deoxycytidine kinase
Mutations:C9S, C45S, C59S, C146S
Chain IDs:A (auth: B), B (auth: A)
Chain Length:279
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase
J.Med.Chem. 51 4219 4225 (2008)
PMID: 18570408 DOI: 10.1021/jm800134t

Abstact

Purine nucleoside analogues of medicinal importance, such as cladribine, require phosphorylation by deoxycytidine kinase (dCK) for pharmacological activity. Structural studies of ternary complexes of human dCK show that the enzyme conformation adjusts to the different hydrogen-bonding properties between dA and dG and to the presence of substituent at the 2-position present in dG and cladribine. Specifically, the carbonyl group in dG elicits a previously unseen conformational adjustment of the active site residues Arg104 and Asp133. In addition, dG and cladribine adopt the anti conformation, in contrast to the syn conformation observed with dA. Kinetic analysis reveals that cladribine is phosphorylated at the highest efficiency with UTP as donor. We attribute this to the ability of cladribine to combine advantageous properties from dA (favorable hydrogen-bonding pattern) and dG (propensity to bind to the enzyme in its anti conformation), suggesting that dA analogues with a substituent at the 2-position are likely to be better activated by human dCK.

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