2ZI5

C4S dCK variant of dCK in complex with L-dA+UDP

Summary for 2ZI5

• Entry DOI: 10.2210/pdb2zi5/pdb
• Related: 1P60 2NO1 2NO7 2ZI3 2ZI4 2ZI6 2ZI7 2ZI9 2ZIA
• Descriptor: Deoxycytidine kinase, URIDINE-5'-DIPHOSPHATE, (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol, ... (4 entities in total)
• Functional Keywords: dck, purine, deoxyadenosine, deoxycytidine kinase, nucleoside, enantiomer, l-da, udp, atp-binding, nucleotide-binding, nucleus, phosphoprotein, transferase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P27707
• Total number of polymer chains: 4
• Total formula weight: 132911.65

Authors

Sabini, E.,Lavie, A. (deposition date: 2008-02-13, release date: 2008-04-22, Last modification date: 2023-11-01)

Primary citation

Sabini, E.,Hazra, S.,Ort, S.,Konrad, M.,Lavie, A.
Structural basis for substrate promiscuity of dCK
J.Mol.Biol., 378:607-621, 2008

PubMed Abstract: Deoxycytidine kinase (dCK) is an essential nucleoside kinase critical for the production of nucleotide precursors for DNA synthesis. This enzyme catalyzes the initial conversion of the nucleosides deoxyadenosine (dA), deoxyguanosine (dG), and deoxycytidine (dC) into their monophosphate forms, with subsequent phosphorylation to the triphosphate forms performed by additional enzymes. Several nucleoside analog prodrugs are dependent on dCK for their pharmacological activation, and even nucleosides of the non-physiological L-chirality are phosphorylated by dCK. In addition to accepting dC and purine nucleosides (and their analogs) as phosphoryl acceptors, dCK can utilize either ATP or UTP as phosphoryl donors. To unravel the structural basis for substrate promiscuity of dCK at both the nucleoside acceptor and nucleotide donor sites, we solved the crystal structures of the enzyme as ternary complexes with the two enantiomeric forms of dA (D-dA, or L-dA), with either UDP or ADP bound to the donor site. The complexes with UDP revealed an open state of dCK in which the nucleoside, either D-dA or L-dA, is surprisingly bound in a manner not consistent with catalysis. In contrast, the complexes with ADP, with either D-dA or L-dA, adopted a closed and catalytically competent conformation. The differential states adopted by dCK in response to the nature of the nucleotide were also detected by tryptophan fluorescence experiments. Thus, we are in the unique position to observe differential effects at the acceptor site due to the nature of the nucleotide at the donor site, allowing us to rationalize the different kinetic properties observed with UTP to those with ATP.

PubMed: 18377927
DOI: 10.1016/j.jmb.2008.02.061

Experimental method

X-RAY DIFFRACTION (1.77 Å)