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2.7.1.74: deoxycytidine kinase

This is an abbreviated version!
For detailed information about deoxycytidine kinase, go to the full flat file.

Word Map on EC 2.7.1.74

Reaction

NTP
+
deoxycytidine
=
NDP
 +
dCMP

Synonyms

2'-deoxycytidine kinase, ara-C kinase, arabinofuranosylcytosine kinase, dC kinase, dCK, deoxycytidine kinase, deoxycytidine-cytidine kinase, dNTP:deoxycytidine 5'-phosphotransferase, kinase, deoxycytidine (phosphorylating), NTP:deoxycytidine 5'-phosphotransferase

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.1 Phosphotransferases with an alcohol group as acceptor
                2.7.1.74 deoxycytidine kinase

Crystallization

Crystallization on EC 2.7.1.74 - deoxycytidine kinase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure model construction, using the crystal structure of deoxyguanosine kinase, EC 2.7.1.113, as a template, for docking simulations of enzyme with purine nucleosides and analogues, overview
-
dCK in complex with acyclovir at the nucleoside phosphoryl acceptor site, and UDP at the phosphoryl donor site, hanging drop vapour diffusion method, 20 mg/ml protein with 5 mM UDP and 5 mM acyclovir is mixed with reservoir solution containing 0.90-1.5 M trisodium citrate dihydrate and 100 mM HEPES, pH 7.5, 12°C, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement
enzyme mutant C9S/C45S/C59S/S74E/R104M/D133A/C146S in complex with L-dT and UDP, hanging drop vapour diffusion method, mixing of 0.001 ml of 9-15 mg/ml protein mixed with 0.001 ml reservoir solution containing 0.9-1.5 M trisodium citrate dihydrate and 100 mM Tris, pH 7.5, room temperature, X-ray diffraction structure determination and analysis at 1.9-2.5 A resolution
hanging drop vapour diffusion method, in complex with 2-chloro-9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-9H-purin-6-amine and ADP
hanging drop vapour diffusion method, in complex with deoxycytidine (dC) and UDP, and in the presence of deoxycytidine but the absence of UDP or ADP
hanging drop vapour diffusion method, mutant enzyme crystallized in complex with its substrates (-)-beta-2’,3’-dideoxy-3’-thiacytidine and troxacitabine
in complex with 5-methyldeoxycytidine and ADP, hanging drop vapor diffusion method
in complex with dCMP, UDP, and Mg2+ ion, as well as with dAMP, UDP and Mg2+ ion, both to 3.4 A resolution. Product complexes with UDP and a dead-end complex with substrate and UDP have similar active-site conformations
in complex with inhibitors 2-(((2-(3-(2-fluoroethoxy)-4-methoxyphenyl)-5-methylthiazol-4-yl)methyl)thio)pyrimidine-4,6-diamine and 1-(5-(4-(((4,6-diaminopyrimidin-2-yl)thio)methyl)-5-propylthiazol-2-yl)-2-methoxyphenoxy)-2-methylpropan-2-ol , hanging drop vapor diffusion method, using 0.9-1.5 M trisodium citrate dehydrate and 25 mM HEPES (pH 7.5), at 12°C
in complex with inhibitors and UDP, hanging drop vapor diffusion method, using 0.9-1.5 M trisodium citrate dehydrate and 25 mM HEPES pH 7.5
mutant C9S/C45S/C59S/C146S in complex with D-2'-deoxycytidine and ADP, L-2'-deoxycytidine and ADP, and with 5-fluoro-1-(2R,5S)-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosine, i.e. emtricitabine, and ADP. The ability of deoxycytidine kinase to phosphorylate the beta-form of enantiomeric nucleosides is due to both the nature of the enzyme’s active site and the nature of the substrates. Most of the binding interactions between substrate and enzyme are directed at the base moiety of the nucleoside
mutant C9S/C45S/C59S/C146S in complex with L-nucleosides (-)-beta-2',3'-dideoxy-3'-thiacytidine and troxacitabine. The nucleoside binding-site tolerates substrates with different chiral configurations by maintaining virtually all of the protein-ligand interactions responsible for productive substrate positioning. The pseudo-symmetry of nucleosides and nucleoside analogs in combination with their conformational flexibility allows the L- and D-enantiomeric forms to adopt similar shapes when bound to the enzyme
mutant enzyme R104M/D133A in complex with L-thymidine, hanging drop vapor diffusion method, using 0.90-1.5 M trisodium citrate dihydrate and 100 mM HEPES, pH 7.5
purified recombinanat Wild-type enzyme in complex with 5-methyldeoxycytidine and ADP, hanging drop vapour diffusion method, mixing of 0.001 ml of 8 mg/ml protein mixed with 0.001 ml reservoir solution containing 0.9-1.5 M trisodium citrate dihydrate and 100 mM Tris, pH 7.5, room temperature, X-ray diffraction structure determination and analysis at 1.96 A resolution
structural studies of ternary complexes. The enzyme conformation adjusts to the different hydrogen-bonding properties between 2'-deoxyadenosine and 2'-deoxyguanosine and to the presence of substituent at the 2-position present in 2'-deoxyguanosine and cladribine. The carbonyl group in 2'-deoxyguansoine elicits a conformational adjustment of the active site residues Arg104 and Asp133. 2'-Deoxyguanosine and cladribine adopt the anti conformation, in contrast to the syn conformation observed with 2'-deoxyadenosine