Catalytic Mechanism of Nucleoside Diphosphate Kinase Investigated Using Nucleotide Analogues, Viscosity Effects, and X-ray Crystallography

Nucleoside diphosphate (NDP) kinases display low specificity with respect to the base moiety of the nucleotides and to the 2‘-position of the ribose, but the 3‘-hydroxyl is found to be important for catalysis. We report in this paper the enzymatic analysis of a series of derivatives of thymidine diphosphate (TDP) where the 3‘-OH group was removed or replaced by fluorine, azido, and amino groups. With Dictyostelium NDP kinase, k cat decreases 15−200-fold from 1100 s-1 with TDP, and (k cat/K m)NDP decreases from 12 × 106 to 103 to 5 × 104 M-1 s-1, depending on the substrate. The poorest substrates are 3‘-deoxyTDP and 3‘-azido-3‘-deoxyTDP, while the best modified substrates are 2‘,3‘-dehydro-3‘-deoxyTDP and 3‘-fluoro-3‘-deoxyTDP. In a similar way, 3‘-fluoro-2‘,3‘-dideoxyUDP was found to be a better substrate than 2‘,3‘-dideoxyUDP, but a much poorer substrate than 2‘-deoxyUDP. (k cat/K m)NDP is sensitive to the viscosity of the solution with TDP as the substrate but not with the modified substrates. To understand the poor catalytic efficiency of the modified nucleotides at a structural level, we determined the crystal structure of Dictyostelium NDP kinase complexed to 3‘-fluoro-2‘,3‘-dideoxyUDP at 2.7 Å resolution. Significant differences are noted as compared to the TDP complex. Substrate-assisted catalysis by the 3‘-OH, which is effective in the NDP kinase reaction, cannot occur with the modified substrate. With TDP, the β-phosphate, which is the leaving group when a γ-phosphate is transferred to His122, hydrogen bonds to the 3‘-hydroxyl group of the sugar; with 3‘-fluoro-2‘,3‘-dideoxyUDP, the β-phosphate hydrogen bonds to Asn119 and moves away from the attacking Nδ of the catalytic His122. Since all anti-AIDS nucleoside drugs are modified at the 3‘-position, these results are relevant to the role of NDP kinase in their cellular metabolism.