X-ray structure of nucleoside diphosphate kinase complexed with thymidine diphosphate and Mg2+ at 2-A resolution

We report the crystal structure of nucleoside diphosphate kinase (NDP kinase) from Dictyostelium discoideum with thymidine diphosphate (dTDP) and Mg2+ bound at the active site. The structure has been refined to an R-factor of 18.3% at 2-A resolution. The base stacks on the aromatic ring of Phe 64 near the protein surface and is wedged between the side chains of Phe 64 and Val 116. The sugar and the pyrophosphate are deeper inside the protein and make numerous H-bonds with protein side chains. There is no backbone interaction with the nucleotide. A Mg2+ ion bridges the alpha- and beta-phosphates and interacts with the protein via water molecules. NDP kinase shows little specificity toward ribonucleotides and deoxyribonucleotides. This property, required by the enzyme biological function, can now be analyzed by comparing the crystal structures of free, ADP-ligated, and dTDP-ligated enzymes. The most significant differences are located in residues 60-64, which adapt their conformation to allow Phe 64 to stack on both types of bases. Nonspecific binding is achieved by the absence of polar interaction between the base and protein atoms. The ribose of ADP and the deoxyribose of dTDP occupy similar positions, their hydroxyl groups interacting with Lys 16 and Asn 119. The H-bond between Lys 16 and the O2' hydroxyl of ADP is replaced by a similar interaction with a water molecule in the dTDP complex. The beta-phosphate position is the same for ADP and dTDP, suggesting that the mechanism of phosphate transfer is the same for all substrates ofNDP kinase.(ABSTRACT TRUNCATED AT 250 WORDS)