Three-dimensional structure of nucleoside diphosphate kinase

Three-dimensional structures are known from X-ray studies of the nucleoside diphosphate (NDP) kinase of many organisms from bacteria to human. All NDP kinases have subunits of about 150 residues with a very similar fold based on the alpha beta sandwich or ferredoxin fold. This fold is found in many nucleotide or polynucleotide-binding proteins with no sequence relationship to NDP kinase. This common fold is augmented here with specific features: a surface alpha-helix hairpin, the Kpn loop, and the C-terminal extension. The alpha-helix hairpin and Kpn loop make up the nucleotide binding site, w hich is unique to NDP kinase and different from that of other kinases or AT Pases. The Kpn loop and the C-terminal extension are also involved in the q uaternary structure. Whereas all known eukaryotic NDP kinases, including mi tochondral enzymes, are hexamers, some bacterial enzymes are tetramers. How ever, hexameric and tetrameric NDP kinases are built from the same dimer. T he structural environment of the active histidine is identical in all. The nucleotide binding site is also fully conserved, except for a feature impli cating C-terminal residues in the hexamer, but not in the tetramer. Structu ral data on the native and phosphorylated enzyme, complexes with substrates , inhibitor, and a transition state analog, give a solid basis to a mechani sm of phosphate transfer in which the largest contributors to catalysis are the 3'-OH of the sugar and the bound Mg2+ in the nucleotide substrate. In contrast, we still lack structural data relating to DNA binding and other f unctions of NDP kinases.