Three-Dimensional Structure of Nucleoside Diphosphate Kinase

Abstract

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 ofabout 150 residues with a very similar fold based on the αβ sandwich orferredoxin fold.This fold is found in many nucleotide or polynucleotide-binding proteins with no sequencerelationship to NDP kinase. This common fold is augmented here with specificfeatures: asurface α-helix hairpin, the Kpn loop, and the C-terminal extension. The α-helix hairpin andKpn loop make up the nucleotide binding site, which is unique to NDP kinase and differentfrom that of other kinases or ATPases. The Kpn loop and the C-terminal extension are alsoinvolved in the quaternary structure. Whereas all known eukaryotic NDP kinases, includingmitochondral enzymes, are hexamers, some bacterial enzymes are tetramers. However,hexameric and tetrameric NDP kinases are built from the same dimer. The structural environmentof the active histidine is identical in all. The nucleotide binding site is also fully conserved,except for a feature implicating C-terminal residues in the hexamer, but not in the tetramer.Structural data on the native and phosphorylated enzyme, complexes with substrates, inhibitor,and a transition state analog, give a solid basis to a mechanism of phosphate transfer in whichthe largest contributors to catalysis are the 3′-OH of the sugar and the bound Mg²⁺ in thenucleotide substrate. In contrast, we still lack structural data relating to DNA binding andother functions of NDP kinases.