Structural and enzymatic characterisation of nucleoside triphosphate diphosphohydrolases from Trifolium repens and Dolichos biflorus

Abstract

Extracellular nucleoside triphosphate diphosphohydrolases (NTPDases) are enzymes that reduce the extracellular nucleotide signal and inactivate the purinogenic signalling pathway. These enzymes, in the presence of a divalent cation sequentially hydrolyses the γ- and β- phosphoanhydride bond from a range of nucleotide di- or triphosphates to the corresponding nucleotide monophosphate.

There is evidence that purinogenic signalling is present in higher plants and it is becoming clear that NTPDases play a role in the early stages of rhizobium infection during nodulation in legumes. To further our understanding of NTPDases, this study investigated the biochemical and structural characteristics of two legume NTPDases believed to be involved in nodulation. The first, 7WC, was isolated from the roots of white clover and the second, DbLnP, from the roots of Dolichos biflorus. DbLnP has been characterised as a carbohydrate binding NTPDase that is directly associated with the perception of rhizobia. Using X-ray crystallography a number of crystal structures of 7WC and DbLnP were determined at resolutions between 1.9 Å and 2.9 Å. For 7WC, structures were determined for an apo- form, an AMP-bound and also bound with the nonhydrolysable ATP analogue AMPPNP. For DbLnP structures were solved with phosphate and Mn2+ bound and another with AMPPNP and Mn2+ bound. Kinetic analysis of a range of substrates together with the analysis of the binding modes of 7WC and DbLnP explained substrate preference for each of the NTPDases. These analyses showed that NTPDases can adopt two conformations depending on substrate and co-factor binding. The central hinge region creates a ‘butterfly’ motion of the domains that reduces the width of the active site cleft. This phenomenon has been previously hypothesised but has not been observed for NTPDases. A model of catalysis is proposed whereby the ‘open’ form first binds substrate in an inactive orientation. Binding of the metal ion induces a conformational change that brings the domains together and allows movement of the phosphate tail deeper into the active site cleft – a reorganisation that is required for catalysis. Hydrolysis occurs via nucleophilic attack on the terminal phosphate. Finally, release of the metal ion allows the ‘open’ conformation to be restored for subsequent catalysis to occur.