Catalytic scaffolds for phosphoryl group transfer

Abstract

A single genome encodes a large number of phosphoryl hydrolases for the purposes of phosphate recycling, primary and secondary metabolism, signal transduction and regulation, and protection from xenobiotics. Phosphate monoester hydrolysis faces a high kinetic barrier, yet there are multiple solutions to the problem both in terms of catalytic mechanisms and three-dimensional structure of the hydrolases. Recent structural and mechanistic findings highlight the trigonal-bipyramidal nature of the transition state for enzyme promoted phosphate monoester hydrolysis and the evolution and role of inserted loops/domains in governing substrate specificity and promiscuity. Important questions remain as to how electrostatics modulate water networks and critical proton-transfer events. How substrate targeting and catalysis is achieved by the independently evolved catalytic platforms is compared and contrasted in this article.

Helices on Interdomain Interface Couple Catalysis in the ATPPase Domain with Allostery in Plasmodium falciparum GMP Synthetase

“…The increase in electrophilicity of C2 of XMP enabled through the formation of the unstable adenyl‐XMP intermediate facilitates attack by ammonia and thereby the replacement of the C2 oxygen with nitrogen. Transfer of AMP from ATP to XMP is an adenylation reaction that is facilitated by the ATP α‐phosphorous undergoing geometric as well as electrostatic changes involving the development of strong negative charges on the non‐bridging oxygen atoms in the transition state . As stabilization of transition state underlies enzymatic rate enhancements, all phosphoryl transfer enzymes, including adenylating enzymes, employ positively charged groups to interact with and neutralize the negative charges on the non‐bridging oxygen atoms .…”

Membrane association of monotopic phosphoglycosyl transferase underpins function

“…The Asp position is enforced by formation of a coordinate bond with the Mg 2+ cofactor 7 . Together, these interactions contribute to the nucleophilic reactivity of the non-coordinating oxygen of Asp93, which is an important feature of covalent catalysis at phosphoryl groups 22 . The difference in geometries enforced by the polytopic and monotopic PGT scaffolds may underlie the mechanistic divergence between the two superfamilies.…”

The evolutionary history of the HUP domain

“…Yet the key to phosphate binding is not necessarily the loop, but rather the N-terminus of the a-helix to which the loop connects: namely, the tip of a1. Indeed, in the simplest PBLs, the tip of the a-helix, together with a few flanking loop residues, provide a nest of hydrogen-bonds that bind the phosphate moieties of various cofactors and substrates, including NTPs, NAD or FAD (Leader and Milner-White 2015; Allen and Dunaway-Mariano 2016). In these cases, the loop can be relatively short, and the loop and helix tip are enriched with Gly residues that donate backbone Hbonds, and Ser or Thr residues that make bidentate Hbonds with both the backbone amide and the sidechain hydroxyl (Longo et al 2020b).…”