Common patterns of hydrolysis initiation in P-loop fold nucleoside triphosphatases

Abstract

In ubiquitous P-loop fold nucleoside triphosphatases (also known as Walker NTPases), hydrolysis of ATP or GTP is triggered by interaction with an activating partner (usually another protein domain), which is accompanied by insertion of stimulatory moieties (usually arginine or lysine residues) into the catalytic sites. After inspecting over 3600 Mg-NTP-containing structures of P-loop NTPases, we identified those with stimulator(s) inserted into catalytic sites and analysed the patterns of stimulatory interactions. In most cases, at least one stimulator twists gamma-phosphate counter-clockwise by linking the oxygen atoms of alpha- and gamma-phosphates; the twisted gamma-phosphate is stabilized by a hydrogen bond with the backbone amino group of the fourth residue of the Walker A motif. In the remaining cases, the stimulators only interact with gamma-phosphate. The all-pervasive mechanistic interactions of diverse stimulators with the gamma phosphate group suggests its twisting/turning as the trigger for NTP hydrolysis.

Common mechanism of activated catalysis in P-loop fold nucleoside triphosphatases -in varietate concordia

“…As it follows from Fig. 9, S5, Table S1, and the data in the accompanying article [41], the structures with TS analogs bound have particularly short H-bonds between HN K-3 and O 2G , as well as between Asp WB and [Ser/Thr] K+1 , which suggests an additional constriction of the catalytic site in the TS.…”

“…Also as a quality control, we have measured distances from [Ser/Thr] K+1 to Mg 2+ , to ensure the correct binding of the Mg 2+ and general reliability of the structure resolution at the binding site (i.e, very long distance would indicate a disturbed catalytic site or resolution at the site that is insufficient for our purposes of comparative analysis), and from [Asp/Glu] WB to Mg 2+ , to identify cases of direct coordination of Mg 2+ by the acidic residue (short distances) or disassembled binding sites (long distances).In addition, we examined the presence of interactions of phosphate chain with NH K-3 group and positively charged moieties in those sites that passed the quality control (the details of analysis are described in the accompanying paper [41] and depicted in Fig. 14 of it.…”

“…In the latter case, the fluoride derivative can be identified as a genuine ADP:AlF3 by the similarity of its geometry to that of the Mn-ADP:AlF3 complex in the Zika virus helicase (PDB ID 5Y6M [145]), see the accompanying paper [41] for details.…”

“…We counted and measured all the bonds in catalytic sites for the two pairs of such structures. One pair of structures consisted of RhoA GTPases in complex with their activator RhoGAP and GDP:AlF4 In the latter case, the fluoride derivative can be identified as a genuine ADP:AlF3 by the similarity of its geometry to that of the Mn-ADP:AlF3 complex in the Zika virus helicase (PDB ID 5Y6M [145]), see the accompanying paper [41] for details.…”

“…Upon this interaction, specific stimulatory moieties, usually Arg or Lys residues ("Arg/Lys fingers", Fig. 1E,F), are inserted into the catalytic sites and promote the cleavage of γ-phosphate, see the accompanying article [41] and [4,15,16,40,[42][43][44][45][46][47][48][49].…”