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

Although P-loop fold n ucleoside tri p hosphatases (also known as Walker NTPases) are ubiquitous, their catalytic mechanism remains obscure. Based on a comparative structural analysis of 3136 Mg-NTP-containing catalytic sites, we propose a common scheme of activated catalysis for P-loop NTPases where a hydrogen bond (H-bond) between the strictly conserved, Mg-coordinating Ser/Thr of the Walker A motif ([Ser/Thr] WA ) and the conserved aspartate of the Walker B motif (Asp WB ) plays the key role. We found that this H-bond is very short in the structures with bound transition state (TS) analogs. We suggest that the proton affinities of these two residues reverse in the TS so that the proton relocates from [Ser/Thr] WA to Asp WB . The anionic [Ser/Thr] WA withdraws then a proton from the (catalytic) water molecule, and the nascent hydroxyl anion attacks gamma-phosphate. When the gamma-phosphate group breaks away, the trapped proton relays from Asp WB , via [Ser/Thr] WA , to beta-phosphate and compensates for its developing negative charge.