Biology subjects

Shalaeva, D. N.

Publications and source records attributed to Shalaeva, D. N..

3 recordsLinked to original sources

bioRxiv2022

Patterns of hydrolysis initiation in P-loop fold nucleoside triphosphatases - united in diversity

In ubiquitous P-loop fold nucleoside triphosphatases (also known as Walker NTPases), hydrolysis of ATP or GTP is initiated by interaction with an activating partner (usually another protein domain), which is accompanied by insertion of stimulatory moiety(ies) (usually arginine or lysine residues) into the catalytic site. 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 ubiquitous mechanistic interaction of diverse stimulators with the gamma phosphate group suggests its twist/rotation as the trigger for NTP hydrolysis.

biochemistry↗

bioRxiv2022

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

Though P-loop fold nucleoside triphosphatases (also known as Walker NTPases) are widespread, their catalytic mechanism remains unclear. Based on a comparative structure analysis of 3136 Mg-NTP-containing catalytic sites, we propose a common scheme of activated catalysis for P-loop NTPases. In this scheme, 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 (AspWB) plays the key role. We found that this H-bond is very short in the structures with bound transition state analogs. Given that a short hydrogen bond (also known as a low-barrier hydrogen bond) implies parity of pK values of the H-bond partners, we suggest that the proton affinities of these two residues reverse upon activation so that the proton relocates from [Ser/Thr]WA to AspWB. The anionic [Ser/Thr]WA alkoxide withdraws then a proton from the would-be nucleophile (either a water molecule or a sugar moiety in some P-loop kinases), and the nascent anion attacks the gamma-phosphate group. When gamma-phosphate breaks away, the trapped proton relays from AspWB, via [Ser/Thr]WA, to beta-phosphate and compensates for its developing negative charge.

biochemistry↗

bioRxiv2018

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases

The activity of cellular nucleoside triphosphatases (NTPases) must be tightly controlled to prevent spontaneous ATP hydrolysis leading to cell death. While most P-loop NTPases require activation by arginine or lysine fingers, some of the apparently ancestral ones are, instead, activated by potassium ions, but not by sodium ions. We combined comparative structure analysis of P-loop NTPases of various classes with molecular dynamics (MD) simulations of Mg-ATP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures, the conserved P-loop motif keeps the triphosphate chains of enzyme-bound NTPs in an extended, catalytically prone conformation, similar to that attained by ATP in water in the presence of potassium or ammonium ions bound between alpha- and gamma-phosphate groups. The smaller sodium ions could not reach both alpha- and gamma-phosphates of a protein-bound extended phosphate chain and therefore are unable to activate most potassium-dependent P-loop NTPases.

evolutionary biology↗