Title:	Catalytic mechanism of P-loop fold nucleoside triphosphatases unraveled by large-scale comparative structure analysis
Authors:	Kozlova, Maria
ORCID of the author:	https://orcid.org/0000-0003-0699-5064
Thesis advisor:	P.D. Dr. Armen Mulkidjanian
Thesis referee:	Prof. Dr. Roland Brandt
Abstract:	Though P-loop fold nucleoside triphosphatases (also known as Walker NTPases) are ubiquitous, their catalytic mechanism remains unclear. In these proteins, 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. Based on our automatized comparative structure analysis of 3136 Mg-NTP-containing catalytic sites, 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. Based on our comparative structure analysis, 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.
URL:	https://doi.org/10.48693/392 https://osnadocs.ub.uni-osnabrueck.de/handle/ds-202309019673
Subject Keywords:	Bioinformatics; ATPases; GTPases; Protein structures; P-loop; Walker ATPase; Walker A motif; Walker B motif; Ras GTPase; ABC transporter; Myosin; Kinesin; ATP synthase; ATP hydrolysis; Proton transport; Enzyme catalysis
Issue Date:	1-Sep-2023
License name:	Attribution-NonCommercial-ShareAlike 3.0 Germany
License url:	http://creativecommons.org/licenses/by-nc-sa/3.0/de/
Type of publication:	Dissertation oder Habilitation [doctoralThesis]
Appears in Collections:	FB05 - E-Dissertationen

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