2022
DOI: 10.1101/2022.06.23.497298
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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 interacti… Show more

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Cited by 2 publications
(52 citation statements)
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“…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.…”
Section: Constriction Of the Catalytic Site In The Transition Statementioning
confidence: 76%
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“…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.…”
Section: Constriction Of the Catalytic Site In The Transition Statementioning
confidence: 76%
“…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.…”
Section: Methodsmentioning
confidence: 99%
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