Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism

DC FieldValueLanguage
dc.contributor.authorShalaeva, Daria N.
dc.contributor.authorCherepanov, Dmitry A.
dc.contributor.authorGalperin, Michael Y.
dc.contributor.authorGolovin, Andrey V.
dc.contributor.authorMulkidjanian, Armen Y.
dc.date.accessioned2021-12-23T16:21:32Z-
dc.date.available2021-12-23T16:21:32Z-
dc.date.issued2018
dc.identifier.issn2050084X
dc.identifier.urihttps://osnascholar.ub.uni-osnabrueck.de/handle/unios/13910-
dc.description.abstractThe ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine `finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.
dc.description.sponsorshipDeutscher Akademischer AustauschdienstDeutscher Akademischer Austausch Dienst (DAAD); Russian Science FoundationRussian Science Foundation (RSF) [14-50-00029]; U.S. National Library of MedicineUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Library of Medicine (NLM); Lomonosov Moscow State University [RFMEFI62117X0011]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [DFG-436-RUS 113/963/0-1]; Bundesministerium fur Bildung und ForschungFederal Ministry of Education & Research (BMBF); Osnabrueck University; Deutscher Akademischer Austauschdienst Ostpartnerschaften programm Daria N Shalaeva; Russian Science Foundation 14-50-00029 (Noah's Ark) Daria N Shalaeva Dmitry A Cherepanov Andrey V Golovin; U.S. National Library of Medicine Intramural Research Program Michael Y Galperin; Lomonosov Moscow State University RFMEFI62117X0011 Andrey V Golovin; Deutsche Forschungsgemeinschaft DFG-436-RUS 113/963/0-1 Armen Y Mulkidjanian; Bundesministerium fur Bildung und Forschung Laseromix Armen Y Mulkidjanian; Osnabrueck University EvoCell Program Armen Y Mulkidjanian; The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
dc.language.isoen
dc.publisherELIFE SCIENCES PUBLICATIONS LTD
dc.relation.ispartofELIFE
dc.subject16S RIBOSOMAL-RNA
dc.subjectATP HYDROLYSIS
dc.subjectBiology
dc.subjectELONGATION-FACTOR TU
dc.subjectESCHERICHIA-COLI
dc.subjectFORCE-FIELD
dc.subjectG DOMAIN
dc.subjectGTPASE ACTIVITY
dc.subjectLife Sciences & Biomedicine - Other Topics
dc.subjectMOLECULAR-DYNAMICS SIMULATION
dc.subjectPHOSPHORYL TRANSFER
dc.subjectSTRUCTURAL BASIS
dc.titleEvolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism
dc.typejournal article
dc.identifier.doi10.7554/eLife.37373
dc.identifier.isiISI:000454486300001
dc.description.volume7
dc.contributor.orcid0000-0002-2265-5572
dc.contributor.orcid0000-0001-5844-3064
dc.contributor.orcid0000-0001-6286-4638
dc.contributor.orcid0000-0003-0582-2612
dc.contributor.orcid0000-0002-8908-4268
dc.contributor.researcheridB-5859-2013
dc.contributor.researcheridAAH-3608-2021
dc.contributor.researcheridJ-8086-2013
dc.contributor.researcheridR-8391-2016
dc.contributor.researcheridABB-4382-2020
dc.publisher.placeSHERATON HOUSE, CASTLE PARK, CAMBRIDGE, CB3 0AX, ENGLAND
dcterms.isPartOf.abbreviationeLife
dcterms.oaStatusGreen Submitted, Green Published, gold
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