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

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Title: Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism
Authors: Shalaeva, Daria N.
Cherepanov, Dmitry A.
Galperin, Michael Y.
Golovin, Andrey V.
Mulkidjanian, Armen Y.
ORCID of the author: https://orcid.org/0000-0001-6286-4638
Abstract: The 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.
Citations: eLife 2018;7:e37373, eLife Sciences Publications, 2018, S. 1-35
URL: https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-201904101401
Subject Keywords: P-loop; nucleoside triphosphatases (NTPases); molecular dynamics simulations
Issue Date: 11-Dec-2018
License name: CC0 1.0 Universal
License url: http://creativecommons.org/publicdomain/zero/1.0/
Type of publication: Einzelbeitrag in einer wissenschaftlichen Zeitschrift [article]
Appears in Collections:FB04 - Hochschulschriften

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