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AMP Binding Stabilizes the KTN Domain of the Shewanella Subscriber access provided by Library, Special Collections and Museums, University of Aberdeen Article AMP binding stabilizes the KTN domain of the Shewanella denitrificans Kef potassium efflux system Christos Pliotas, Samuel C Grayer, Silvia Ekkerman, Anthony KN Chan, Jess Healy, Phedra Marius, Wendy Bartlett, Amjad Khan, wilian augusto cortopassi, Shane A Chandler, Tim Rasmussen, Justin LP Benesch, Robert S. Paton, Timothy D. W. Claridge, Samantha Miller, Ian Rylance Booth, James H. Naismith, and Stuart J. Conway Biochemistry, Just Accepted Manuscript • DOI: 10.1021/acs.biochem.7b00300 • Publication Date (Web): 28 Jun 2017 Downloaded from http://pubs.acs.org on June 28, 2017 Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts. Biochemistry is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties. Page 1 of 54 Biochemistry Nucleotide Binding to Kef 1 2 3 AMP binding stabilizes the KTN domain of the Shewanella denitrificans Kef 4 5 6 potassium efflux system 7 8 9 10 Christos Pliotas,a,† Samuel C. Grayer,b,† Silvia Ekkerman,c,† Anthony K. N. Chan,b,† 11 12 b,‡ a c b b 13 Jess Healy, Phedra Marius, Wendy Bartlett, Amjad Khan, Wilian A. Cortopassi, 14 15 Shane A. Chandler,d Tim Rasmussen,c Justin L. P. Benesch,d Robert S. Paton,b 16 17 Timothy D. W. Claridge,b Samantha Miller,b Ian R. Booth,c,* James H. 18 19 a,e,f,g, b,h, 20 Naismith * and Stuart J. Conway * 21 22 23 24 aBiomedical Sciences Research Complex, University of St Andrews, North Haugh, St 25 26 27 Andrews, KY16 9ST, UK 28 29 bDepartment of Chemistry, Chemistry Research Laboratory, University of Oxford, 30 31 Mansfield Road, Oxford, OX1 3TA, UK 32 33 c 34 School of Medicine, Medical Sciences and Nutrition, Foresterhill, Aberdeen, AB25 35 36 2ZD, UK 37 38 d 39 Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University 40 41 of Oxford, South Parks Road, Oxford, OX1 3QZ, UK 42 43 eBiotherapy Centre, Sichuan University, Chengdu, China. 44 45 f 46 RCaH, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0FA. 47 48 gDivision of Structural Biology, University of Oxford, Henry Wellcome Building for 49 50 Genomic Medicine, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 51 52 53 7BN. 54 55 hFreiburg Institute for Advanced Studies – FRIAS, Albert-Ludwigs-Universität 56 57 Freiburg, Albertstr. 19, 79104 Freiburg, Germany. 58 59 60 1 ACS Paragon Plus Environment Biochemistry Page 2 of 54 Nucleotide Binding to Kef 1 2 3 †These authors contributed equally to this work. 4 5 ‡ 6 Current address: Department of Pharmaceutical and Biological Chemistry, UCL 7 8 School of Pharmacy, University College London, 29/39 Brunswick Square, WC1N, 9 10 11 1AX, UK 12 13 *To whom correspondence should be addressed. 14 15 Stuart Conway: [email protected]; +44(0)1865 285109. 16 17 18 James Naismith: [email protected]; +44(0)1235567701. 19 20 Ian Booth: [email protected]; +44 (0)1224 437396. 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 2 ACS Paragon Plus Environment Page 3 of 54 Biochemistry Nucleotide Binding to Kef 1 2 3 Abstract 4 5 6 Ligand binding is one of the most fundamental properties of proteins. Ligand 7 8 functions fall into three basic types: substrates, regulatory molecules, and co-factors 9 10 11 essential to protein stability, reactivity, or enzyme-substrate complex formation. The 12 13 regulation of potassium ion movement in bacteria is predominantly under the control 14 15 of regulatory ligands that gate the relevant channels and transporters, which possess 16 17 18 subunits or domains that contain Rossmann folds (RFs). Here we demonstrate that 19 20 AMP is bound to both RFs of the dimeric bacterial Kef potassium efflux system 21 22 (Kef), where it plays a structural role. We conclude that AMP binds with high affinity 23 24 25 ensuring that the site is fully occupied at all times in the cell. Loss of the ability to 26 27 bind AMP, we demonstrate, causes protein, and likely dimer, instability and 28 29 consequent loss of function. Regulation of Kef system function is via the reversible 30 31 32 binding of comparatively low affinity glutathione-based ligands at the interface 33 34 between the dimer subunits. We propose this interfacial binding site is itself 35 36 37 stabilised, at least in part, by AMP binding. 38 39 40 41 42 43 44 Keywords 45 46 Biophysical studies, crystallography, protein dimers, membrane protein, nucleotide 47 48 49 50 51 52 53 54 55 56 57 58 59 60 3 ACS Paragon Plus Environment Biochemistry Page 4 of 54 Nucleotide Binding to Kef 1 2 3 A fundamental property of proteins, by which they express their function in the cell, 4 5 6 is the binding of ligands, usually ions or molecules of small mass relative to that of 7 8 the protein itself. At least three different roles are ascribed to the binding of ligands: 9 10 11 firstly, the ligand is a substrate or essential cofactor for an enzyme; secondly, ligand 12 13 binding may be purely regulatory bringing about changes in protein activity; and 14 15 thirdly ligands may stabilize a protein fold. The roles are not mutually exclusive and 16 17 18 can be combined. The activation of ligand-gated channels is usually brought about by 19 20 an allosteric transition upon ligand binding at a point distant from the pore; the 21 22 changes in the concentration of the ligand may reflect the biological state of either the 23 24 25 cell or the environment. Regulation of ion flow is critical throughout biology and, for 26 27 potassium ions (K+), ligand-gated channels and transporters are central to the 28 29 modulation of cellular K+ pools. 30 31 32 33 34 In bacteria, both K+ channels, which play an important role in K+ influx, and K+ 35 36 + 37 efflux systems that control the response of the bacterial cell to electrophiles, have K 38 39 transport and NAD-binding (KTN) domains. These domains may be covalently 40 41 attached to the pore or may be separately expressed entities that form non-covalent 42 43 44 associations with the pore. Some are hybrid systems utilizing a combination of KTN 45 46 domains that are part of the integral pore-forming subunit together with KTN 47 48 domains expressed separately from an internal start codon on the same mRNA as the 49 50 1,2 51 pore protein. Another major structural variation is that for the channels (e.g. 52 53 TrkAH, KtrAB and MthK) octameric rings of KTN domains modulate ion flux, 54 55 56 whereas for the Kef systems, dimeric assemblies dominate the known architectures. A 57 58 conserved feature of KTN domains is a Rossmann fold, a feature known to be 59 60 4 ACS Paragon Plus Environment Page 5 of 54 Biochemistry Nucleotide Binding to Kef 1 2 3 associated with nucleotide binding since its first identification in NAD(H)-binding 4 5 3 6 lactate dehydrogenase. 7 8 9 10 11 In Escherichia coli, and most other bacteria, multiple transport systems and channels 12 + 13 effect control over the K pool, including the Kef systems, which are gated by 14 15 glutathione (GSH) and its electrophilic conjugates (GSX). In Gram-positive bacteria 16 17 18 similar protective systems might exist which employ electrophilic conjugates of other 19 20 species-specific thiols,4 for example bacillithiol.5-7 Whereas the activity of most K+ 21 22 transport systems causes modulation of the cytoplasmic pH in the alkaline direction, 23 24 8,9 25 the Kef systems cause acidification in response to cell-damaging electrophiles. The 26 27 ~600 residue Kef proteins form dimers of an ~380 amino acid membrane domain, 28 29 which may contain up to 12 trans-membrane spans, although these are poorly defined 30 31 32 from a structural perspective. A short hydrophilic linker (20-26 amino acids) connects 33 34 the membrane domain to two further domains: an ~150 residue KTN domain, and a 35 36 37 further, less well-conserved, domain of variable length at the extreme C-terminus of 38 39 the protein.
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