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      Dimerization facilitates the conformational transitions for bacterial phosphotransferase enzyme I autophosphorylation in an allosteric manner

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          Abstract

          The bacterial phosphotransferase system is central to sugar uptake and phosphorylation. Enzyme I ( EI), the first enzyme of the system, autophosphorylates as a dimer using phosphoenolpyruvate ( PEP), but it is not clearly understood how dimerization activates the enzyme activity. Here, we show that EI dimerization is important for proper conformational transitions and the domain association required for the autophosphorylation. EI(G356S) with reduced dimerization affinity and lower autophosphorylation activity revealed that significantly hindered conformational transitions are required for the phosphoryl transfer reaction. The G356S mutation does not change the binding affinity for PEP, but perturbs the domain association accompanying large interdomain motions that bring the active site His189 close to PEP. The interface for the domain association is separate from the dimerization interface, demonstrating that dimerization can prime the conformational change in an allosteric manner.

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          Most cited references22

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          The changing landscape of protein allostery.

          It is becoming increasingly clear that the fundamental capacity to undergo conformational change in response to ligand binding is intrinsic to proteins. This property confers on proteins the ability to be allosterically modulated in order to shift substrate binding affinities, alter enzymatic activity or regulate protein-protein interaction. How this allosteric modulation occurs--the pathways of communication, the shifting of conformational ensembles and the altered molecular dynamics--has received considerable attention during the past two years. Recent progress has helped outline the molecular origins of allostery in proteins as diverse as Hsp70 molecular chaperones and signal integrating proteins, such as WASP. In addition, allosteric properties have been successfully engineered into proteins for drug design or the development of novel biosensors. Methodological advances have provided exciting prospects for new insights and new biological roles of allosteric systems have been uncovered.
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            Principles of Allosteric Interactions in Cell Signaling

            Linking cell signaling events to the fundamental physicochemical basis of the conformational behavior of single molecules and ultimately to cellular function is a key challenge facing the life sciences. Here we outline the emerging principles of allosteric interactions in cell signaling, with emphasis on the following points. (1) Allosteric efficacy is not a function of the chemical composition of the allosteric pocket but reflects the extent of the population shift between the inactive and active states. That is, the allosteric effect is determined by the extent of preferred binding, not by the overall binding affinity. (2) Coupling between the allosteric and active sites does not decide the allosteric effect; however, it does define the propagation pathways, the allosteric binding sites, and key on-path residues. (3) Atoms of allosteric effectors can act as “driver” or “anchor” and create attractive “pulling” or repulsive “pushing” interactions. Deciphering, quantifying, and integrating the multiple co-occurring events present daunting challenges to our scientific community.
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              Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering.

              The solution structures of free Enzyme I (EI, ∼128 kDa, 575 × 2 residues), the first enzyme in the bacterial phosphotransferase system, and its complex with HPr (∼146 kDa) have been solved using novel methodology that makes use of prior structural knowledge (namely, the structures of the dimeric EIC domain and the isolated EIN domain both free and complexed to HPr), combined with residual dipolar coupling (RDC), small- (SAXS) and wide- (WAXS) angle X-ray scattering and small-angle neutron scattering (SANS) data. The calculational strategy employs conjoined rigid body/torsion/Cartesian simulated annealing, and incorporates improvements in calculating and refining against SAXS/WAXS data that take into account complex molecular shapes in the description of the solvent layer resulting in a better representation of the SAXS/WAXS data. The RDC data orient the symmetrically related EIN domains relative to the C(2) symmetry axis of the EIC dimer, while translational, shape, and size information is provided by SAXS/WAXS. The resulting structures are independently validated by SANS. Comparison of the structures of the free EI and the EI-HPr complex with that of the crystal structure of a trapped phosphorylated EI intermediate reveals large (∼70-90°) hinge body rotations of the two subdomains comprising the EIN domain, as well as of the EIN domain relative to the dimeric EIC domain. These large-scale interdomain motions shed light on the structural transitions that accompany the catalytic cycle of EI.
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                Author and article information

                Contributors
                jysuh@snu.ac.kr
                Journal
                FEBS Open Bio
                FEBS Open Bio
                10.1002/(ISSN)2211-5463
                FEB4
                FEBS Open Bio
                John Wiley and Sons Inc. (Hoboken )
                2211-5463
                17 July 2017
                August 2017
                : 7
                : 8 ( doiID: 10.1111/feb4.2017.7.issue-8 )
                : 1208-1216
                Affiliations
                [ 1 ] Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Korea
                [ 2 ] Institute for Biomedical Sciences Shinshu University Nagano Japan
                Author notes
                [*] [* ] Correspondence

                J.‐Y. Suh, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, 1 Gwanak‐ro, Gwanak‐gu, Seoul National University, Seoul 08826, Korea

                Fax: +82 2 877 4906

                Tel: +82 2 880 4879

                E‐mail: jysuh@ 123456snu.ac.kr

                [†]

                These authors contributed equally to this work

                Article
                FEB412260
                10.1002/2211-5463.12260
                5537066
                f6eb0274-2bc7-49bd-bc80-386992e330b6
                © 2017 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 04 April 2017
                : 21 June 2017
                : 21 June 2017
                Page count
                Figures: 6, Tables: 1, Pages: 9, Words: 4820
                Funding
                Funded by: Cooperative Research Program for Agriculture Science & Technology Development
                Funded by: Rural Development Administration
                Award ID: PJ011112
                Funded by: New & Renewable Energy Core Technology Program
                Funded by: Korea Institute of Energy Technology Evaluation and Planning
                Funded by: Ministry of Trade, Industry & Energy, Republic of Korea
                Award ID: 20143030090940
                Funded by: Korea Basic Science Institute
                Funded by: National Center for Inter‐University Research Facilities
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                feb412260
                August 2017
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.1.4 mode:remove_FC converted:31.07.2017

                allostery,conformational transition,dimerization,phosphotransferase system

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