Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

Nithianantham, Stanley; Shilton, Brian H

doi:10.1016/j.jmb.2008.08.022

Title: Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling

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Abstract

The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motif V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis ismore »« less

Authors:

Nithianantham, Stanley; Shilton, Brian H ^[1]

Publication Date:: Wed Sep 28 00:00:00 EDT 2011

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Org.:: FOREIGN

OSTI Identifier:: 1023636

Resource Type:: Journal Article

Journal Name:: Journal of Molecular Biology

Additional Journal Information:: Journal Volume: 383; Journal Issue: (2) ; 11, 2008; Journal ID: ISSN 0022-2836

Publisher:: Elsevier

Country of Publication:: United States

Language:: ENGLISH

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ADP; AFFINITY; ATP; CONFORMATIONAL CHANGES; COUPLING; CROSS-LINKING; CRYSTAL STRUCTURE; DATA; ESCHERICHIA COLI; FUNCTIONS; HYDROLYSIS; INTERACTIONS; RNA; SUBSTRATES

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                    Nithianantham, Stanley, and Shilton, Brian H. Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling.  United States: N. p., 2011. 
        Web.  doi:10.1016/j.jmb.2008.08.022.

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                    Nithianantham, Stanley, & Shilton, Brian H. Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling.  United States.  https://doi.org/10.1016/j.jmb.2008.08.022

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                    Nithianantham, Stanley, and Shilton, Brian H. 2011.  
        "Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling".  United States.  https://doi.org/10.1016/j.jmb.2008.08.022.

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@article{osti_1023636,

  title        = {Analysis of the Isolated SecA DEAD Motor Suggests a Mechanism for Chemical-Mechanical Coupling},

  author       = {Nithianantham, Stanley and Shilton, Brian H},

  abstractNote = {The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motif V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.},

  doi          = {10.1016/j.jmb.2008.08.022},

  url          = {https://www.osti.gov/biblio/1023636},
  journal      = {Journal of Molecular Biology},

  issn         = {0022-2836},

  number       = (2) ; 11, 2008,

  volume       = 383,

  place        = {United States},

  year         = {Wed Sep 28 00:00:00 EDT 2011},

  month        = {Wed Sep 28 00:00:00 EDT 2011}

}

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