Literature DB >> 21282052

The nuts and bolts of ring-translocase structure and mechanism.

Artem Y Lyubimov1, Melania Strycharska, James M Berger.   

Abstract

Ring-shaped, oligomeric translocases are multisubunit enzymes that couple the hydrolysis of Nucleoside TriPhosphates (NTPs) to directed movement along extended biopolymer substrates. These motors help unwind nucleic acid duplexes, unfold protein chains, and shepherd nucleic acids between cellular and/or viral compartments. Substrates are translocated through a central pore formed by a circular array of catalytic subunits. Cycles of nucleotide binding, hydrolysis, and product release help reposition translocation loops in the pore to direct movement. How NTP turnover allosterically induces these conformational changes, and the extent of mechanistic divergence between motor families, remain outstanding problems. This review examines the current models for ring-translocase function and highlights the fundamental gaps remaining in our understanding of these molecular machines.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21282052      PMCID: PMC3070846          DOI: 10.1016/j.sbi.2011.01.002

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  51 in total

1.  Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.

Authors:  M R Singleton; M R Sawaya; T Ellenberger; D B Wigley
Journal:  Cell       Date:  2000-06-09       Impact factor: 41.582

2.  Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU.

Authors:  J Wang; J J Song; I S Seong; M C Franklin; S Kamtekar; S H Eom; C H Chung
Journal:  Structure       Date:  2001-11       Impact factor: 5.006

3.  ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal.

Authors:  C Lee; M P Schwartz; S Prakash; M Iwakura; A Matouschek
Journal:  Mol Cell       Date:  2001-03       Impact factor: 17.970

4.  Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding.

Authors:  R R Wei; J P Richardson
Journal:  J Mol Biol       Date:  2001-12-14       Impact factor: 5.469

5.  Mutations in the rho transcription termination factor that affect RNA tracking.

Authors:  Yi Xu; Harold Kohn; William R Widger
Journal:  J Biol Chem       Date:  2002-05-28       Impact factor: 5.157

6.  Evolutionary history and higher order classification of AAA+ ATPases.

Authors:  Lakshminarayan M Iyer; Detlef D Leipe; Eugene V Koonin; L Aravind
Journal:  J Struct Biol       Date:  2004 Apr-May       Impact factor: 2.867

7.  DNA-induced switch from independent to sequential dTTP hydrolysis in the bacteriophage T7 DNA helicase.

Authors:  Donald J Crampton; Sourav Mukherjee; Charles C Richardson
Journal:  Mol Cell       Date:  2006-01-20       Impact factor: 17.970

8.  Importance of F1-ATPase residue alpha-Arg-376 for catalytic transition state stabilization.

Authors:  S Nadanaciva; J Weber; S Wilke-Mounts; A E Senior
Journal:  Biochemistry       Date:  1999-11-23       Impact factor: 3.162

9.  Evolution and classification of P-loop kinases and related proteins.

Authors:  Detlef D Leipe; Eugene V Koonin; L Aravind
Journal:  J Mol Biol       Date:  2003-10-31       Impact factor: 5.469

10.  Mcm4,6,7 uses a "pump in ring" mechanism to unwind DNA by steric exclusion and actively translocate along a duplex.

Authors:  Daniel L Kaplan; Megan J Davey; Mike O'Donnell
Journal:  J Biol Chem       Date:  2003-09-17       Impact factor: 5.157

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  70 in total

1.  The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase.

Authors:  Sebastian Glatt; Juliette Létoquart; Céline Faux; Nicholas M I Taylor; Bertrand Séraphin; Christoph W Müller
Journal:  Nat Struct Mol Biol       Date:  2012-02-19       Impact factor: 15.369

2.  ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote.

Authors:  Artem Y Lyubimov; Alessandro Costa; Franziska Bleichert; Michael R Botchan; James M Berger
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-09       Impact factor: 11.205

3.  Bacterial and Eukaryotic Replisome Machines.

Authors:  Nina Yao; Mike O'Donnell
Journal:  JSM Biochem Mol Biol       Date:  2016-05-30

4.  Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution.

Authors:  Wen Ma; Klaus Schulten
Journal:  J Am Chem Soc       Date:  2015-02-19       Impact factor: 15.419

Review 5.  The Eukaryotic CMG Helicase at the Replication Fork: Emerging Architecture Reveals an Unexpected Mechanism.

Authors:  Huilin Li; Michael E O'Donnell
Journal:  Bioessays       Date:  2018-02-06       Impact factor: 4.345

6.  Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.

Authors:  Stefan M Giovan; Robert G Scharein; Andreas Hanke; Stephen D Levene
Journal:  J Chem Phys       Date:  2014-11-07       Impact factor: 3.488

Review 7.  Spiraling in Control: Structures and Mechanisms of the Hsp104 Disaggregase.

Authors:  James Shorter; Daniel R Southworth
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-08-01       Impact factor: 10.005

8.  Ligand-induced and small-molecule control of substrate loading in a hexameric helicase.

Authors:  Michael R Lawson; Kevin Dyer; James M Berger
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-07       Impact factor: 11.205

9.  Nucleotide-dependent control of internal strains in ring-shaped AAA+ motors.

Authors:  Wonmuk Hwang; Matthew J Lang
Journal:  Cell Mol Bioeng       Date:  2012-12-14       Impact factor: 2.321

Review 10.  The ring-shaped hexameric helicases that function at DNA replication forks.

Authors:  Michael E O'Donnell; Huilin Li
Journal:  Nat Struct Mol Biol       Date:  2018-01-29       Impact factor: 15.369

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