Literature DB >> 30582519

Mechanisms of opening and closing of the bacterial replicative helicase.

Jillian Chase1,2, Andrew Catalano1, Alex J Noble3, Edward T Eng3, Paul Db Olinares4, Kelly Molloy4, Danaya Pakotiprapha5,6, Martin Samuels6, Brian Chait4, Amedee des Georges1,2,7,8, David Jeruzalmi1,2,8,9.   

Abstract

Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
© 2018, Chase et al.

Entities:  

Keywords:  DNA replication; DnaB replicative helicase; E. coli; biochemistry; chemical biology; cryogenic electron microscopy; helicase loader; molecular biophysics; replication initiation; structural biology

Mesh:

Substances:

Year:  2018        PMID: 30582519      PMCID: PMC6391071          DOI: 10.7554/eLife.41140

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  126 in total

1.  The bacterial replicative helicase DnaB evolved from a RecA duplication.

Authors:  D D Leipe; L Aravind; N V Grishin; E V Koonin
Journal:  Genome Res       Date:  2000-01       Impact factor: 9.043

2.  Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.

Authors:  E Krissinel; K Henrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

3.  Molecular replacement with MOLREP.

Authors:  Alexei Vagin; Alexei Teplyakov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21

4.  Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances.

Authors:  Eric D Merkley; Steven Rysavy; Abdullah Kahraman; Ryan P Hafen; Valerie Daggett; Joshua N Adkins
Journal:  Protein Sci       Date:  2014-04-03       Impact factor: 6.725

5.  Primase directs the release of DnaC from DnaB.

Authors:  Magdalena Makowska-Grzyska; Jon M Kaguni
Journal:  Mol Cell       Date:  2010-01-15       Impact factor: 17.970

Review 6.  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

Review 7.  oriC-encoded instructions for the initiation of bacterial chromosome replication.

Authors:  Marcin Wolański; Rafał Donczew; Anna Zawilak-Pawlik; Jolanta Zakrzewska-Czerwińska
Journal:  Front Microbiol       Date:  2015-01-06       Impact factor: 5.640

8.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.

Authors:  Dari Kimanius; Björn O Forsberg; Sjors Hw Scheres; Erik Lindahl
Journal:  Elife       Date:  2016-11-15       Impact factor: 8.140

9.  Real-space refinement in PHENIX for cryo-EM and crystallography.

Authors:  Pavel V Afonine; Billy K Poon; Randy J Read; Oleg V Sobolev; Thomas C Terwilliger; Alexandre Urzhumtsev; Paul D Adams
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-05-30       Impact factor: 7.652

10.  The crystal structure of the Thermus aquaticus DnaB helicase monomer.

Authors:  Scott Bailey; William K Eliason; Thomas A Steitz
Journal:  Nucleic Acids Res       Date:  2007-07-01       Impact factor: 16.971

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  6 in total

Review 1.  A structural view of bacterial DNA replication.

Authors:  Aaron J Oakley
Journal:  Protein Sci       Date:  2019-04-17       Impact factor: 6.725

2.  Mechanisms of opening and closing of the bacterial replicative helicase.

Authors:  Jillian Chase; Andrew Catalano; Alex J Noble; Edward T Eng; Paul Db Olinares; Kelly Molloy; Danaya Pakotiprapha; Martin Samuels; Brian Chait; Amedee des Georges; David Jeruzalmi
Journal:  Elife       Date:  2018-12-24       Impact factor: 8.140

Review 3.  Convergent evolution in two bacterial replicative helicase loaders.

Authors:  Jillian Chase; James Berger; David Jeruzalmi
Journal:  Trends Biochem Sci       Date:  2022-03-26       Impact factor: 14.264

4.  Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM.

Authors:  Paul Dominic B Olinares; Jin Young Kang; Eliza Llewellyn; Courtney Chiu; James Chen; Brandon Malone; Ruth M Saecker; Elizabeth A Campbell; Seth A Darst; Brian T Chait
Journal:  Structure       Date:  2020-11-19       Impact factor: 5.006

5.  Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase.

Authors:  Stéphanie Marsin; Yazid Adam; Claire Cargemel; Jessica Andreani; Sonia Baconnais; Pierre Legrand; Ines Li de la Sierra-Gallay; Adeline Humbert; Magali Aumont-Nicaise; Christophe Velours; Françoise Ochsenbein; Dominique Durand; Eric Le Cam; Hélène Walbott; Christophe Possoz; Sophie Quevillon-Cheruel; Jean-Luc Ferat
Journal:  Nucleic Acids Res       Date:  2021-06-21       Impact factor: 16.971

6.  DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation.

Authors:  Sabrina Adam; Hiwot Anteneh; Maximilian Hornisch; Vincent Wagner; Jiuwei Lu; Nicole E Radde; Pavel Bashtrykov; Jikui Song; Albert Jeltsch
Journal:  Nat Commun       Date:  2020-07-24       Impact factor: 14.919

  6 in total

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