title: Nucleotide and partner-protein control of bacterial replicative helicase structure and function.
abstract: Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple methods to investigate the bacterial replicative helicase, DnaB. A 3.3 Å crystal structure of Aquifex aeolicus DnaB, complexed with nucleotide, reveals a newly discovered conformational state for this motor protein. Electron microscopy and small angle X-ray scattering studies confirm the state seen crystallographically, showing that the DnaB ATPase domains and an associated N-terminal collar transition between two physical states in a nucleotide-dependent manner. Mutant helicases locked in either collar state are active but display different capacities to support critical activities such as duplex translocation and primase-dependent RNA synthesis. Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors.
authors.affiliation: Biophysics Program, University of California, Berkeley, Berkeley, CA 94720-3220, USA.
authors.forename: Melania S
authors.initials: MS
authors.lastname: Strycharska
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Arias-Palomo
authors.affiliation: The James H Clark Center, Stanford School of Medicine, Stanford, CA 94305, USA.
authors.forename: Artem Y
authors.initials: AY
authors.lastname: Lyubimov
authors.affiliation: Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Erzberger
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Valerie L
authors.initials: VL
authors.lastname: O'Shea
authors.affiliation: Biophysics Program, University of California, Berkeley, Berkeley, CA 94720-3220, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3220, USA.
authors.forename: Carlos J
authors.initials: CJ
authors.lastname: Bustamante
authors.affiliation: Biophysics Program, University of California, Berkeley, Berkeley, CA 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3220, USA. Electronic address: jmberger@jhmi.edu.
authors.forename: James M
authors.initials: JM
authors.lastname: Berger
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004261:DNA Replication; D004269:DNA, Bacterial / Q000096:biosynthesis*; D053488:DnaB Helicases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006868:Hydrolysis; D008854:Microscopy, Electron; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009711:Nucleotides / Q000378:metabolism*; D011487:Protein Conformation; D012329:RNA, Bacterial / Q000096:biosynthesis; D011994:Recombinant Proteins / Q000378:metabolism; D013329:Structure-Activity Relationship
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C071702:DnaC protein, E coli; D029968:Escherichia coli Proteins; D009711:Nucleotides; D012329:RNA, Bacterial; D011994:Recombinant Proteins; D000255:Adenosine Triphosphate; C506730:dnaB protein, E coli; D053488:DnaB Helicases