2D7E

Crystal structure of N-terminal domain of PriA from E.coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.

Sasaki, K.Ose, T.Okamoto, N.Maenaka, K.Tanaka, T.Masai, H.Saito, M.Shirai, T.Kohda, D.

(2007) EMBO J. 26: 2584-2593

  • DOI: 10.1038/sj.emboj.7601697
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes ...

    In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli
      Sasaki, K.,Ose, T.,Tanaka, T.,Mizukoshi, T.,Ishigaki, T.,Maenaka, K.,Masai, H.,Kohda, D.
      (2006) Biochim.Biophys.Acta 1764: 157


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA. Electronic address: glander@scripps.edu.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5G 1L6, Canada.,From the Bioconversion Group and.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260; acohen@slac.stanford.edu guc9@pitt.edu.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.,Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. Electronic address: bwiedenheft@gmail.com.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.,Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK; Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.,the Polymer Chemistry Group, Research Institute for Sustainable Chemistry, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan, and.,Departments of Biochemistry and Molecular Genetics, MaRS Centre, West Tower, Floor 16, Toronto, ON, M5G 1M1, Canada.,JAN Scientific Inc., Seattle, WA 98105.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada. Electronic address: derek.bowie@mcgill.ca.,Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Cancer institute, the Affiliated Hospital of Qingdao University, Qingdao Cancer Institute and School of Basic Medicine, Qingdao University, 266021, Qingdao, China.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada. sli@uwo.ca.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico.,Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15260.,Integrated Program in Neuroscience, McGill University, Montréal, QC H3A 2B4, Canada; Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,the Bio-based Materials Chemistry Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.,Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States.,Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioner's Road East, London, ON, N6C 2V5, Canada. sli@uwo.ca.,the Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.,From the Bioconversion Group and inoue-h@aist.go.jp.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; acohen@slac.stanford.edu guc9@pitt.edu.,Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Primosomal protein N'
A, B, C, D
105Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: priA
EC: 3.6.4.-
Find proteins for P17888 (Escherichia coli (strain K12))
Go to UniProtKB:  P17888
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.247 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 111.570α = 90.00
b = 111.570β = 90.00
c = 260.550γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-02-27
    Type: Data collection, Database references