2DWL

Crystal structure of the PriA protein complexed with oligonucleotides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.302 
  • 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:  
    2DWL, 2DWN, 2DWM, 2D7H, 2D7G, 2D7E

  • 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 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 ...

    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.


    Organizational Affiliation

    Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Primosomal protein NC [auth A], D [auth B], E [auth C], F [auth D]105Escherichia coliMutation(s): 0 
EC: 3.6.1 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for P17888 (Escherichia coli (strain K12))
Explore P17888 
Go to UniProtKB:  P17888
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*(DC))-3'A [auth E], B [auth F]2N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.302 
    • R-Value Work: 0.247 
    • Space Group: H 3 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 111.51α = 90
    b = 111.51β = 90
    c = 260.46γ = 120
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    MOLREPphasing
    CNSrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

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