4B5I

Product complex of Neisseria AP endonuclease in presence of metal ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.

Lu, D.Silhan, J.MacDonald, J.T.Carpenter, E.P.Jensen, K.Tang, C.M.Baldwin, G.S.Freemont, P.S.

(2012) Proc Natl Acad Sci U S A 109: 16852-16857

  • DOI: 10.1073/pnas.1206563109
  • Primary Citation of Related Structures:  
    4B5F, 4B5G, 4B5H, 4B5I, 4B5J, 4B5M

  • PubMed Abstract: 
  • Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonuclease ...

    Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures.


    Organizational Affiliation

    Centre for Structural Biology, Division of Molecular Biosciences and Department of Microbiology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE EXODEOXYRIBONUCLEASEA259Neisseria meningitidisMutation(s): 0 
EC: 3.1.11.2
Find proteins for Q7DD47 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q7DD47 
Go to UniProtKB:  Q7DD47
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*TP*AP*CP)-3'U5Neisseria meningitidis
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'V11Neisseria meningitidis
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(*3DRP*CP*AP*TP*CP*GP)-3'X6Neisseria meningitidis
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        MN
        Query on MN

        Download CCD File 
        A
        MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.56 Å
        • R-Value Free: 0.252 
        • R-Value Work: 0.205 
        • R-Value Observed: 0.207 
        • Space Group: P 43 21 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 69.09α = 90
        b = 69.09β = 90
        c = 119.67γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2012-10-17
          Type: Initial release
        • Version 1.1: 2012-10-31
          Changes: Database references
        • Version 1.2: 2018-02-28
          Changes: Database references