4B5M

Neisseria AP endonuclease bound to the substrate with a cytosine orphan base


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.758 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 

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:  

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE EXODEOXYRIBONUCLEASE
A, B, C
259Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Gene Names: exoA
EC: 3.1.11.2
Find proteins for Q7DD47 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q7DD47
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*3DRP*CP*AP*TP*CP*GP)-3'L,M,N6Neisseria meningitidis
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*AP*CP)-3'U,W,Y5Neisseria meningitidis
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'V,X,Z11Neisseria meningitidis
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
L, M, N
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.758 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.050α = 90.00
b = 77.050β = 90.00
c = 382.580γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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