4B5G

Substrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXODEOXYRIBONUCLEASE
A, B, C
259Neisseria meningitidisMutation(s): 0 
EC: 3.1.11.2
Find proteins for Q7DD47 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q7DD47
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'U, W,Y11Neisseria meningitidis
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'V, X,Z11Neisseria meningitidis
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.241α = 90
b = 75.241β = 90
c = 380.683γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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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