Apurinic Apyrimidinic (AP) endonuclease (NApe) from Neisseria Meningitidis

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.123 

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Ap Endonuclease Paralogues with Distinct Activities in DNA Repair and Bacterial Pathogenesis.

Carpenter, E.P.Corbett, A.Thomson, H.Adacha, J.Jensen, K.Bergeron, J.Kasampalidis, I.Exley, R.Winterbotham, M.Tang, C.Baldwin, G.S.Freemont, P.

(2007) EMBO J 26: 1363

  • DOI: https://doi.org/10.1038/sj.emboj.7601593
  • Primary Citation of Related Structures:  
    2JC4, 2JC5

  • PubMed Abstract: 

    Oxidative stress is a principal cause of DNA damage, and mechanisms to repair this damage are among the most highly conserved of biological processes. Oxidative stress is also used by phagocytes to attack bacterial pathogens in defence of the host. We have identified and characterised two apurinic/apyrimidinic (AP) endonuclease paralogues in the human pathogen Neisseria meningitidis. The presence of multiple versions of DNA repair enzymes in a single organism is usually thought to reflect redundancy in activities that are essential for cellular viability. We demonstrate here that these two AP endonuclease paralogues have distinct activities in DNA repair: one is a typical Neisserial AP endonuclease (NApe), whereas the other is a specialised 3'-phosphodiesterase Neisserial exonuclease (NExo). The lack of AP endonuclease activity of NExo is shown to be attributable to the presence of a histidine side chain, blocking the abasic ribose-binding site. Both enzymes are necessary for survival of N. meningitidis under oxidative stress and during bloodstream infection. The novel functional pairing of NExo and NApe is widespread among bacteria and appears to have evolved independently on several occasions.

  • Organizational Affiliation

    Centre for Structural Biology, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EXODEOXYRIBONUCLEASE259Neisseria meningitidisMutation(s): 0 
Find proteins for Q7DD47 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q7DD47 
Go to UniProtKB:  Q7DD47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DD47
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.156α = 90
b = 79.511β = 107.22
c = 41.045γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other