4B5J

Neisseria AP endonuclease bound to the substrate with an orphan Adenine base

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 

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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) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site ...

    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 LengthOrganismDetailsImage
PUTATIVE EXODEOXYRIBONUCLEASEA259Neisseria meningitidisMutation(s): 0 
EC: 3.1.11.2
UniProt
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'B [auth U]11Neisseria meningitidis
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3'C [auth V]11Neisseria meningitidis
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.88α = 90
b = 69.88β = 90
c = 122.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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