2JC5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/sj.emboj.7601593
  • Primary Citation of Related Structures:  

  • 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. W ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXODEOXYRIBONUCLEASE
A
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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCN
Query on BCN

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Download CCD File 
A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

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Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.120 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.156α = 90.00
b = 79.511β = 107.22
c = 41.045γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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