2JC4

3'-5' exonuclease (NExo) from Neisseria Meningitidis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXODEOXYRIBONUCLEASE IIIA256Neisseria meningitidisMutation(s): 0 
EC: 3.1.11.2
UniProt
Find proteins for Q9K100 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9K100 
Go to UniProtKB:  Q9K100
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K100
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
2HP
Query on 2HP
Download Ideal Coordinates CCD File 
G [auth A]DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.193α = 90
b = 58.618β = 90
c = 88.635γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

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