Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.28 kDa 
• Atom Count: 2594 
• Residue Count: 278 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

4B5J

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

• DOI: 10.2210/pdb4B5J/pdb
• NDB: NA2067

• Classification: HYDROLASE/DNA
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-03 Released: 2012-10-17 
• Deposition Author(s): Lu, D., Silhan, J., MacDonald, J.T., Carpenter, E.P., Jensen, K., Tang, C.M., Baldwin, G.S., Freemont, P.S.

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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 

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

• PubMed: 23035246 
• 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) 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PUTATIVE EXODEOXYRIBONUCLEASE	A	259	Neisseria meningitidis	Mutation(s): 0  EC: 3.1.11.2
Find proteins for Q7DD47 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q7DD47  Go to UniProtKB:  Q7DD47

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'	U	11	Neisseria meningitidis

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3'	V	11	Neisseria meningitidis

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 = 69.88	α = 90
b = 69.88	β = 90
c = 122.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-03 
• Released Date: 2012-10-17 
Deposition Author(s): Lu, D., Silhan, J., MacDonald, J.T., Carpenter, E.P., Jensen, K., Tang, C.M., Baldwin, G.S., Freemont, P.S.

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