› 4b5i

X-ray diffraction
2.56Å resolution

Product complex of Neisseria AP endonuclease in presence of metal ions

Released:
DOI: 10.2210/pdb4b5i/pdb
PDB entry 4b5i coloured by chain, front view.
PDB entry 4b5i coloured by chain, side view.
PDB entry 4b5i coloured by chain, top view.
Source organism: Neisseria meningitidis
Primary publication:
Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS
Proc Natl Acad Sci U S A 109 16852-7 (2012)
PMID: 23035246

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117238 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease/exonuclease/phosphatase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 259 amino acids
Theoretical weight: 29.7 KDa
Source organism: Neisseria meningitidis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7DD47 (Residues: 1-259; Coverage: 100%)
Gene names: NMB2082, exoA
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
5'-D(*GP*CP*TP*AP*CP)-3' Chain: U
Molecule details ›
Chain: U
Length: 5 nucleotides
Theoretical weight: 1.48 KDa
Source organism: Neisseria meningitidis
Expression system: Not provided
5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3' Chain: V
Molecule details ›
Chain: V
Length: 11 nucleotides
Theoretical weight: 3.41 KDa
Source organism: Neisseria meningitidis
Expression system: Not provided
5'-D(*3DRP*CP*AP*TP*CP*GP)-3' Chain: X
Molecule details ›
Chain: X
Length: 6 nucleotides
Theoretical weight: 1.66 KDa
Source organism: Neisseria meningitidis
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 69.09Å b: 69.09Å c: 119.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.252
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Recognition and repair of chemically heterogeneous structures at DNA ends.
Andres et al. (2015)
1 more

1 mention without citation

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Lu et al. (2012)