› 2jc4

X-ray diffraction
1.9Å resolution

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

Released:
DOI: 10.2210/pdb2jc4/pdb
PDB entry 2jc4 coloured by chain, front view.
PDB entry 2jc4 coloured by chain, side view.
PDB entry 2jc4 coloured by chain, top view.
Source organism: Neisseria meningitidis
Primary publication:
AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis.
Carpenter EP, Corbett A, Thomson H, Adacha J, Jensen K, Bergeron J, Kasampalidis I, Exley R, Winterbotham M, Tang C, Baldwin GS, Freemont P
EMBO J 26 1363-72 (2007)
PMID: 17318183

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191734 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endonuclease/exonuclease/phosphatase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 256 amino acids
Theoretical weight: 29.19 KDa
Source organism: Neisseria meningitidis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9K100 (Residues: 1-256; Coverage: 100%)
Gene names: NMB0399, xthA
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand NA 2 x NA
Ligand 1PE 1 x 1PE
Ligand ACT 1 x ACT
Ligand 2HP 1 x 2HP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.1
Spacegroup: P212121
Unit cell:
a: 46.193Å b: 58.618Å c: 88.635Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.152 0.152 0.202
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Mechanisms of avoidance of host immunity by Neisseria meningitidis and its effect on vaccine development.
Lo et al. (2009)
3 more

1 mention without citation

Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis.
Silhan et al. (2018)