› 4js4

X-ray diffraction
3.1Å resolution

Crystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotide

Released:
DOI: 10.2210/pdb4js4/pdb
PDB entry 4js4 coloured by chain, front view.
PDB entry 4js4 coloured by chain, side view.
PDB entry 4js4 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.
Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE
OpenAccess logo Nucleic Acids Res 41 5887-97 (2013)
PMID: 23609540

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

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-117708 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Exodeoxyribonuclease I Chains: A, B
Molecule details ›
Chains: A, B
Length: 478 amino acids
Theoretical weight: 54.85 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P04995 (Residues: 1-475; Coverage: 100%)
Gene names: JW1993, b2011, cpeA, sbcB, xonA
Sequence domains:
Structure domains:
dT16 oligonucleotide Chains: C, D
Molecule details ›
Chains: C, D
Length: 16 nucleotides
Theoretical weight: 4.97 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P43
Unit cell:
a: 91.413Å b: 91.413Å c: 162.518Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.225 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Processivity in Bacterial Glycosyltransferases.
Yakovlieva et al. (2020)
1 more

2 mentions without citation

Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.
Korada et al. (2013)
1 more