› 1qum

X-ray diffraction
1.55Å resolution

CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA

Released:
DOI: 10.2210/pdb1qum/pdb
PDB entry 1qum coloured by chain, front view.
PDB entry 1qum coloured by chain, side view.
PDB entry 1qum coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.
Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA
Cell 98 397-408 (1999)
PMID: 10458614

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114473 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease 4 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 31.52 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6C1 (Residues: 1-285; Coverage: 100%)
Gene names: JW2146, b2159, nfo
Sequence domains: Xylose isomerase-like TIM barrel
Structure domains: Divalent-metal-dependent TIM barrel enzymes
5'-D(*CP*GP*TP*CP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*(3DR)P*CP*GP*AP*CP*GP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 4.01 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL1-5
Spacegroup: C2
Unit cell:
a: 133.12Å b: 58.727Å c: 51.146Å
α: 90° β: 94.97° γ: 90°
R-values:
R R work R free
0.203 0.203 0.254
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

30 review citations

Cellular responses to DNA damage.
Norbury et al. (2001)
29 more

19 mentions without citation

AdoMet-dependent methylation, DNA methyltransferases and base flipping.
Cheng et al. (2001)
18 more