› 4k1g

X-ray diffraction
1.9Å resolution

Structure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a alphadA:T basepair

Released:
DOI: 10.2210/pdb4k1g/pdb
PDB entry 4k1g coloured by chain, front view.
PDB entry 4k1g coloured by chain, side view.
PDB entry 4k1g coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases.
Mazouzi A, Vigouroux A, Aikeshev B, Brooks PJ, Saparbaev MK, Morera S, Ishchenko AA
Proc Natl Acad Sci U S A 110 E3071-80 (2013)
PMID: 23898172

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117718 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 285 amino acids
Theoretical weight: 31.45 KDa
Source organism: Escherichia coli K-12
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
DNA (5'-D(*GP*CP*GP*TP*CP*C)-3') Chains: E, M
Molecule details ›
Chains: E, M
Length: 6 nucleotides
Theoretical weight: 1.79 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3') Chains: F, N
Molecule details ›
Chains: F, N
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3') Chains: H, O
Molecule details ›
Chains: H, O
Length: 9 nucleotides
Theoretical weight: 2.75 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 5 x ZN
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2221
Unit cell:
a: 117.95Å b: 136.66Å c: 112.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.212
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Oxidatively induced DNA damage and its repair in cancer.
Dizdaroglu M. (2015)
11 more

4 mentions without citation

Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases.
Prorok et al. (2021)
3 more