› 4fs2

X-ray diffraction
2.05Å resolution

Base pairing mechanism of N2,3-ethenoguanine with dCTP by human polymerase iota

Released:
DOI: 10.2210/pdb4fs2/pdb
PDB entry 4fs2 coloured by chain, front view.
PDB entry 4fs2 coloured by chain, side view.
PDB entry 4fs2 coloured by chain, top view.
Source organisms:
Primary publication:
Basis of miscoding of the DNA adduct N2,3-ethenoguanine by human Y-family DNA polymerases.
Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY, Rizzo CJ, Egli M, Guengerich FP
J Biol Chem 287 35516-35526 (2012)
PMID: 22910910

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117511 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA polymerase iota Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 47.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UNA4 (Residues: 26-445; Coverage: 57%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
DNA (5'-D(*TP*CP*TP*(EFG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3') Chains: B, C
Molecule details ›
Chains: B, C
Length: 18 nucleotides
Theoretical weight: 5.53 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand NA 1 x NA
Ligand DCP 1 x DCP
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P6522
Unit cell:
a: 97.298Å b: 97.298Å c: 202.906Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.214 0.261
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Inflammation-induced DNA damage, mutations and cancer.
Kay et al. (2019)
4 more

2 mentions without citation

Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases.
Zhao et al. (2017)
1 more