› 3k5m

X-ray diffraction
2.04Å resolution

Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ternary complex

Released:
DOI: 10.2210/pdb3k5m/pdb
PDB entry 3k5m coloured by chain, front view.
PDB entry 3k5m coloured by chain, side view.
PDB entry 3k5m coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural insight into translesion synthesis by DNA Pol II.
Wang F, Yang W
Cell 139 1279-89 (2009)
PMID: 20064374

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-116468 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase II Chain: A
Molecule details ›
Chain: A
Length: 786 amino acids
Theoretical weight: 90.46 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P21189 (Residues: 1-783; Coverage: 100%)
Gene names: JW0059, b0060, dinA, polB
Sequence domains:
Structure domains:
DNA (5'-D(*AP*GP*TP*CP*CP*TP*GP*(3DR)P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3') Chain: T
Molecule details ›
Chain: T
Length: 20 nucleotides
Theoretical weight: 5.99 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.01 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DG3 1 x DG3
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 73.109Å b: 95.228Å c: 144.735Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.243 0.26
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

14 review citations

Translesion DNA polymerases.
Goodman et al. (2013)
13 more

4 mentions without citation

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism.
Yang et al. (2018)
3 more