› 3k57

X-ray diffraction
2.08Å resolution

Crystal structure of E.coli Pol II-normal DNA-dATP ternary complex

Released:
DOI: 10.2210/pdb3k57/pdb
PDB entry 3k57 coloured by chain, front view.
PDB entry 3k57 coloured by chain, side view.
PDB entry 3k57 coloured by chain, top view.
Source organism: Escherichia coli K-12
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-116464 (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 K-12
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(*G*TP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided
DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 1 x DTP
Ligand MG 2 x MG
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 80.425Å b: 99.888Å c: 125.745Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.204 0.216
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

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

7 mentions without citation

Structural insights into eukaryotic DNA replication.
Doublié et al. (2014)
6 more