› 3lzi

X-ray diffraction
2.3Å resolution

RB69 DNA Polymerase (Y567A) ternary complex with dATP Opposite 7,8-dihydro-8-oxoguanine

Released:
DOI: 10.2210/pdb3lzi/pdb
PDB entry 3lzi coloured by chain, front view.
PDB entry 3lzi coloured by chain, side view.
PDB entry 3lzi coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine .
Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH
Biochemistry 49 4116-25 (2010)
PMID: 20411947

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-116544 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 903 amino acids
Theoretical weight: 104.56 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(P*TP*CP*AP*(8OG)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 1 x DTP
Ligand CA 5 x CA
2 modified residues:
Ligand 8OG 1 x 8OG
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 78.148Å b: 117.603Å c: 130.681Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.258
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine.
Beard et al. (2010)
2 more

2 mentions without citation

Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor.
Wang et al. (2013)
1 more