› 1zyq

X-ray diffraction
2.7Å resolution

T7 DNA polymerase in complex with 8oG and incoming ddATP

Released:
DOI: 10.2210/pdb1zyq/pdb
PDB entry 1zyq coloured by chain, front view.
PDB entry 1zyq coloured by chain, side view.
PDB entry 1zyq coloured by chain, top view.
Source organisms:
Primary publication:
A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine.
Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T
Structure 13 1653-9 (2005)
PMID: 16271888

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114967 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA-directed DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 698 amino acids
Theoretical weight: 79.03 KDa
Source organism: Escherichia phage T7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00581 (Residues: 1-704; Coverage: 99%)
Gene name: 5
Sequence domains: DNA polymerase family A
Structure domains:
Thioredoxin 1 Chain: B
Molecule details ›
Chain: B
Length: 108 amino acids
Theoretical weight: 11.69 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AA25 (Residues: 2-109; Coverage: 99%)
Gene names: JW5856, b3781, fipA, trxA, tsnC
Sequence domains: Thioredoxin
Structure domains: Glutaredoxin
5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DDG))-3' Chain: P
Molecule details ›
Chain: P
Length: 22 nucleotides
Theoretical weight: 6.76 KDa
5'-D(*CP*CP*CP*(8OG)P*CP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3' Chain: T
Molecule details ›
Chain: T
Length: 26 nucleotides
Theoretical weight: 7.94 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand DAD 1 x DAD
2 modified residues:
Ligand DDG 1 x DDG
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C, null
Spacegroup: P21212
Unit cell:
a: 106.148Å b: 213.007Å c: 52.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.224 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

3 review citations

Biological properties of single chemical-DNA adducts: a twenty year perspective.
Delaney et al. (2008)
2 more

2 mentions without citation

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