› 1x9w

X-ray diffraction
2.3Å resolution

T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide.

Released:
DOI: 10.2210/pdb1x9w/pdb
PDB entry 1x9w coloured by chain, front view.
PDB entry 1x9w coloured by chain, side view.
PDB entry 1x9w coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T
Proc Natl Acad Sci U S A 101 16186-91 (2004)
PMID: 15528277

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-114797 (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: 79.09 KDa
Source organism: Escherichia phage T7
Expression system: Escherichia coli
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(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*GP*AP*(2DT))-3' Chain: C
Molecule details ›
Chain: C
Length: 22 nucleotides
Theoretical weight: 6.93 KDa
5'-D(*CP*CP*CP*(AFG)*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*TP*CP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 26 nucleotides
Theoretical weight: 7.94 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
2 modified residues:
Ligand 2DT 1 x 2DT
Ligand AFG 1 x AFG

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P21212
Unit cell:
a: 105.944Å b: 213.559Å c: 52.168Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.258
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Motors, switches, and contacts in the replisome.
Hamdan et al. (2009)
3 more

1 mention without citation

Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.
Dutta et al. (2004)