› 1sl0

X-ray diffraction
3.2Å resolution

Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide

Released:
DOI: 10.2210/pdb1sl0/pdb
PDB entry 1sl0 coloured by chain, front view.
PDB entry 1sl0 coloured by chain, side view.
PDB entry 1sl0 coloured by chain, top view.
Source organisms:
Primary publication:
Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Li Y, Dutta S, Doublié S, Bdour HM, Taylor JS, Ellenberger T
Nat Struct Mol Biol 11 784-90 (2004)
PMID: 15235589

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-114602 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA-directed DNA polymerase Chains: A, C
Molecule details ›
Chains: A, C
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 Chains: B, D
Molecule details ›
Chains: B, D
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*(2DT))-3' Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 21 nucleotides
Theoretical weight: 6.43 KDa
5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3' Chains: T, U
Molecule details ›
Chains: T, U
Length: 25 nucleotides
Theoretical weight: 7.92 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand DAD 2 x DAD
2 modified residues:
Ligand 2DT 2 x 2DT
Ligand TTD 2 x TTD

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 54.266Å b: 105.466Å c: 213.931Å
α: 90° β: 91.57° γ: 90°
R-values:
R R work R free
0.282 0.282 0.351
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.
Prakash et al. (2005)
8 more

3 mentions without citation

Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase.
Luo et al. (2007)
2 more