› 1sl2

X-ray diffraction
2.3Å resolution

Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide

Released:
DOI: 10.2210/pdb1sl2/pdb
PDB entry 1sl2 coloured by chain, front view.
PDB entry 1sl2 coloured by chain, side view.
PDB entry 1sl2 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-114604 (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(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*TP*(2DA))-3' Chain: P
Molecule details ›
Chain: P
Length: 22 nucleotides
Theoretical weight: 6.74 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' Chain: T
Molecule details ›
Chain: T
Length: 25 nucleotides
Theoretical weight: 7.92 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand DAD 1 x DAD
2 modified residues:
Ligand 2DA 1 x 2DA
Ligand TTD 1 x TTD

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 104.983Å b: 212.599Å c: 51.945Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.246 0.279
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

4 mentions without citation

Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer.
Vasquez-Del Carpio et al. (2011)
3 more