› 3lwl

X-ray diffraction
2.25Å resolution

Structure of Klenow fragment of Taq polymerase in complex with an abasic site

Released:
DOI: 10.2210/pdb3lwl/pdb
PDB entry 3lwl coloured by chain, front view.
PDB entry 3lwl coloured by chain, side view.
PDB entry 3lwl coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Replication through an abasic DNA lesion: structural basis for adenine selectivity.
Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs K, Welte W, Marx A
EMBO J 29 1738-47 (2010)
PMID: 20400942

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-116540 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase I, thermostable Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 60.94 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P19821 (Residues: 293-832; Coverage: 65%)
Gene names: pol1, polA
Sequence domains:
Structure domains:
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*(3DR)P*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.79 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand DDS 1 x DDS
Ligand MG 1 x MG
Ligand ACT 5 x ACT
Ligand GOL 7 x GOL
Ligand NA 4 x NA
1 modified residue:
Ligand 2DA 1 x 2DA

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P3121
Unit cell:
a: 110.228Å b: 110.228Å c: 91.265Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.188 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

DNA polymerase delta in DNA replication and genome maintenance.
Prindle et al. (2012)
4 more

4 mentions without citation

DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesions.
Zahn et al. (2011)
3 more