› 3m8s

X-ray diffraction
2.2Å resolution

Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-methylated dTTP

Released:
DOI: 10.2210/pdb3m8s/pdb
PDB entry 3m8s coloured by chain, front view.
PDB entry 3m8s coloured by chain, side view.
PDB entry 3m8s coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Structures of DNA polymerases caught processing size-augmented nucleotide probes.
Betz K, Streckenbach F, Schnur A, Exner T, Welte W, Diederichs K, Marx A
Angew Chem Int Ed Engl 49 5181-4 (2010)
PMID: 20572212

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-507688 (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*(DOC))-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Thermus aquaticus
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.95 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand HXB 1 x HXB
Ligand MG 2 x MG
Ligand GOL 3 x GOL
Ligand PEG 1 x PEG
Ligand 15P 1 x 15P
Ligand ACT 4 x ACT
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3121
Unit cell:
a: 108.742Å b: 108.742Å c: 90.755Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.17 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

DNA polymerases and cancer.
Lange et al. (2011)
2 more

1 mention without citation

Structural insights into DNA replication without hydrogen bonds.
Betz et al. (2013)