› 3py8

X-ray diffraction
1.74Å resolution

Crystal structure of a mutant of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with DNA and ddCTP

Released:
DOI: 10.2210/pdb3py8/pdb
PDB entry 3py8 coloured by chain, front view.
PDB entry 3py8 coloured by chain, side view.
PDB entry 3py8 coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Learning from directed evolution: Thermus aquaticus DNA polymerase mutants with translesion synthesis activity.
Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A
Chembiochem 12 1574-80 (2011)
PMID: 21480455

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-116725 (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: 60.95 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*A*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
Source organism: Thermus aquaticus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand DCT 1 x DCT
Ligand GOL 2 x GOL
Ligand MN 5 x MN
Ligand MG 1 x MG
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P3121
Unit cell:
a: 108.61Å b: 108.61Å c: 90.57Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.169 0.199
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.
Currin et al. (2015)
2 more

2 mentions without citation

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron et al. (2016)
1 more