› 5ihe

X-ray diffraction
2.5Å resolution

D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)

Released:
DOI: 10.2210/pdb5ihe/pdb
PDB entry 5ihe coloured by chain, front view.
PDB entry 5ihe coloured by chain, side view.
PDB entry 5ihe coloured by chain, top view.
Source organism: Pyrococcus abyssi GE5
Primary publication:
Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.
Sauguet L, Raia P, Henneke G, Delarue M
Nat Commun 7 12227 (2016)
PMID: 27548043

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194173 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA polymerase II small subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 475 amino acids
Theoretical weight: 53.61 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V2F3 (Residues: 145-619; Coverage: 77%)
Gene names: PAB2266, PYRAB01210, polB
Sequence domains: Calcineurin-like phosphoesterase

Ligands and Environments

6 bound ligands:
Ligand D5M 2 x D5M
Ligand FE 2 x FE
Ligand ZN 2 x ZN
Ligand CA 3 x CA
Ligand ACT 2 x ACT
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 85.969Å b: 91.415Å c: 145.209Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.225
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Archaeal DNA Replication.
Greci et al. (2020)
3 more

4 mentions without citation

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.
Sauguet et al. (2016)
3 more