3v7k

X-ray diffraction
2.27Å resolution

Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex

Released:
Source organism: Rattus norvegicus
Entry authors: Rangarajan S, Jaeger J

Function and Biology Details

Reactions catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-117030 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 340 amino acids
Theoretical weight: 39.06 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P06766 (Residues: 4-335; Coverage: 99%)
Gene name: Polb
Sequence domains:
Structure domains:
DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.48 KDa
Source organism: Rattus norvegicus
Expression system: Not provided
DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*A)-3') Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.3 KDa
Source organism: Rattus norvegicus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 56.464Å b: 75.508Å c: 117.359Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.225 0.277
Expression systems:
  • Escherichia coli
  • Not provided