› 2jef

X-ray diffraction
2.17Å resolution

The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus solfataricus DNA Polymerase IV: Steady-state and Pre-steady-state and X-Ray Crystallography of Correct and Incorrect Pairing

Released:
DOI: 10.2210/pdb2jef/pdb
PDB entry 2jef coloured by chain, front view.
PDB entry 2jef coloured by chain, side view.
PDB entry 2jef coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Molecular basis of selectivity of nucleoside triphosphate incorporation opposite O6-benzylguanine by sulfolobus solfataricus DNA polymerase Dpo4: steady-state and pre-steady-state kinetics and x-ray crystallography of correct and incorrect pairing.
Eoff RL, Angel KC, Egli M, Guengerich FP
J Biol Chem 282 13573-84 (2007)
PMID: 17337730

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115424 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 41.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*DOC)-3' Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.37 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*CP*AP*CP*BZGP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.46 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DGT 1 x DGT
Ligand CA 3 x CA
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P21212
Unit cell:
a: 93.99Å b: 102.66Å c: 52.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.267
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Mass spectrometry of structurally modified DNA.
Tretyakova et al. (2013)
5 more

3 mentions without citation

Structural diversity of the Y-family DNA polymerases.
Pata JD. (2010)
2 more