› 2v9w

X-ray diffraction
3Å resolution

Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand

Released:
DOI: 10.2210/pdb2v9w/pdb
PDB entry 2v9w coloured by chain, front view.
PDB entry 2v9w coloured by chain, side view.
PDB entry 2v9w coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene.
Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M
J Biol Chem 282 36421-33 (2007)
PMID: 17951245

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-115865 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
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 *CP*TP*G)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4.12 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 18 nucleotides
Theoretical weight: 5.38 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand DCT 2 x DCT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 52.704Å b: 186.744Å c: 52.73Å
α: 90° β: 110.06° γ: 90°
R-values:
R R work R free
0.218 0.218 0.29
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

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

3 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
2 more