› 2va3

X-ray diffraction
2.98Å 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/pdb2va3/pdb
PDB entry 2va3 coloured by chain, front view.
PDB entry 2va3 coloured by chain, side view.
PDB entry 2va3 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-507194 (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 *CP*TP*A)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.11 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*TP*CP*AP*DFTP*TP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.36 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
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 94.62Å b: 103.566Å c: 52.645Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.231 0.282
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

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

2 mentions without citation

The steric hypothesis for DNA replication and fluorine hydrogen bonding revisited in light of structural data.
Egli M. (2012)
1 more