› 2w8l

X-ray diffraction
3Å resolution

Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation

Released:
DOI: 10.2210/pdb2w8l/pdb
PDB entry 2w8l coloured by chain, front view.
PDB entry 2w8l coloured by chain, side view.
PDB entry 2w8l coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Versatility of Y-family Sulfolobus solfataricus DNA polymerase Dpo4 in translesion synthesis past bulky N2-alkylguanine adducts.
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP
J Biol Chem 284 3563-76 (2009)
PMID: 19059910

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115900 (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*N2GP*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: 5.51 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21212
Unit cell:
a: 95.919Å b: 103.832Å c: 52.493Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.282
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

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

2 mentions without citation

Versatility of Y-family Sulfolobus solfataricus DNA polymerase Dpo4 in translesion synthesis past bulky N2-alkylguanine adducts.
Zhang et al. (2009)
1 more