› 2w9b

X-ray diffraction
2.28Å resolution

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

Released:
DOI: 10.2210/pdb2w9b/pdb
PDB entry 2w9b coloured by chain, front view.
PDB entry 2w9b coloured by chain, side view.
PDB entry 2w9b coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes.
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP
J Biol Chem 284 17687-99 (2009)
PMID: 19542237

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-218926 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 41.11 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:
DNA polymerase IV Chain: B
Molecule details ›
Chain: 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 *TP*TP*CP*DOCP)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 14 nucleotides
Theoretical weight: 4.37 KDa
5'-D(*TP*CP*AP*TP*M2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' Chains: E, F
Molecule details ›
Chains: E, F
Length: 18 nucleotides
Theoretical weight: 5.42 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 4 x MG
2 modified residues:
Ligand DOC 2 x DOC
Ligand O2G 2 x O2G

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 51.794Å b: 101.776Å c: 97.268Å
α: 90° β: 91.95° γ: 90°
R-values:
R R work R free
0.239 0.239 0.251
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

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

3 mentions without citation

Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes.
Zhang et al. (2009)
2 more