› 2bq3

X-ray diffraction
2Å resolution

DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine

Released:
DOI: 10.2210/pdb2bq3/pdb
PDB entry 2bq3 coloured by chain, front view.
PDB entry 2bq3 coloured by chain, side view.
PDB entry 2bq3 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine.
Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP
J Biol Chem 280 29750-64 (2005)
PMID: 15965231

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-115124 (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*A)-3' Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.41 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*CP*AP*TP*GNEP*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: 5.41 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21212
Unit cell:
a: 93.679Å b: 102.852Å c: 53.178Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.239 0.27
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

Mechanism of a genetic glissando: structural biology of indel mutations.
Garcia-Diaz et al. (2006)
12 more

3 mentions without citation

Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
Dimitri et al. (2008)
2 more