› 2xc9

X-ray diffraction
2.2Å resolution

BINARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE AND 1, N2-ETHENOGUANINE MODIFIED DNA, MAGNESIUM FORM

Released:
DOI: 10.2210/pdb2xc9/pdb
PDB entry 2xc9 coloured by chain, front view.
PDB entry 2xc9 coloured by chain, side view.
PDB entry 2xc9 coloured by chain, top view.
Source organisms:
Primary publication:
Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus.
Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M
Acta Crystallogr Sect F Struct Biol Cryst Commun 66 1013-8 (2010)
PMID: 20823515

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-115920 (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*G)-3' Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.43 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*AP*CP*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: 5.4 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21212
Unit cell:
a: 93.722Å b: 102.125Å c: 53.004Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.221 0.25
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesions.
Zahn et al. (2011)
1 more

2 mentions without citation

Translesion DNA Synthesis.
Vaisman et al. (2012)
1 more