› 2j6u

X-ray diffraction
2.5Å resolution

Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dGTP.

Released:
DOI: 10.2210/pdb2j6u/pdb
PDB entry 2j6u coloured by chain, front view.
PDB entry 2j6u coloured by chain, side view.
PDB entry 2j6u coloured by chain, top view.
Source organisms:
Primary publication:
Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred.
Eoff RL, Irimia A, Egli M, Guengerich FP
J Biol Chem 282 1456-67 (2007)
PMID: 17105728

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-115419 (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*T)-3' Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.4 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*AP*C G32P*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: 5.39 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand DGT 1 x DGT
1 modified residue:
Ligand 6OG 1 x 6OG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 92.318Å b: 102.285Å c: 52.485Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.265
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

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

1 mention without citation

Translesion DNA Synthesis.
Vaisman et al. (2012)