› 3v6k

X-ray diffraction
3.6Å resolution

Replication of N2,3-Ethenoguanine by DNA Polymerases

Released:
DOI: 10.2210/pdb3v6k/pdb
PDB entry 3v6k coloured by chain, front view.
PDB entry 3v6k coloured by chain, side view.
PDB entry 3v6k coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Replication of N2,3-ethenoguanine by DNA polymerases.
Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP
Angew Chem Int Ed Engl 51 5466-9 (2012)
PMID: 22488769

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-117025 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, J
Molecule details ›
Chains: A, J
Length: 347 amino acids
Theoretical weight: 39.84 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-342; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(P*GP*AP*AP*GP*GP*AP*TP*TP*CP*(2DT))-3') Chains: K, P
Molecule details ›
Chains: K, P
Length: 10 nucleotides
Theoretical weight: 3.07 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*C)-3') Chains: B, M
Molecule details ›
Chains: B, M
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand CA 7 x CA
Ligand NA 4 x NA
1 modified residue:
Ligand 2DT 2 x 2DT

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 51.855Å b: 110.953Å c: 100.238Å
α: 90° β: 102.7° γ: 90°
R-values:
R R work R free
0.234 0.229 0.303
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

A rescue act: Translesion DNA synthesis past N(2) -deoxyguanosine adducts.
Nair et al. (2015)
1 more