› 2v4r

X-ray diffraction
2.5Å resolution

Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine

Released:
DOI: 10.2210/pdb2v4r/pdb
PDB entry 2v4r coloured by chain, front view.
PDB entry 2v4r coloured by chain, side view.
PDB entry 2v4r coloured by chain, top view.
Source organisms:
Primary publication:
Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondialdehyde-deoxyguanosine adduct.
Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ
Biochemistry 48 7079-88 (2009)
PMID: 19492857

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-115863 (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*C)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*AP*CP*M1GP*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: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DGT 1 x DGT
Ligand CA 3 x CA
1 modified residue:
Ligand M1G 1 x M1G

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21212
Unit cell:
a: 93.545Å b: 102.537Å c: 52.176Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.218 0.273
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Chemistry and structural biology of DNA damage and biological consequences.
Stone et al. (2011)
1 more

2 mentions without citation

Structural and functional analysis of Sulfolobus solfataricus Y-family DNA polymerase Dpo4-catalyzed bypass of the malondialdehyde-deoxyguanosine adduct.
Eoff et al. (2009)
1 more