› 1s97

X-ray diffraction
2.4Å resolution

DPO4 with GT mismatch

Released:
DOI: 10.2210/pdb1s97/pdb
PDB entry 1s97 coloured by chain, front view.
PDB entry 1s97 coloured by chain, side view.
PDB entry 1s97 coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Dpo4 is hindered in extending a G.T mismatch by a reverse wobble.
Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK
Nat Struct Mol Biol 11 457-62 (2004)
PMID: 15077104

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-114579 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
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*CP*TP*G)-3' Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 13 nucleotides
Theoretical weight: 4.12 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 18 nucleotides
Theoretical weight: 5.38 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand DCT 4 x DCT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 104.433Å b: 100.644Å c: 110.426Å
α: 90° β: 94.89° γ: 90°
R-values:
R R work R free
0.236 0.218 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.
Prakash et al. (2005)
5 more

2 mentions without citation

Structural diversity of the Y-family DNA polymerases.
Pata JD. (2010)
1 more