› 4qwb

X-ray diffraction
1.8Å resolution

CRYSTAL STRUCTURE of DPO4 LINKER REGION P236A MUTANT WITH AN INCOMING D-dCDP

Released:
DOI: 10.2210/pdb4qwb/pdb
PDB entry 4qwb coloured by chain, front view.
PDB entry 4qwb coloured by chain, side view.
PDB entry 4qwb coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z
Nucleic Acids Res 42 9984-95 (2014)
PMID: 25104018

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-118037 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 343 amino acids
Theoretical weight: 39.19 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-343; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*(DOC))-3') Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.51 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand YYY 1 x YYY
Ligand CA 4 x CA
Ligand ACT 4 x ACT
Ligand GOL 3 x GOL
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21212
Unit cell:
a: 96.95Å b: 102.34Å c: 52.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.271
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Ribonucleotides in bacterial DNA.
Schroeder et al. (2015)
1 more

2 mentions without citation

Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum: structural and functional insights into thiosulfate oxidation.
Brito et al. (2015)
1 more