› 4qwc

X-ray diffraction
2.4Å resolution

Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus in Comples with DNA and L-DCDP

Released:
DOI: 10.2210/pdb4qwc/pdb
PDB entry 4qwc coloured by chain, front view.
PDB entry 4qwc coloured by chain, side view.
PDB entry 4qwc coloured by chain, top view.
Source organisms:
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-118038 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, D
Molecule details ›
Chains: A, D
Length: 343 amino acids
Theoretical weight: 39.22 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*C)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: synthetic construct
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') Chains: C, F
Molecule details ›
Chains: C, F
Length: 18 nucleotides
Theoretical weight: 5.51 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 5 x CA
Ligand ACT 3 x ACT
Ligand LTP 2 x LTP
1 modified residue:
Ligand DOC 2 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 98.44Å b: 101.93Å c: 105.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.227 0.277
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