› 4qw8

X-ray diffraction
2.29Å resolution

TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND D-DCTP

Released:
DOI: 10.2210/pdb4qw8/pdb
PDB entry 4qw8 coloured by chain, front view.
PDB entry 4qw8 coloured by chain, side view.
PDB entry 4qw8 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-118034 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 349 amino acids
Theoretical weight: 40.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DCP 1 x DCP
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21212
Unit cell:
a: 98.073Å b: 102.317Å c: 52.495Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.215 0.235
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing.
Ruiz et al. (2022)
9 other articles

3 mentions without citation

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