› 2imw

X-ray diffraction
2.05Å resolution

Mechanism of Template-Independent Nucleotide Incorporation Catalyzed by a Template-Dependent DNA Polymerase

Released:
DOI: 10.2210/pdb2imw/pdb
PDB entry 2imw coloured by chain, front view.
PDB entry 2imw coloured by chain, side view.
PDB entry 2imw coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase.
Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor JS, Yang W, Suo Z
J Mol Biol 365 590-602 (2007)
PMID: 17095011

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-115404 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: P
Molecule details ›
Chain: P
Length: 348 amino acids
Theoretical weight: 39.75 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-348; Coverage: 99%)
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: S
Molecule details ›
Chain: S
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
5'-D(*TP*AP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 15 nucleotides
Theoretical weight: 4.46 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 2 x CA
Ligand DDS 1 x DDS
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 98.057Å b: 101.857Å c: 52.38Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.23 0.284
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Investigating the biochemical impact of DNA damage with structure-based probes: abasic sites, photodimers, alkylation adducts, and oxidative lesions.
Dahlmann et al. (2009)
1 more

2 mentions without citation

Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase.
Fiala et al. (2007)
1 more