› 1jxl

X-ray diffraction
2.1Å resolution

Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Released:
DOI: 10.2210/pdb1jxl/pdb
PDB entry 1jxl coloured by chain, front view.
PDB entry 1jxl coloured by chain, side view.
PDB entry 1jxl coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
Ling H, Boudsocq F, Woodgate R, Yang W
Cell 107 91-102 (2001)
PMID: 11595188

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-114038 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli BL21(DE3)
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*TP*T)-3' Chain: P
Molecule details ›
Chain: P
Length: 12 nucleotides
Theoretical weight: 3.81 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU)P*CP*CP*CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.87 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand EDO 1 x EDO
Ligand CA 1 x CA
Ligand MG 3 x MG
Ligand DG3 1 x DG3
1 modified residue:
Ligand BRU 2 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9B
Spacegroup: P21212
Unit cell:
a: 97.12Å b: 101.88Å c: 52.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.278 0.221 0.278
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

72 review citations

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

13 mentions without citation

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