› 3rr5

X-ray diffraction
3.02Å resolution

DNA ligase from the archaeon Thermococcus sp. 1519

Released:
DOI: 10.2210/pdb3rr5/pdb
PDB entry 3rr5 coloured by chain, front view.
PDB entry 3rr5 coloured by chain, side view.
PDB entry 3rr5 coloured by chain, top view.
Source organism: Thermococcus sp. 1519
Primary publication:
ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.
Petrova T, Bezsudnova EY, Boyko KM, Mardanov AV, Polyakov KM, Volkov VV, Kozin M, Ravin NV, Shabalin IG, Skryabin KG, Stekhanova TN, Kovalchuk MV, Popov VO
Acta Crystallogr Sect F Struct Biol Cryst Commun 68 1440-7 (2012)
PMID: 23192021

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = 5'-adenosyl [DNA ligase]-N(epsilon)-phosphono-L-lysine + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111010 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 570 amino acids
Theoretical weight: 64.89 KDa
Source organism: Thermococcus sp. 1519
Expression system: Escherichia coli
UniProt:
  • Canonical: C0LJI8 (Residues: 2-559; Coverage: 100%)
Gene name: lig
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 76.95Å b: 85.6Å c: 105.96Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.233 0.31
Expression system: Escherichia coli

Quick links

Citations

3 review citations

From Structure-Function Analyses to Protein Engineering for Practical Applications of DNA Ligase.
Tanabe et al. (2015)
2 more

3 mentions without citation

Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology.
Chambers et al. (2015)
2 more