› 4eq5

X-ray diffraction
2.85Å resolution

DNA ligase from the archaeon Thermococcus sibiricus

Released:
DOI: 10.2210/pdb4eq5/pdb
Model geometry
Fit model/data
PDB entry 4eq5 coloured by chain, front view.
PDB entry 4eq5 coloured by chain, side view.
PDB entry 4eq5 coloured by chain, top view.
Source organism: Thermococcus sibiricus MM 739
Primary publication:
Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus.
Petrova TE, Bezsudnova EY, Dorokhov BD, Slutskaya ES, Polyakov KM, Dorovatovskiy PV, Ravin NV, Skryabin KG, Kovalchuk MV, Popov VO
Acta Crystallogr Sect F Struct Biol Cryst Commun 68 163-5 (2012)
PMID: 22297989

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-111550 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 571 amino acids
Theoretical weight: 64.82 KDa
Source organism: Thermococcus sibiricus MM 739
Expression system: Escherichia coli
UniProt:
  • Canonical: C6A2U9 (Residues: 2-560; Coverage: 100%)
Gene names: TSIB_0885, lig
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: KURCHATOV SNC BEAMLINE K4.4
Spacegroup: P212121
Unit cell:
a: 58.59Å b: 87.54Å c: 126.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.277 0.273 0.358
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Biotechnological applications of archaeal enzymes from extreme environments.
Cabrera et al. (2018)
2 more

2 mentions without citation

ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain.
Petrova et al. (2012)
1 more