› 3gde

X-ray diffraction
2.3Å resolution

The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus

Released:
DOI: 10.2210/pdb3gde/pdb
PDB entry 3gde coloured by chain, front view.
PDB entry 3gde coloured by chain, side view.
PDB entry 3gde coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Primary publication:
ATP-dependent DNA ligase from Archaeoglobus fulgidus displays a tightly closed conformation.
Kim DJ, Kim O, Kim HW, Kim HS, Lee SJ, Suh SW
Acta Crystallogr Sect F Struct Biol Cryst Commun 65 544-50 (2009)
PMID: 19478428

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-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-128151 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 558 amino acids
Theoretical weight: 63.93 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O29632 (Residues: 1-555; Coverage: 100%)
Gene names: AF_0623, lig
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand PO4 4 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P41212
Unit cell:
a: 94.355Å b: 94.355Å c: 197.416Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.215 0.277
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

4 mentions without citation

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