› 2cfm

X-ray diffraction
1.8Å resolution

ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS

Released:
DOI: 10.2210/pdb2cfm/pdb
PDB entry 2cfm coloured by chain, front view.
PDB entry 2cfm coloured by chain, side view.
PDB entry 2cfm coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
The closed structure of an archaeal DNA ligase from Pyrococcus furiosus.
Nishida H, Kiyonari S, Ishino Y, Morikawa K
J Mol Biol 360 956-67 (2006)
PMID: 16820169

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-157532 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 561 amino acids
Theoretical weight: 64.62 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P56709 (Residues: 1-561; Coverage: 100%)
Gene names: PF1635, lig
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand AMP 1 x AMP
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6B
Spacegroup: P21
Unit cell:
a: 60.866Å b: 87.399Å c: 62.648Å
α: 90° β: 109.22° γ: 90°
R-values:
R R work R free
0.204 0.204 0.231
Expression system: Escherichia coli BL21

Quick links

Citations

7 review citations

DNA ligases: progress and prospects.
Shuman S. (2009)
6 more

9 mentions without citation

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