› 4d05

X-ray diffraction
1.65Å resolution

Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant bacterium

Released:
DOI: 10.2210/pdb4d05/pdb
PDB entry 4d05 coloured by chain, front view.
PDB entry 4d05 coloured by chain, side view.
PDB entry 4d05 coloured by chain, top view.
Source organism: Psychromonas sp. SP041
Primary publication:
Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface.
Williamson A, Rothweiler U, Schr��der Leiros HK
Acta Crystallogr. D Biol. Crystallogr. 70 3043-56 (2014)
PMID: 25372693

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-100820 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Atp-dependent dna ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 258 amino acids
Theoretical weight: 29.8 KDa
Source organism: Psychromonas sp. SP041
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0A6YVN6 (Residues: 1-258; Coverage: 100%)
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 9 x SO4
Ligand AMP 2 x AMP
Ligand MG 1 x MG
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 178.427Å b: 43.976Å c: 89.633Å
α: 90° β: 105.92° γ: 90°
R-values:
R R work R free
0.147 0.145 0.192
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.
Williamson et al. (2020)
6 other articles

4 mentions without citation

Enzyme-adenylate structure of a bacterial ATP-dependent DNA ligase with a minimized DNA-binding surface.
Williamson et al. (2014)
3 more