› 6gdr

X-ray diffraction
2.33Å resolution

DNA binding with a minimal scaffold: Structure-function analysis of Lig E DNA ligases

Released:
DOI: 10.2210/pdb6gdr/pdb
PDB entry 6gdr coloured by chain, front view.
PDB entry 6gdr coloured by chain, side view.
PDB entry 6gdr coloured by chain, top view.
Source organism: Alteromonas mediterranea
Primary publication:
DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.
Williamson A, Grgic M, Leiros HS
Nucleic Acids Res 46 8616-8629 (2018)
PMID: 30007325

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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103499 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
ATP-dependent DNA ligase family profile domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 33.02 KDa
Source organism: Alteromonas mediterranea
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1J0SCU0 (Residues: 21-317; Coverage: 100%)
Gene name: BM525_03130
Sequence domains:
DNA (5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Alteromonas mediterranea
Expression system: Escherichia coli
DNA Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3 KDa
Source organism: Alteromonas mediterranea
Expression system: Escherichia coli
DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.34 KDa
Source organism: Alteromonas mediterranea
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand PO4 2 x PO4
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Unit cell:
a: 65.024Å b: 71.207Å c: 117.16Å
α: 90° β: 94.82° γ: 90°
R-values:
R R work R free
0.22 0.218 0.264
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Temperature adaptation of DNA ligases from psychrophilic organisms.
Berg et al. (2019)
3 more

5 mentions without citation

Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.
Williamson et al. (2020)
4 more