› 5tt5

X-ray diffraction
1.55Å resolution

Escherichia coli LigA (K115M) in complex with NAD+

Released:
DOI: 10.2210/pdb5tt5/pdb
PDB entry 5tt5 coloured by chain, front view.
PDB entry 5tt5 coloured by chain, side view.
PDB entry 5tt5 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD+-dependent polynucleotide ligases.
Unciuleac MC, Goldgur Y, Shuman S
Proc Natl Acad Sci U S A 114 2592-2597 (2017)
PMID: 28223499

Function and Biology Details

Reaction catalysed: 
(1a) NAD(+) + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + beta-nicotinamide D-nucleotide
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147189 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase Chain: A
Molecule details ›
Chain: A
Length: 691 amino acids
Theoretical weight: 76.18 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P15042 (Residues: 1-671; Coverage: 100%)
Gene names: JW2403, b2411, dnaL, lig, ligA, lop, pdeC
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 1 x NAD
2 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 40.907Å b: 94.312Å c: 150.927Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.205
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)
7 other articles

4 mentions without citation

Genetically encoded tools for measuring and manipulating metabolism.
Choe et al. (2022)
3 more