› 6kdu

X-ray diffraction
2.2Å resolution

Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis

Released:
DOI: 10.2210/pdb6kdu/pdb
PDB entry 6kdu coloured by chain, front view.
PDB entry 6kdu coloured by chain, side view.
PDB entry 6kdu coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD+-dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity.
Afsar M, Shukla A, Kumar N, Ramachandran R
Acta Crystallogr D Struct Biol 77 776-789 (2021)
PMID: 34076591

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:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161892 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase A Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 36.85 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P9WNV1 (Residues: 8-328; Coverage: 47%)
Gene names: MTV012.28c, Rv3014c, lig, ligA
Sequence domains: NAD-dependent DNA ligase adenylation domain

Ligands and Environments

3 bound ligands:
Ligand AMP 1 x AMP
Ligand NMN 1 x NMN
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 11.2C
Spacegroup: P6122
Unit cell:
a: 96.168Å b: 96.168Å c: 200.835Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.21 0.244
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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Citations

1 mention without citation

Increased survival in puppies affected by Canine Parvovirus type II using an immunomodulator as a therapeutic aid.
Muñoz et al. (2021)