› 6lw8

X-ray diffraction
2.4Å 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/pdb6lw8/pdb
PDB entry 6lw8 coloured by chain, front view.
PDB entry 6lw8 coloured by chain, side view.
PDB entry 6lw8 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Structure based identification of first-in-class fragment inhibitors that target the NMN pocket of M. tuberculosis NAD+-dependent DNA ligase A.
Shukla A, Afsar M, Kumar N, Kumar S, Ramachandran R
J Struct Biol 213 107655 (2021)
PMID: 33197566

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161893 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA ligase A Chain: A
Molecule details ›
Chain: A
Length: 334 amino acids
Theoretical weight: 37.61 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P9WNV1 (Residues: 1-328; Coverage: 48%)
Gene names: MTV012.28c, Rv3014c, lig, ligA
Sequence domains: NAD-dependent DNA ligase adenylation domain

Ligands and Environments

3 bound ligands:
Ligand GOL 1 x GOL
Ligand EWO 1 x EWO
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Spacegroup: P6122
Unit cell:
a: 95.39Å b: 95.39Å c: 201.683Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.241 0.239 0.27
Expression system: Escherichia coli BL21

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