› 7k72

X-ray diffraction
2.05Å resolution

Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD

Released:
DOI: 10.2210/pdb7k72/pdb
PDB entry 7k72 coloured by chain, front view.
PDB entry 7k72 coloured by chain, side view.
PDB entry 7k72 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Entry author: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 336 amino acids
Theoretical weight: 37.81 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
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


Cofactor: Ligand NAD 4 x NAD
3 bound ligands:
Ligand MG 9 x MG
Ligand CA 2 x CA
Ligand MPD 5 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P1
Unit cell:
a: 50.94Å b: 63.81Å c: 120.73Å
α: 96.22° β: 89.55° γ: 111.97°
R-values:
R R work R free
0.169 0.168 0.206
Expression system: Escherichia coli BL21(DE3)

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