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X-ray diffraction
1.47Å resolution

Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct 3-(Aminomethyl)-4-bromo-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP

Released:
DOI: 10.2210/pdb5ags/pdb
PDB entry 5ags coloured by chain, front view.
PDB entry 5ags coloured by chain, side view.
PDB entry 5ags coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium tuberculosis That Target Leucyl-tRNA Synthetase.
Palencia A, Li X, Bu W, Choi W, Ding CZ, Easom EE, Feng L, Hernandez V, Houston P, Liu L, Meewan M, Mohan M, Rock FL, Sexton H, Zhang S, Zhou Y, Wan B, Wang Y, Franzblau SG, Woolhiser L, Gruppo V, Lenaerts AJ, O'Malley T, Parish T, Cooper CB, Waters MG, Ma Z, Ioerger TR, Sacchettini JC, Rullas J, Angulo-Barturen I, Pérez-Herrán E, Mendoza A, Barros D, Cusack S, Plattner JJ, Alley MR
Antimicrob Agents Chemother 60 6271-80 (2016)
PMID: 27503647

Function and Biology Details

Reaction catalysed: 
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161431 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Leucine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 24.89 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P9WFV1 (Residues: 309-513; Coverage: 21%)
Gene names: MTCY21D4.04, Rv0041, leuS
Sequence domains: Leucyl-tRNA synthetase, editing domain
Structure domains: Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

Ligands and Environments

2 bound ligands:
Ligand MET 1 x MET
Ligand 38Y 1 x 38Y
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 44.75Å b: 62.16Å c: 76.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.206
Expression system: Escherichia coli K-12

Quick links

Citations

20 review citations

Antibiotics in the clinical pipeline in October 2019.
Butler et al. (2020)
19 more

2 mentions without citation

Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium tuberculosis That Target Leucyl-tRNA Synthetase.
Palencia et al. (2016)
1 more