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› 7ens

X-ray diffraction
2.2Å resolution

Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Indolmycin and ATP

Released:
DOI: 10.2210/pdb7ens/pdb
Model geometry
Fit model/data
PDB entry 7ens coloured by chain, front view.
PDB entry 7ens coloured by chain, side view.
PDB entry 7ens coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents.
Yang Y, Xu Y, Yue Y, Wang H, Cui Y, Pan M, Zhang X, Zhang L, Li H, Xu M, Tang Y, Chen S
ACS Chem Biol 17 39-53 (2022)
PMID: 34908399

Function and Biology Details

Reaction catalysed: 
tRNA(Trp) + L-tryptophan + ATP = L-tryptophyl-tRNA(Trp) + AMP +diphosphate + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161426 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 344 amino acids
Theoretical weight: 37.38 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WFT3 (Residues: 1-336; Coverage: 100%)
Gene names: MTV016.36c, Rv3336c, trpS
Sequence domains: tRNA synthetases class I (W and Y)

Ligands and Environments

3 bound ligands:
Ligand ATP 1 x ATP
Ligand MG 1 x MG
Ligand 5BX 1 x 5BX
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P6522
Unit cell:
a: 61.752Å b: 61.752Å c: 334.653Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.225 0.251
Expression system: Escherichia coli

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Citations

2 citation in other articles

An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening.
Xiang et al. (2023)
1 more

1 mention without citation

Morphology of Lymphoid Tissue in the Lungs of Guinea Pigs Infected with Mycobacterium bovis against the Background of Vaccine Immunity and the Action of Betulin and Its Derivatives.
Koshkin et al. (2022)