5AGS | pdb_00005ags

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

• PDB DOI: https://doi.org/10.2210/pdb5AGS/pdb

• Classification: LIGASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2015-02-03 Released: 2016-03-09 
• Deposition Author(s): Palencia, A., Li, X., Alley, M.R.K., Ding, C., Easom, E.E., Hernandez, V., Meewan, M., Mohan, M., Rock, F.L., Franzblau, S.G., Wang, Y., Lenaerts, A.J., Parish, T., Cooper, C.B., Waters, M.G., Ma, Z., Mendoza, A., Barros, D., Cusack, S., Plattner, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium Tuberculosis that Target Leucyl-tRNA Synthetase.

Palencia, A., Li, X., Bu, W., Choi, W., Ding, C.Z., Easom, E.E., Feng, L., Hernandez, V., Houston, P., Liu, L., Meewan, M., Mohan, M., Rock, F.L., Sexton, H., Zhang, S., Zhou, Y., Wan, B., Wang, Y., Franzblau, S.G., Woolhiser, L., Gruppo, V., Lenaerts, A.J., O'Malley, T., Parish, T., Cooper, C.B., Waters, M.G., Ma, Z., Ioerger, T.R., Sacchettini, J.C., Rullas, J., Angulo-Barturen, I., Perez-Herran, E., Mendoza, A., Barros, D., Cusack, S., Plattner, J.J., Alley, M.R.K.

(2016) Antimicrob Agents Chemother 60: 6271

• PubMed: 27503647 
• DOI: https://doi.org/10.1128/AAC.01339-16
• Primary Citation Related Structures: 
  5AGR, 5AGS, 5AGT


• PubMed Abstract: 
  

  The recent development and spread of extensively drug-resistant and totally drug-resistant resistant (TDR) strains of Mycobacterium tuberculosis highlight the need for new antitubercular drugs. Protein synthesis inhibitors have played an important role in the treatment of tuberculosis (TB) starting with the inclusion of streptomycin in the first combination therapies. Although parenteral aminoglycosides are a key component of therapy for multidrug-resistant TB, the oxazolidinone linezolid is the only orally available protein synthesis inhibitor that is effective against TB. Here, we show that small-molecule inhibitors of aminoacyl-tRNA synthetases (AARSs), which are known to be excellent antibacterial protein synthesis targets, are orally bioavailable and effective against M. tuberculosis in TB mouse infection models. We applied the oxaborole tRNA-trapping (OBORT) mechanism, which was first developed to target fungal cytoplasmic leucyl-tRNA synthetase (LeuRS), to M. tuberculosis LeuRS. X-ray crystallography was used to guide the design of LeuRS inhibitors that have good biochemical potency and excellent whole-cell activity against M. tuberculosis Importantly, their good oral bioavailability translates into in vivo efficacy in both the acute and chronic mouse models of TB with potency comparable to that of the frontline drug isoniazid.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Grenoble, France.
Anacor Pharmaceuticals, Palo Alto, California, USA.
Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA.
Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA.
Global Alliance for TB Drug Development, New York, New York, USA.
Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
Tres Cantos Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Spain.
Anacor Pharmaceuticals, Palo Alto, California, USA [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.66 kDa 
• Atom Count: 1,851 
• Modeled Residue Count: 192 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEUCYL-TRNA SYNTHETASE	A	232	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 6.1.1.4
UniProt
Find proteins for P9WFV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFV1  Go to UniProtKB:  P9WFV1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
38Y	C [auth A]	3-(AMINOMETHYL)-4-BROMO-7-ETHOXYBENZO[C][1,2]OXABOROL-1(3H)-OL-MODIFIED ADENOSINE C20 H25 B Br N6 O9 P SFZDVNHRQSVZOB-CDUMDVBJSA-N
MET	B [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.75	α = 90
b = 62.16	β = 90
c = 76.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Palencia, A., Li, X., Alley, M.R.K., Ding, C., Easom, E.E., Hernandez, V., Meewan, M., Mohan, M., Rock, F.L., Franzblau, S.G., Wang, Y., Lenaerts, A.J., Parish, T., Cooper, C.B., Waters, M.G., Ma, Z., Mendoza, A., Barros, D., Cusack, S., Plattner, J.J.

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 1.2: 2016-10-05
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Data collection
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description