4PY2 | pdb_00004py2

Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA

• PDB DOI: https://doi.org/10.2210/pdb4PY2/pdb

• Classification: ligase/ligase inhibitor
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-25 Released: 2015-04-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.211 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis.

Ojo, K.K., Ranade, R.M., Zhang, Z., Dranow, D.M., Myers, J.B., Choi, R., Nakazawa Hewitt, S., Edwards, T.E., Davies, D.R., Lorimer, D., Boyle, S.M., Barrett, L.K., Buckner, F.S., Fan, E., Van Voorhis, W.C.

(2016) PLoS One 11: e0160350-e0160350

• PubMed: 27500735 
• DOI: https://doi.org/10.1371/journal.pone.0160350
• Primary Citation Related Structures: 
  4DLP, 4PY2, 5K0S, 5K0T


• PubMed Abstract: 
  

  We investigated Brucella melitensis methionyl-tRNA-synthetase (BmMetRS) with molecular, structural and phenotypic methods to learn if BmMetRS is a promising target for brucellosis drug development. Recombinant BmMetRS was expressed, purified from wild type Brucella melitensis biovar Abortus 2308 strain ATCC/CRP #DD-156 and screened by a thermal melt assay against a focused library of one hundred previously classified methionyl-tRNA-synthetase inhibitors of the blood stage form of Trypanosoma brucei. Three compounds showed appreciable shift of denaturation temperature and were selected for further studies on inhibition of the recombinant enzyme activity and cell viability against wild type B. melitensis strain 16M. BmMetRS protein complexed with these three inhibitors resolved into three-dimensional crystal structures and was analyzed. All three selected methionyl-tRNA-synthetase compounds inhibit recombinant BmMetRS enzymatic functions in an aminoacylation assay at varying concentrations. Furthermore, growth inhibition of B. melitensis strain 16M by the compounds was shown. Inhibitor-BmMetRS crystal structure models were used to illustrate the molecular basis of the enzyme inhibition. Our current data suggests that BmMetRS is a promising target for brucellosis drug development. However, further studies are needed to optimize lead compound potency, efficacy and safety as well as determine the pharmacokinetics, optimal dosage, and duration for effective treatment.

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Organizational Affiliation: 
• Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America.
Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.
Beryllium, Bainbridge Island, Washington, United States of America.
Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 182.52 kDa 
• Atom Count: 12,210 
• Modeled Residue Count: 1,477 
• Deposited Residue Count: 1,608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase	A, B, C	536	Brucella abortus 2308	Mutation(s): 0  Gene Names: metG, BAB1_1014 EC: 6.1.1.10
UniProt
Find proteins for Q2YQ76 (Brucella abortus (strain 2308)) Explore Q2YQ76  Go to UniProtKB:  Q2YQ76

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
43E	D [auth A], F [auth B], K [auth C]	1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea C15 H17 Cl2 N3 O S DGBJLEREWKGWML-UHFFFAOYSA-N
EDO	E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.211 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34PY2

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.01	α = 110.47
b = 99.48	β = 87.24
c = 104	γ = 99.99

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2025-10-22
  Changes: Structure summary