Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.15 kDa 
• Atom Count: 8,570 
• Modelled Residue Count: 903 
• Deposited Residue Count: 968 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 3ZJT

Ternary complex of E.coli leucyl-tRNA synthetase, tRNA(Leu)574 and the benzoxaborole AN3017 in the editing conformation

• PDB DOI: 10.2210/pdb3ZJT/pdb
• NDB: NA2332

• Classification: LIGASE/RNA
• Organism(s): Escherichia coli, Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-01-18 Released: 2013-04-17 
• Deposition Author(s): Cusack, S., Palencia, A., Crepin, T., Hernandez, V., Akama, T., Baker, S.J., Bu, W., Feng, L., Freund, Y.R., Liu, L., Meewan, M., Mohan, M., Mao, W., Rock, F.L., Sexton, H., Sheoran, A., Zhang, Y., Zhang, Y., Zhou, Y., Nieman, J.A., Anugula, M.R., Keramane, E.M., Savariraj, K., Reddy, D.S., Sharma, R., Subedi, R., Singh, R., OLeary, A., Simon, N.L., DeMarsh, P.L., Mushtaq, S., Warner, M., Livermore, D.M., Alley, M.R.K., Plattner, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria.

Hernandez, V., Crepin, T., Palencia, A., Cusack, S., Akama, T., Baker, S.J., Bu, W., Feng, L., Freund, Y.R., Liu, L., Meewan, M., Mohan, M., Mao, W., Rock, F.L., Sexton, H., Sheoran, A., Zhang, Y., Zhang, Y., Zhou, Y., Nieman, J.A., Anugula, M.R., Keramane, E.M., Savariraj, K., Reddy, D.S., Sharma, R., Subedi, R., Singh, R., O'Leary, A., Simon, N.L., De Marsh, P.L., Mushtaq, S., Warner, M., Livermore, D.M., Alley, M.R.K., Plattner, J.J.

(2013) Antimicrob Agents Chemother 57: 1394

• PubMed: 23295920 
• DOI: 10.1128/AAC.02058-12
• Primary Citation of Related Structures:  
  3ZJT, 3ZJU, 3ZJV


• PubMed Abstract: 
  

Gram-negative bacteria cause approximately 70% of the infections in intensive care units. A growing number of bacterial isolates responsible for these infections are resistant to currently available antibiotics and to many in development. Most agents under development are modifications of existing drug classes, which only partially overcome existing resistance mechanisms. Therefore, new classes of Gram-negative antibacterials with truly novel modes of action are needed to circumvent these existing resistance mechanisms. We have previously identified a new a way to inhibit an aminoacyl-tRNA synthetase, leucyl-tRNA synthetase (LeuRS), in fungi via the oxaborole tRNA trapping (OBORT) mechanism. Herein, we show how we have modified the OBORT mechanism using a structure-guided approach to develop a new boron-based antibiotic class, the aminomethylbenzoxaboroles, which inhibit bacterial leucyl-tRNA synthetase and have activity against Gram-negative bacteria by largely evading the main efflux mechanisms in Escherichia coli and Pseudomonas aeruginosa. The lead analogue, AN3365, is active against Gram-negative bacteria, including Enterobacteriaceae bearing NDM-1 and KPC carbapenemases, as well as P. aeruginosa. This novel boron-based antibacterial, AN3365, has good mouse pharmacokinetics and was efficacious against E. coli and P. aeruginosa in murine thigh infection models, which suggest that this novel class of antibacterials has the potential to address this unmet medical need.

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Organizational Affiliation: 

Anacor Pharmaceuticals Inc., Palo Alto, CA, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEUCYL-TRNA SYNTHETASE	A	880	Escherichia coli	Mutation(s): 0  EC: 6.1.1.4
UniProt
Find proteins for P07813 (Escherichia coli (strain K12)) Explore P07813  Go to UniProtKB:  P07813

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TRNALEU5 UAA ISOACCEPTOR	B	88	Escherichia coli K-12

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.9	α = 90
b = 118.8	β = 90
c = 140.4	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: 2013-04-17 
Deposition Author(s): Cusack, S., Palencia, A., Crepin, T., Hernandez, V., Akama, T., Baker, S.J., Bu, W., Feng, L., Freund, Y.R., Liu, L., Meewan, M., Mohan, M., Mao, W., Rock, F.L., Sexton, H., Sheoran, A., Zhang, Y., Zhang, Y., Zhou, Y., Nieman, J.A., Anugula, M.R., Keramane, E.M., Savariraj, K., Reddy, D.S., Sharma, R., Subedi, R., Singh, R., OLeary, A., Simon, N.L., DeMarsh, P.L., Mushtaq, S., Warner, M., Livermore, D.M., Alley, M.R.K., Plattner, J.J.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release