2V0G | pdb_00002v0g

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A tRNA(leu) transcript with 5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1- BENZOXABOROLE (AN2690) forming an adduct to the ribose of adenosine- 76 in the enzyme editing site.

• PDB DOI: https://doi.org/10.2210/pdb2V0G/pdb
• NAKB: 2V0G

• Classification: LIGASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-14 Released: 2007-07-03 
• Deposition Author(s): Rock, F., Mao, W., Yaremchuk, A., Tukalo, M., Crepin, T., Zhou, H., Zhang, Y., Hernandez, V., Akama, T., Baker, S., Plattner, J., Shapiro, L., Martinis, S.A., Benkovic, S.J., Cusack, S., Alley, M.R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.314 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site.

Rock, F., Mao, W., Yaremchuk, A., Tukalo, M., Crepin, T., Zhou, H., Zhang, Y., Hernandez, V., Akama, T., Baker, S., Plattner, J., Shapiro, L., Martinis, S.A., Benkovic, S.J., Cusack, S., Alley, M.R.K.

(2007) Science 316: 1759

• PubMed: 17588934 
• DOI: https://doi.org/10.1126/science.1142189
• Primary Citation Related Structures: 
  2V0C, 2V0G


• PubMed Abstract: 
  

  Aminoacyl-transfer RNA (tRNA) synthetases, which catalyze the attachment of the correct amino acid to its corresponding tRNA during translation of the genetic code, are proven antimicrobial drug targets. We show that the broad-spectrum antifungal 5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690), in development for the treatment of onychomycosis, inhibits yeast cytoplasmic leucyl-tRNA synthetase by formation of a stable tRNA(Leu)-AN2690 adduct in the editing site of the enzyme. Adduct formation is mediated through the boron atom of AN2690 and the 2'- and 3'-oxygen atoms of tRNA's3'-terminal adenosine. The trapping of enzyme-bound tRNA(Leu) in the editing site prevents catalytic turnover, thus inhibiting synthesis of leucyl-tRNA(Leu) and consequentially blocking protein synthesis. This result establishes the editing site as a bona fide target for aminoacyl-tRNA synthetase inhibitors.

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Organizational Affiliation: 
• Anacor Pharmaceuticals, Incorporated, 1060 East Meadow Circle, Palo Alto, CA 94303, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 258.29 kDa 
• Atom Count: 17,604 
• Modeled Residue Count: 1,904 
• Deposited Residue Count: 1,922 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINOACYL-TRNA SYNTHETASE	A, C [auth D]	878	Thermus thermophilus	Mutation(s): 0  EC: 6.1.1.4
UniProt
Find proteins for Q7SIE4 (Thermus thermophilus) Explore Q7SIE4  Go to UniProtKB:  Q7SIE4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TRNALEU	B, D [auth F]	83	Thermus thermophilus

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	H [auth A], V [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
LEU	E [auth A], P [auth D]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
SO4	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth D], R [auth D], S [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A], G [auth A], T [auth D], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.314 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.05	α = 90
b = 125.8	β = 118.71
c = 173.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Rock, F., Mao, W., Yaremchuk, A., Tukalo, M., Crepin, T., Zhou, H., Zhang, Y., Hernandez, V., Akama, T., Baker, S., Plattner, J., Shapiro, L., Martinis, S.A., Benkovic, S.J., Cusack, S., Alley, M.R.K.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description