6Q89

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Leucyl)-Sulfamoyl)Adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.

Nautiyal, M.De Graef, S.Pang, L.Gadakh, B.Strelkov, S.V.Weeks, S.D.Van Aerschot, A.

(2019) Eur.J.Med.Chem. 173: 154-166

  • DOI: 10.1016/j.ejmech.2019.04.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (aaRSs) catalyse the ATP-dependent coupling of an amino acid to its cognate tRNA. Being vital for protein translation aaRSs are considered a promising target for the development of novel antimicrobial agents. 5'-O-(N-aminoa ...

    Aminoacyl-tRNA synthetases (aaRSs) catalyse the ATP-dependent coupling of an amino acid to its cognate tRNA. Being vital for protein translation aaRSs are considered a promising target for the development of novel antimicrobial agents. 5'-O-(N-aminoacyl)-sulfamoyl adenosine (aaSA) is a non-hydrolysable analogue of the aaRS reaction intermediate that has been shown to be a potent inhibitor of this enzyme family but is prone to chemical instability and enzymatic modification. In an attempt to improve the molecular properties of this scaffold we synthesized a series of base substituted aaSA analogues comprising cytosine, uracil and N 3 -methyluracil targeting leucyl-, tyrosyl- and isoleucyl-tRNA synthetases. In in vitro assays seven out of the nine inhibitors demonstrated K i app values in the low nanomolar range. To complement the biochemical studies, X-ray crystallographic structures of Neisseria gonorrhoeae leucyl-tRNA synthetase and Escherichia coli tyrosyl-tRNA synthetase in complex with the newly synthesized compounds were determined. These highlighted a subtle interplay between the base moiety and the target enzyme in defining relative inhibitory activity. Encouraged by this data we investigated if the pyrimidine congeners could escape a natural resistance mechanism, involving acetylation of the amine of the aminoacyl group by the bacterial N-acetyltransferases RimL and YhhY. With RimL the pyrimidine congeners were less susceptible to inactivation compared to the equivalent aaSA, whereas with YhhY the converse was true. Combined the various insights resulting from this study will pave the way for the further rational design of aaRS inhibitors.


    Organizational Affiliation

    Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium. Electronic address: arthur.vanaerschot@kuleuven.be.,Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium.,Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium; Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium.,Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucine--tRNA ligase
A
877Neisseria gonorrhoeaeMutation(s): 1 
Gene Names: leuS
EC: 6.1.1.4
Find proteins for A0A5K1KQ39 (Neisseria gonorrhoeae)
Go to UniProtKB:  A0A5K1KQ39
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LSS
Query on LSS

Download SDF File 
Download CCD File 
A
5'-O-(L-leucylsulfamoyl)adenosine
5-O-N-LEUCYL-SULFAMOYLADENOSINE
C16 H25 N7 O7 S
XFEDFDTWJLGMBO-LEJQEAHTSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.942α = 90.00
b = 82.935β = 90.00
c = 228.519γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG077814N
Research Foundation - FlandersBelgiumG0A4616N
Research Foundation - FlandersBelgium1109117N

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references
  • Version 1.2: 2019-05-01
    Type: Data collection