4YCU

Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.

Fang, P.Han, H.Wang, J.Chen, K.Chen, X.Guo, M.

(2015) Chem. Biol. 22: 734-744

  • DOI: 10.1016/j.chembiol.2015.05.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves ...

    Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.,Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA. Electronic address: pfang@scripps.edu.,Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA; Department of Cell and Molecular Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA. Electronic address: guomin@scripps.edu.,Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA; School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine--tRNA ligase
A, B
513Homo sapiensMutation(s): 0 
Gene Names: KARS (KIAA0070)
EC: 2.7.7.-, 6.1.1.6
Find proteins for Q15046 (Homo sapiens)
Go to Gene View: KARS
Go to UniProtKB:  Q15046
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
C
42Homo sapiensMutation(s): 0 
Gene Names: AIMP2 (JTV1)
Find proteins for Q13155 (Homo sapiens)
Go to Gene View: AIMP2
Go to UniProtKB:  Q13155
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
A, B
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
KRS
Query on KRS

Download SDF File 
Download CCD File 
A, B
cladosporin
(3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KRSIC50: >20000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 96.194α = 90.00
b = 99.847β = 90.00
c = 268.987γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM100136
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM106134

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.2: 2018-10-10
    Type: Data collection, Database references, Structure summary