5ELO

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and cladosporin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.

Baragana, B.Forte, B.Choi, R.Nakazawa Hewitt, S.Bueren-Calabuig, J.A.Pisco, J.P.Peet, C.Dranow, D.M.Robinson, D.A.Jansen, C.Norcross, N.R.Vinayak, S.Anderson, M.Brooks, C.F.Cooper, C.A.Damerow, S.Delves, M.Dowers, K.Duffy, J.Edwards, T.E.Hallyburton, I.Horst, B.G.Hulverson, M.A.Ferguson, L.Jimenez-Diaz, M.B.Jumani, R.S.Lorimer, D.D.Love, M.S.Maher, S.Matthews, H.McNamara, C.W.Miller, P.O'Neill, S.Ojo, K.K.Osuna-Cabello, M.Pinto, E.Post, J.Riley, J.Rottmann, M.Sanz, L.M.Scullion, P.Sharma, A.Shepherd, S.M.Shishikura, Y.Simeons, F.R.C.Stebbins, E.E.Stojanovski, L.Straschil, U.Tamaki, F.K.Tamjar, J.Torrie, L.S.Vantaux, A.Witkowski, B.Wittlin, S.Yogavel, M.Zuccotto, F.Angulo-Barturen, I.Sinden, R.Baum, J.Gamo, F.J.Maser, P.Kyle, D.E.Winzeler, E.A.Myler, P.J.Wyatt, P.G.Floyd, D.Matthews, D.Sharma, A.Striepen, B.Huston, C.D.Gray, D.W.Fairlamb, A.H.Pisliakov, A.V.Walpole, C.Read, K.D.Van Voorhis, W.C.Gilbert, I.H.

(2019) Proc Natl Acad Sci U S A 

  • DOI: https://doi.org/10.1073/pnas.1814685116
  • Primary Citation of Related Structures:  
    5ELN, 5ELO, 6AGT, 6HCU, 6HCV, 6HCW

  • PubMed Abstract: 

    Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage Plasmodium falciparum and Cryptosporidium parvum in cell-culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase ( Pf KRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both Pf KRS1 and C. parvum KRS ( Cp KRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED 90 = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between Pf KRS1 and Cp KRS. This series of compounds inhibit Cp KRS and C. parvum and Cryptosporidium hominis in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for Pf KRS1 and Cp KRS vs. (human) Hs KRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.


  • Organizational Affiliation

    Wellcome Centre for Anti-Infectives Research, Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, DD1 5EH Dundee, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B, C, D
535Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: cgd4_2370
EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CR27 
Go to UniProtKB:  Q5CR27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CR27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KRS
Query on KRS

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D]
cladosporin
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
G [auth A],
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
S [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.22α = 90
b = 120.72β = 90.23
c = 143.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description