5ELO | pdb_00005elo

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 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

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 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.

Macromolecule Content 

  • Total Structure Weight: 248.23 kDa 
  • Atom Count: 18,226 
  • Modeled Residue Count: 1,995 
  • Deposited Residue Count: 2,140 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1 21 1
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

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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