6HJE

Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Designed mono- and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography.

Amaral, P.A.Autheman, D.de Melo, G.D.Gouault, N.Cupif, J.F.Goyard, S.Dutra, P.Coatnoan, N.Cosson, A.Monet, D.Saul, F.Haouz, A.Uriac, P.Blondel, A.Minoprio, P.

(2018) PLoS Negl Trop Dis 12: e0006853-e0006853

  • DOI: 10.1371/journal.pntd.0006853
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chagas disease, caused by Trypanosoma cruzi, affects millions of people in South America and no satisfactory therapy exists, especially for its life threatening chronic phase. We targeted the Proline Racemase of T. cruzi, which is present in all stag ...

    Chagas disease, caused by Trypanosoma cruzi, affects millions of people in South America and no satisfactory therapy exists, especially for its life threatening chronic phase. We targeted the Proline Racemase of T. cruzi, which is present in all stages of the parasite life cycle, to discover new inhibitors against this disease. The first published crystal structures of the enzyme revealed that the catalytic site is too small to allow any relevant drug design. In previous work, to break through the chemical space afforded to virtual screening and drug design, we generated intermediate models between the open (ligand free) and closed (ligand bound) forms of the enzyme. In the present work, we co-crystallized the enzyme with the selected inhibitors and found that they were covalently bound to the catalytic cysteine residues in the active site, thus explaining why these compounds act as irreversible inhibitors. These results led us to the design of a novel, more potent specific inhibitor, NG-P27. Co-crystallization of this new inhibitor with the enzyme allowed us to confirm the predicted protein functional motions and further characterize the chemical mechanism. Hence, the catalytic Cys300 sulfur atom of the enzyme attacks the C2 carbon of the inhibitor in a coupled, regiospecific-stereospecific Michael reaction with trans-addition of a proton on the C3 carbon. Strikingly, the six different conformations of the catalytic site in the crystal structures reported in this work had key similarities to our intermediate models previously generated by inference of the protein functional motions. These crystal structures span a conformational interval covering roughly the first quarter of the opening mechanism, demonstrating the relevance of modeling approaches to break through chemical space in drug design.


    Organizational Affiliation

    Institut Pasteur, Unité de Bioinformatique Structurale, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France.,Université de Rennes 1, Equipe Chimie organique et interfaces (CORINT), UMR 6226 Sciences Chimiques de Rennes, Rennes, France.,Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosomatidés, Département Infection et Epidémiologie, Paris, France.,Institut Pasteur, Plateforme de Cristallographie, Département de Biologie Structurale et Chimie, CNRS-UMR 3528, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proline racemase A
A, B
414Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
Gene Names: PA45-A
EC: 5.1.1.4
Find proteins for Q4DA80 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DA80
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
7N0
Query on 7N0

Download SDF File 
Download CCD File 
A, B
2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid
C7 H10 O3
OLLLIBGOZUPLOK-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.233α = 90.00
b = 90.640β = 126.04
c = 85.394γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE16-0001-01

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release