1W62

proline racemase in complex with one molecule of pyrrole-2-carboxylic acid (hemi form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase.

Buschiazzo, A.Goytia, M.Schaeffer, F.Degrave, W.Shepard, W.Gregoire, C.Chamond, N.Cosson, A.Berneman, A.Coatnoan, N.Alzari, P.M.Minoprio, P.

(2006) Proc Natl Acad Sci U S A 103: 1705-1710

  • DOI: 10.1073/pnas.0509010103
  • Primary Citation of Related Structures:  
    1W62, 1W61

  • PubMed Abstract: 
  • Amino acid racemases catalyze the stereoinversion of the chiral C alpha to produce the d-enantiomers that participate in biological processes, such as cell wall construction in prokaryotes. Within this large protein family, bacterial proline racemase ...

    Amino acid racemases catalyze the stereoinversion of the chiral C alpha to produce the d-enantiomers that participate in biological processes, such as cell wall construction in prokaryotes. Within this large protein family, bacterial proline racemases have been extensively studied as a model of enzymes acting with a pyridoxal-phosphate-independent mechanism. Here we report the crystal structure of the proline racemase from the human parasite Trypanosoma cruzi (TcPRACA), a secreted enzyme that triggers host B cell polyclonal activation, which prevents specific humoral immune responses and is crucial for parasite evasion and fate. The enzyme is a homodimer, with each monomer folded in two symmetric alpha/beta subunits separated by a deep crevice. The structure of TcPRACA in complex with a transition-state analog, pyrrole-2-carboxylic acid, reveals the presence of one reaction center per monomer, with two Cys residues optimally located to perform acid/base catalysis through a carbanion stabilization mechanism. Mutation of the catalytic Cys residues abolishes the enzymatic activity but preserves the mitogenic properties of the protein. In contrast, inhibitor binding promotes the closure of the interdomain crevice and completely abrogates B cell proliferation, suggesting that the mitogenic properties of TcPRACA depend on the exposure of transient epitopes in the ligand-free enzyme.


    Organizational Affiliation

    Unité de Biochimie Structurale, Centre National de la Recherche Scientifique/Institut Pasteur, 25 Rue du Dr. Roux, F-75724 Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proline racemase AAB414Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: PA45-ATc00.1047053506795.80
EC: 5.1.1.4
Find proteins for Q4DA80 (Trypanosoma cruzi (strain CL Brener))
Explore Q4DA80 
Go to UniProtKB:  Q4DA80
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYC
Query on PYC

Download CCD File 
A
PYRROLE-2-CARBOXYLATE
C5 H4 N O2
WRHZVMBBRYBTKZ-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PYCKa:  4600000   M^-1  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.018α = 90
b = 89.382β = 125.98
c = 84.456γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-06-13
    Changes: Data collection, Database references, Source and taxonomy, Structure summary