Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 91.70 kDa 
• Atom Count: 5554 
• Modelled Residue Count: 713 
• Deposited Residue Count: 828 
• Unique protein chains: 1

1W62

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

• PDB DOI: 10.2210/pdb1W62/pdb

• Classification: RACEMASE
• Organism(s): Trypanosoma cruzi strain CL Brener
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-12 Released: 2006-02-03 
• Deposition Author(s): Buschiazzo, A., Alzari, P.

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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 

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

• PubMed: 16446443 
• DOI: 10.1073/pnas.0509010103
• Primary Citation of Related Structures:  
  1W61, 1W62


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline racemase A	A, B	414	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: PA45-A, Tc00.1047053506795.80 EC: 5.1.1.4
UniProt
Find proteins for Q4DA80 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DA80  Go to UniProtKB:  Q4DA80

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYC	C [auth A]	PYRROLE-2-CARBOXYLATE C5 H4 N O2 WRHZVMBBRYBTKZ-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
PYC	Binding MOAD:  1W62	Ka: 4.60e+6 (M^-1) from 1 assay(s)

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 = 136.018	α = 90
b = 89.382	β = 125.98
c = 84.456	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-12 
• Released Date: 2006-02-03 
Deposition Author(s): Buschiazzo, A., Alzari, P.

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