4I71

Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with a trypanocidal compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor

Giannese, F.Berg, M.Van der Veken, P.Castagna, V.Tornaghi, P.Augustyns, K.Degano, M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1553-1566

  • DOI: 10.1107/S0907444913010792
  • Primary Citation of Related Structures:  
    4I72, 4I73, 4I74, 4I75, 4I70, 4I71

  • PubMed Abstract: 
  • Sleeping sickness is a deadly disease that primarily affects sub-Saharan Africa and is caused by protozoan parasites of the Trypanosoma genus. Trypanosomes are purine auxotrophs and their uptake pathway has long been appreciated as an attractive target for drug design ...

    Sleeping sickness is a deadly disease that primarily affects sub-Saharan Africa and is caused by protozoan parasites of the Trypanosoma genus. Trypanosomes are purine auxotrophs and their uptake pathway has long been appreciated as an attractive target for drug design. Recently, one tight-binding competitive inhibitor of the trypanosomal purine-specific nucleoside hydrolase (IAGNH) showed remarkable trypanocidal activity in a murine model of infection. Here, the enzymatic characterization of T. brucei brucei IAGNH is presented, together with its high-resolution structures in the unliganded form and in complexes with different inhibitors, including the trypanocidal compound UAMC-00363. A description of the crucial contacts that account for the high-affinity inhibition of IAGNH by iminoribitol-based compounds is provided and the molecular mechanism underlying the conformational change necessary for enzymatic catalysis is identified. It is demonstrated for the first time that metalorganic complexes can compete for binding at the active site of nucleoside hydrolase enzymes, mimicking the positively charged transition state of the enzymatic reaction. Moreover, we show that divalent metal ions can act as noncompetitive IAGNH inhibitors, stabilizing a nonproductive conformation of the catalytic loop. These results open a path for rational improvement of the potency and the selectivity of existing compounds and suggest new scaffolds that may be used as blueprints for the design of novel antitrypanosomal compounds.


    Related Citations: 
    • Transition-state complex of the purine-specific nucleoside hydrolase of T. vivax: enzyme conformational changes and implications for catalysis
      Versees, W., Barlow, J., Steyaert, J.
      (2006) J Mol Biol 359: 331
    • Structure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei
      Vandemeulebroucke, A., Minici, C., Bruno, I., Muzzolini, L., Tornaghi, P., Parkin, D.W., Versees, W., Steyaert, J., Degano, M.
      (2010) Biochemistry 49: 8999
    • Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism
      Parkin, D.W.
      (1996) J Biol Chem 271: 21713

    Organizational Affiliation

    Biocrystallography Unit, Department of Immunology, Transplantation and Infectious Diseases, Scientific Institute San Raffaele, via Olgettina 58, 20132 Milano, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-adenosine-guanosine-nucleoside hydrolaseA330Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb927.3.2960
EC: 3.2.2.1
Find proteins for Q57ZL6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57ZL6 
Go to UniProtKB:  Q57ZL6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGV
Query on AGV

Download Ideal Coordinates CCD File 
B [auth A](2R,3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidine-3,4-diol
C12 H17 N5 O3
RCLRGJMFVIDWTM-VHSKPIJISA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], G [auth A], H [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AGVKi:  18   nM  Binding MOAD
AGVKi :  18   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.36α = 90
b = 72.35β = 90
c = 133.28γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references