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 PISA (software)

Macromolecule Content

• Total Structure Weight: 36.84 kDa 
• Atom Count: 2875 
• Modelled Residue Count: 325 
• Deposited Residue Count: 330 
• Unique protein chains: 1

4I71

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

• PDB DOI: 10.2210/pdb4I71/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-30 Released: 2013-08-07 
• Deposition Author(s): Giannese, F., Degano, M.

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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 

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

• PubMed: 23897478 
• DOI: 10.1107/S0907444913010792
• Primary Citation of Related Structures:  
  4I70, 4I71, 4I72, 4I73, 4I74, 4I75


• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-adenosine-guanosine-nucleoside hydrolase	A	330	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb927.3.2960 EC: 3.2.2.1
UniProt
Find proteins for Q57ZL6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q57ZL6  Go to UniProtKB:  Q57ZL6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGV	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
TRS	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NI	D [auth A], E [auth A], G [auth A], H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AGV	Binding MOAD:  4I71	Ki: 18 (nM) from 1 assay(s)
	PDBBind:  4I71	Ki: 18 (nM) from 1 assay(s)

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 = 66.36	α = 90
b = 72.35	β = 90
c = 133.28	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-30 
• Released Date: 2013-08-07 
Deposition Author(s): Giannese, F., Degano, M.

Revision History  

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