4I71

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

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.

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

PubMed: 23897478 Search on PubMed
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. 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
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
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
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGV Query on AGV Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	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 SDF format, chain F [auth A] MOL2 format, chain F [auth A]	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 SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	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 SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction