Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 76.25 kDa 
• Atom Count: 5465 
• Residue Count: 631 
• Unique protein chains: 1

1HOZ

CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE-PREFERRING NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX

• DOI: 10.2210/pdb1HOZ/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-12-12 Released: 2001-12-12 
• Deposition Author(s): Versees, W., Decanniere, K., Pelle, R., Depoorter, J., Parkin, D.W., Steyaert, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Literature

Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax.

Versees, W., Decanniere, K., Pelle, R., Depoorter, J., Brosens, E., Parkin, D.W., Steyaert, J.

(2001) J Mol Biol 307: 1363-1379

• PubMed: 11292348 
• DOI: 10.1006/jmbi.2001.4548
• Primary Citation of Related Structures:  
  1HP0, 1HOZ


• PubMed Abstract: 
  

The purine salvage pathway of parasitic protozoa is currently considered as a target for drug development because these organisms cannot synthesize purines de novo. Insight into the structure and mechanism of the involved enzymes can aid in the development of potent inhibitors, leading to new curative drugs. Nucleoside hydrolases are key enzymes in the purine salvage pathway of Trypanosomatidae, and they are especially attractive because they have no equivalent in mammalian cells. We cloned, expressed and purified a nucleoside hydrolase from Trypanosoma vivax. The substrate activity profile establishes the enzyme to be a member of the inosine-adenosine-guanosine-preferring nucleoside hydrolases (IAG-NH). We solved the crystal structure of the enzyme at 1.6 A resolution using MAD techniques. The complex of the enzyme with the substrate analogue 3-deaza-adenosine is presented. These are the first structures of an IAG-NH reported in the literature. The T. vivax IAG-NH is a homodimer, with each subunit consisting of ten beta-strands, 12 alpha-helices and three small 3(10)-helices. Six of the eight strands of the central beta-sheet form a motif resembling the Rossmann fold. Superposition of the active sites of this IAG-NH and the inosine-uridine-preferring nucleoside hydrolase (IU-NH) of Crithidia fasciculata shows the molecular basis of the different substrate specificity distinguishing these two classes of nucleoside hydrolases. An "aromatic stacking network" in the active site of the IAG-NH, absent from the IU-NH, imposes the purine specificity. Asp10 is the proposed general base in the reaction mechanism, abstracting a proton from a nucleophilic water molecule. Asp40 (replaced by Asn39 in the IU-NH) is positioned appropriately to act as a general acid and to protonate the purine leaving group. The second general acid, needed for full enzymatic activity, is probably part of a flexible loop located in the vicinity of the active site.

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Organizational Affiliation: 

Dienst Ultrastructuur, Vlaams Interuniversitair instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, Sint-Genesius-Rode, B-1640, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INOSINE-ADENOSINE-GUANOSINE-PREFERRING NUCLEOSIDE HYDROLASE	A, B	339	Trypanosoma vivax	Mutation(s): 0  EC: 3.2.2.1
Find proteins for Q9GPQ4 (Trypanosoma vivax) Explore Q9GPQ4  Go to UniProtKB:  Q9GPQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.09	α = 90
b = 74	β = 104.56
c = 82	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-12-12 
• Released Date: 2001-12-12 
Deposition Author(s): Versees, W., Decanniere, K., Pelle, R., Depoorter, J., Parkin, D.W., Steyaert, J.

Revision History 

• Version 1.0: 2001-12-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance