3FZ0

Inosine-Guanosine Nucleoside Hydrolase (IG-NH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 8999-9010

  • DOI: 10.1021/bi100697d
  • Also Cited By: 4I75, 4I74, 4I73, 4I72, 4I71, 4I70

  • PubMed Abstract: 
  • Trypanosomes are purine-auxotrophic parasites that depend upon nucleoside hydrolase (NH) activity to salvage nitrogenous bases necessary for nucleic acid and cofactor synthesis. Nonspecific and purine-specific NHs have been widely studied, yet little ...

    Trypanosomes are purine-auxotrophic parasites that depend upon nucleoside hydrolase (NH) activity to salvage nitrogenous bases necessary for nucleic acid and cofactor synthesis. Nonspecific and purine-specific NHs have been widely studied, yet little is known about the 6-oxopurine-specific isozymes, although they are thought to play a primary role in the catabolism of exogenously derived nucleosides. Here, we report the first functional and structural characterization of the inosine-guanosine-specific NH from Trypanosoma brucei brucei. The enzyme shows near diffusion-limited efficiency coupled with a clear specificity for 6-oxopurine nucleosides achieved through a catalytic selection of these substrates. Pre-steady-state kinetic analysis reveals ordered product release, and a rate-limiting structural rearrangement that is associated with the release of the product, ribose. The crystal structure of this trypanosomal NH determined to 2.5 Å resolution reveals distinctive features compared to those of both purine- and pyrimidine-specific isozymes in the framework of the conserved and versatile NH fold. Nanomolar iminoribitol-based inhibitors identified in this study represent important lead compounds for the development of novel therapeutic strategies against trypanosomal diseases.


    Related Citations: 
    • Guanosine-inosine-preferring nucleoside N-glycohydrolase from Crithidia fasciculata
      Estupinan, B.,Schramm, V.L.
      (1994) J.Biol.Chem. 269: 23068


    Organizational Affiliation

    Department of Molecular and Cellular Interactions and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside hydrolase, putative
A, B, C, D
360Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 2 
EC: 3.2.2.1
Find proteins for Q57X73 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q57X73
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BTB
Query on BTB

Download SDF File 
Download CCD File 
A, B, C, D
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 124.690α = 90.00
b = 116.040β = 90.00
c = 204.760γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
MOLREPphasing
REFMACrefinement
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance