1TCV

Crystal Structure of the Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with Non-detergent Sulfobetaine 195 and acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures for the Potential Drug Target Purine Nucleoside Phosphorylase from Schistosoma mansoni Causal Agent of Schistosomiasis.

Pereira, H.D.Franco, G.R.Cleasby, A.Garratt, R.C.

(2005) J.Mol.Biol. 353: 584-599

  • DOI: 10.1016/j.jmb.2005.08.045
  • Primary Citation of Related Structures:  
  • Also Cited By: 3FB1, 3FAZ, 3F8W, 3E0Q

  • PubMed Abstract: 
  • Despite the availability of effective chemotherapy, schistosomiasis continues to be one of the major parasitic infections to affect the human population worldwide. Currently, little is known of the structural biology of the parasites that are respons ...

    Despite the availability of effective chemotherapy, schistosomiasis continues to be one of the major parasitic infections to affect the human population worldwide. Currently, little is known of the structural biology of the parasites that are responsible for the disease and few attempts have been made to develop second generation drugs, which may become essential if resistance to those currently available becomes an issue. Here, we describe three crystal structures for the enzyme purine nucleoside phosphorylase (PNP) from Schistosoma mansoni, a component of the purine salvage pathway. PNP is known to be essential for the recovery of purine bases and nucleosides in schistosomes, due to an absence of the enzymes for de novo synthesis, making it a sensitive point in the parasite's metabolism. In all three structures reported here, acetate occupies part of the base-binding site and is directly bound to the conserved glutamic acid at position 203. One of the structures presents the crystallization additive sulfobetaine 195 (NDSB195) occupying simultaneously the ribose and phosphate binding sites, whilst a second presents only phosphate in the latter. The observation of sulfobetaine specifically bound to the protein active site was unexpected and is unique to this structure as far as we are aware. Considerable flexibility is observed in the active site, principally due to variable structural disorder in the regions centered on residues 64 and 260. This conformational plasticity extends to the way in which both NDSB195 and phosphate bind to the individual monomers of the trimeric structure reported here. Differences between the parasite and human enzymes are limited principally to the base-binding site, where the substitution of V245 in the mammalian enzymes by S247 introduces additional hydrogen bonding potential to the site. This is satisfied in the structures described here by a water molecule whose presence is normally observed only in complexes with 6-oxopurines. Residue Y202, which replaces F200 in human PNP, is able to reach over the ribose-binding site to interact with H259 and is predicted to form an additional hydrogen bond with the 5' hydroxyl of nucleoside substrates.


    Related Citations: 
    • Cloning, expression and preliminary crystallographic studies of the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni
      Pereira, H.M.,Cleasby, A.,Pena, S.D.,Franco, G.R.,Garratt, R.C.
      (2003) Acta Crystallogr.,Sect.D 59: 1096


    Organizational Affiliation

    Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, CEP 13560-970, São Carlos-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
purine-nucleoside phosphorylase
A, B, C
287Schistosoma mansoniMutation(s): 0 
EC: 2.4.2.1
Find proteins for Q9BMI9 (Schistosoma mansoni)
Go to UniProtKB:  Q9BMI9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDS
Query on NDS

Download SDF File 
Download CCD File 
A, B, C
ETHYL DIMETHYL AMMONIO PROPANE SULFONATE
C7 H17 N O3 S
NNCRHRDBFDCWPA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.755α = 90.00
b = 122.059β = 90.00
c = 129.761γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
CCP4data scaling
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance