4TXL

Crystal structure of uridine phosphorylase from Schistosoma mansoni in complex with uracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Analysis of two Schistosoma mansoni uridine phosphorylases isoforms suggests the emergence of a protein with a non-canonical function.

da Silva Neto, A.M.Torini de Souza, J.R.Romanello, L.Cassago, A.Serrao, V.H.DeMarco, R.Brandao-Neto, J.Garratt, R.C.Pereira, H.D.

(2016) Biochimie 125: 12-22

  • DOI: 10.1016/j.biochi.2016.02.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Reports of Schistosoma mansoni strains resistant to praziquantel, the only therapeutic strategy available for the treatment of schistosomiasis, have motivated the scientific community towards the search for new possible therapies. Biochemical charact ...

    Reports of Schistosoma mansoni strains resistant to praziquantel, the only therapeutic strategy available for the treatment of schistosomiasis, have motivated the scientific community towards the search for new possible therapies. Biochemical characterization of the parasite's metabolism is an essential component for the rational development of new therapeutic alternatives. One of the so far uncharacterized enzymes is uridine phosphorylase (UP) (EC 2.4.2.3), for which the parasite genome presents two isoforms (SmUPa and SmUPb) that share 92% sequence identity. In this paper, we present crystal structures for SmUPa and SmUPb in their free states as well as bound to different ligands. This we have complemented by enzyme kinetic characterization and phylogenetic analyses. Both enzymes present an overall fold and active site structure similar to other known UPs. The kinetic analyses showed conclusively that SmUPa is a regular uridine phosphorylase but by contrast SmUPb presented no detectable activity. This is particularly noteworthy given the high level of sequence identity between the two isoforms and is probably the result of the significant differences observed for SmUPb in the vicinity of the active site itself, suggesting that it is not a UP at all. On the other hand, it was not possible to identify an alternative function for SmUPb, although our phylogenetic analyses and expression data suggest that SmUPb is still functional and plays a role in parasite metabolism. The unusual UPb isoform may open up new opportunities for understanding unique features of S. mansoni metabolism.


    Organizational Affiliation

    São Carlos Institute of Physics, São Paulo University, São Carlos, São Paulo, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase
C, D, A, B
296Schistosoma mansoniMutation(s): 0 
EC: 2.4.2.3
Find proteins for G4VGI0 (Schistosoma mansoni)
Go to UniProtKB:  G4VGI0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
URA
Query on URA

Download SDF File 
Download CCD File 
A, B, C, D
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.850α = 90.00
b = 108.530β = 90.00
c = 118.670γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
GDAdata collection
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FAPESPBrazil2012/14223-9

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2016-05-25
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description