4TXJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1016/j.biochi.2016.02.007
  • Primary Citation of Related Structures:  
    4TXH, 4TXJ, 4TXL, 4TXM, 4TXN, 5CYF, 5CYG

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D
296Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_082430
EC: 2.4.2.3
UniProt
Find proteins for G4VGI0 (Schistosoma mansoni)
Explore G4VGI0 
Go to UniProtKB:  G4VGI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4VGI0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
THM
Query on THM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
L [auth D]
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
K [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.82α = 90
b = 108.08β = 90
c = 116.06γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
GDAdata collection
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2012/14223-9

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2016-05-25
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2019-04-17
    Changes: Author supporting evidence, Data collection, Polymer sequence
  • Version 2.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description