4TXL | pdb_00004txl

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 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4TXL

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 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.

Macromolecule Content 

  • Total Structure Weight: 131.43 kDa 
  • Atom Count: 9,748 
  • Modeled Residue Count: 1,145 
  • Deposited Residue Count: 1,184 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uridine phosphorylaseA [auth C],
B [auth D],
C [auth A],
D [auth B]
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
URA

Query on URA



Download:Ideal Coordinates CCD File
F [auth C],
H [auth D],
J [auth A],
L [auth B]
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth C],
G [auth D],
I [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.220 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.85α = 90
b = 108.53β = 90
c = 118.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
GDAdata collection
xia2data scaling

Structure Validation

View Full Validation Report



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