3NBQ

Human uridine phosphorylase 1 (hUPP1) with 5-fluorouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active site conformational dynamics in human uridine phosphorylase 1.

Roosild, T.P.Castronovo, S.

(2010) Plos One 5: e12741-e12741

  • DOI: 10.1371/journal.pone.0012741

  • PubMed Abstract: 
  • Uridine phosphorylase (UPP) is a central enzyme in the pyrimidine salvage pathway, catalyzing the reversible phosphorolysis of uridine to uracil and ribose-1-phosphate. Human UPP activity has been a focus of cancer research due to its role in activat ...

    Uridine phosphorylase (UPP) is a central enzyme in the pyrimidine salvage pathway, catalyzing the reversible phosphorolysis of uridine to uracil and ribose-1-phosphate. Human UPP activity has been a focus of cancer research due to its role in activating fluoropyrimidine nucleoside chemotherapeutic agents such as 5-fluorouracil (5-FU) and capecitabine. Additionally, specific molecular inhibitors of this enzyme have been found to raise endogenous uridine concentrations, which can produce a cytoprotective effect on normal tissues exposed to these drugs. Here we report the structure of hUPP1 bound to 5-FU at 2.3 A resolution. Analysis of this structure reveals new insights as to the conformational motions the enzyme undergoes in the course of substrate binding and catalysis. The dimeric enzyme is capable of a large hinge motion between its two domains, facilitating ligand exchange and explaining observed cooperativity between the two active sites in binding phosphate-bearing substrates. Further, a loop toward the back end of the uracil binding pocket is shown to flexibly adjust to the varying chemistry of different compounds through an "induced-fit" association mechanism that was not observed in earlier hUPP1 structures. The details surrounding these dynamic aspects of hUPP1 structure and function provide unexplored avenues to develop novel inhibitors of this protein with improved specificity and increased affinity. Given the recent emergence of new roles for uridine as a neuron protective compound in ischemia and degenerative diseases, such as Alzheimer's and Parkinson's, inhibitors of hUPP1 with greater efficacy, which are able to boost cellular uridine levels without adverse side-effects, may have a wide range of therapeutic applications.


    Organizational Affiliation

    Department of Drug Development, Nevada Cancer Institute, Las Vegas, Nevada, United States of America. troosild@nvcancer.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase 1
A, B, C, D
328Homo sapiensMutation(s): 0 
Gene Names: UPP1 (UP)
EC: 2.4.2.3
Find proteins for Q16831 (Homo sapiens)
Go to Gene View: UPP1
Go to UniProtKB:  Q16831
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URF
Query on URF

Download SDF File 
Download CCD File 
A, B, C, D
5-FLUOROURACIL
C4 H3 F N2 O2
GHASVSINZRGABV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.317α = 90.00
b = 85.281β = 90.00
c = 260.581γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
DENZOdata reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-06-03 
  • Released Date: 2010-10-06 
  • Deposition Author(s): Roosild, T.P.

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description