1RXC

E. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium

Caradoc-Davies, T.T.Cutfield, S.M.Lamont, I.L.Cutfield, J.F.

(2004) J.Mol.Biol. 337: 337-354

  • DOI: 10.1016/j.jmb.2004.01.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uridine phosphorylase (UP) is a key enzyme in the pyrimidine salvage pathway that catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine levels and produces a protective ...

    Uridine phosphorylase (UP) is a key enzyme in the pyrimidine salvage pathway that catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine levels and produces a protective effect ("uridine rescue") against the toxicity of the chemotherapeutic agent 5-fluorouracil without reducing its antitumour activity. We have investigated UP-substrate interactions by determining the crystal structures of native Escherichia coli UP (two forms), and complexes with 5-fluorouracil/ribose 1-phosphate, 2-deoxyuridine/phosphate and thymidine/phosphate. These hexameric structures confirm the overall structural similarity of UP to E.coli purine nucleoside phosphorylase (PNP) whereby, in the presence of substrate, each displays a closed conformation resulting from a concerted movement that closes the active site cleft. However, in contrast to PNP where helix segmentation is the major conformational change between the open and closed forms, in UP more extensive changes are observed. In particular a swinging movement of a flap region consisting of residues 224-234 seals the active site. This overall change in conformation results in compression of the active site cleft. Gln166 and Arg168, part of an inserted segment not seen in PNP, are key residues in the uracil binding pocket and together with a tightly bound water molecule are seen to be involved in the substrate specificity of UP. Enzyme activity shows a twofold dependence on potassium ion concentration. The presence of a potassium ion at the monomer/monomer interface induces some local rearrangement, which results in dimer stabilisation. The conservation of key residues and interactions with substrate in the phosphate and ribose binding pockets suggest that ribooxocarbenium ion formation during catalysis of UP may be similar to that proposed for E.coli PNP.


    Organizational Affiliation

    Department of Biochemistry, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin 9001, New Zealand. tom.caradoc-davies@stonebow.otago.ac.nz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase
A, B, C, D, E, F, G, H, I, J, K, L
253Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: udp
EC: 2.4.2.3
Find proteins for P12758 (Escherichia coli (strain K12))
Go to UniProtKB:  P12758
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, E, I, K
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
J
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
URF
Query on URF

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Download CCD File 
B, C, D, E, F, I, K, L
5-FLUOROURACIL
C4 H3 F N2 O2
GHASVSINZRGABV-UHFFFAOYSA-N
 Ligand Interaction
R1P
Query on R1P

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Download CCD File 
B, C, D, E, F, I, K, L
RIBOSE-1-PHOSPHATE
C5 H11 O8 P
YXJDFQJKERBOBM-TXICZTDVSA-N
 Ligand Interaction
5UD
Query on 5UD

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Download CCD File 
J
5-FLUOROURIDINE
C9 H11 F N2 O6
FHIDNBAQOFJWCA-UAKXSSHOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 90.188α = 90.00
b = 191.701β = 118.50
c = 91.909γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
MOSFLMdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance