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

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

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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: https://doi.org/10.1016/j.jmb.2004.01.039
  • Primary Citation of Related Structures:  
    1RXC, 1RXS, 1RXU, 1RXY, 1T0U

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
253Escherichia coliMutation(s): 0 
Gene Names: UDP
Find proteins for P12758 (Escherichia coli (strain K12))
Explore P12758 
Go to UniProtKB:  P12758
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12758
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5UD

Download Ideal Coordinates CCD File 
C9 H11 F N2 O6
Query on R1P

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EA [auth K]
HA [auth L]
N [auth B]
P [auth C]
S [auth D]
EA [auth K],
HA [auth L],
N [auth B],
P [auth C],
S [auth D],
U [auth E],
X [auth F],
Z [auth I]
C5 H11 O8 P
Query on URF

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BA [auth I]
GA [auth K]
IA [auth L]
O [auth B]
R [auth C]
BA [auth I],
GA [auth K],
IA [auth L],
O [auth B],
R [auth C],
T [auth D],
W [auth E],
Y [auth F]
C4 H3 F N2 O2
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Query on K

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AA [auth I],
FA [auth K],
M [auth A],
Q [auth C],
V [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.188α = 90
b = 191.701β = 118.5
c = 91.909γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-13
    Changes: Data collection, Database references, Structure summary