3KVV

Trapping of an oxocarbenium ion intermediate in UP crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Glycal formation in crystals of uridine phosphorylase.

Paul, D.O'Leary, S.E.Rajashankar, K.Bu, W.Toms, A.Settembre, E.C.Sanders, J.M.Begley, T.P.Ealick, S.E.

(2010) Biochemistry 49: 3499-3509

  • DOI: 10.1021/bi902073b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure ...

    Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine phosphorylase
A, B, C, D, E, F
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R2B
Query on R2B

Download SDF File 
Download CCD File 
A, B, C, D, E, F
1,4-anhydro-D-erythro-pent-1-enitol
C5 H8 O4
WGCMRWDTTZWXPL-UHNVWZDZSA-N
 Ligand Interaction
URF
Query on URF

Download SDF File 
Download CCD File 
A, B, C, D, E, F
5-FLUOROURACIL
C4 H3 F N2 O2
GHASVSINZRGABV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.173 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 92.864α = 90.00
b = 92.864β = 90.00
c = 145.016γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance