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XPRTASE FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Escherichia coli xanthine phosphoribosyltransferase.

Vos, S.de Jersey, J.Martin, J.L.

(1997) Biochemistry 36: 4125-4134

  • DOI: 10.1021/bi962640d
  • Primary Citation of Related Structures:  
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  • PubMed Abstract: 
  • Xanthine phosphoribosyltransferase (XPRT; EC 2.4.2.22) from Escherichia coli is a tetrameric enzyme having 152 residues per subunit. XPRT catalyzes the transfer of the phosphoribosyl group from 5-phospho-alpha-D-ribosyl 1-pyrophosphate (PRib-PP) to t ...

    Xanthine phosphoribosyltransferase (XPRT; EC 2.4.2.22) from Escherichia coli is a tetrameric enzyme having 152 residues per subunit. XPRT catalyzes the transfer of the phosphoribosyl group from 5-phospho-alpha-D-ribosyl 1-pyrophosphate (PRib-PP) to the 6-oxopurine bases guanine, xanthine, and hypoxanthine to form GMP, XMP, and IMP, respectively. Crystals grown in the absence of substrate or product were used to determine the structure of XPRT at a resolution of 1.8 A, by multiple isomorphous replacement. The core structure of XPRT includes a five-stranded parallel beta-sheet surrounded by three alpha-helices, which is similar to that observed in other known phosphoribosyltransferase (PRTase) structures. The XPRT structure also has several interesting features. A glutamine residue in the purine binding site may be responsible for the altered 6-oxopurine base specificity seen in this enzyme compared to other 6-oxopurine PRTases. Also, we observe both a magnesium ion and a sulfate ion bound at the PRib-PP binding site of XPRT. The sulfate ion interacts with Arg-37 which has a cis-peptide conformation, and the magnesium ion interacts with Asp-89, a highly conserved acidic residue in the PRib-PP binding site motif. The XPRT structure also incorporates a feature which has not been observed in other PRTase structures. The C-terminal 12 residues of XPRT adopt an unusual extended conformation and make interactions with a neighboring subunit. The very last residue, Arg-152, could form part of the active site of a symmetry-related subunit in the XPRT tetramer.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Crystallographic Studies of Escherichia Coli Xanthine Phosphoribosyltransferase
      Vos, S., De Jersey, J., Martin, J.L.
      (1996) J Struct Biol 116: 330

    Organizational Affiliation

    Department of Biochemistry, The University of Queensland, Brisbane, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASEAB152Escherichia coliMutation(s): 0 
EC: 2.4.2.22 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for P0A9M5 (Escherichia coli (strain K12))
Explore P0A9M5 
Go to UniProtKB:  P0A9M5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.2α = 90
b = 92.7β = 90
c = 53.2γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model