1QK5

TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase with Xmp, Pyrophosphate and Two Mg2+ Ions Bound: Insights Into the Catalytic Mechanism

Heroux, A.White, E.L.Ross, L.J.Davis, R.L.Borhani, D.W.

(1999) Biochemistry 38: 14495

  • Also Cited By: 1QK4, 1QK3

  • PubMed Abstract: 
  • The crystal structure of the Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase (HGPRT)-xanthosine 5'-monophosphate (XMP)-pyrophosphate-Mg(2+) ternary complex has been determined at 1. 60 A resolution. This biproduct, post-transition st ...

    The crystal structure of the Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase (HGPRT)-xanthosine 5'-monophosphate (XMP)-pyrophosphate-Mg(2+) ternary complex has been determined at 1. 60 A resolution. This biproduct, post-transition state structure is of a T. gondii HGPRT mutant (Asp150Ala or D150A). The D150A mutant has reduced activity (k(cat) lower by 11-, 296-, and 8.6-fold for hypoxanthine, guanine, and xanthine, respectively) compared to wild-type T. gondii HGPRT. The Michaelis constants for purine bases are altered only slightly, whereas those for alpha-D-5-phosphoribosyl 1-pyrophosphate (PRPP) are lower by approximately 6.5-fold. The ternary complex crystallizes in space group C222(1) (a = 55.21 A, b = 112.25 A, and c = 144.28 A) with two subunits in the asymmetric unit; the HGPRT tetramer is completed by the application of 2-fold crystallographic symmetry. All active sites contain XMP ¿bound in a fashion similar to that of the guanosine 5'-monophosphate (GMP) and inosine 5'-monophosphate (IMP) complexes reported in the preceding article [Héroux, A., et al. (1999) Biochemistry 38, 14485-14494]¿, pyrophosphate, and two Mg(2+) ions. Each Mg(2+) ion is octahedrally coordinated by two terminal pyrophosphate oxygen atoms and several ordered water molecules. This structure shows how HGPRT uses two Mg(2+) ions to orient and activate the pyrophosphate moiety of PRPP for attack by a purine base, and why mutation in humans of the residue corresponding to Asp206, the only HGPRT amino acid that directly contacts the Mg(2+) ions, causes Lesch-Nyhan syndrome (HGPRT(Kinston), D193N). The Leu78-Lys79 peptide bond in the active site adopts the cis configuration, which it must to bind PRPP or pyrophosphate. The contribution of cis-trans isomerization of this peptide bond to the energetics of substrate binding and product release is discussed. A comprehensive description of the HGPRT reaction mechanism is also proposed.


    Related Citations: 
    • Isolation and Sequencing of a Cdna Encoding the Hypoxanthine-Guanine Phosphoribosyltransferase from Toxoplasma Gondii
      Vasanthakumar, G.,Van Ginkel, S.,Parish, G.
      (1994) Gene 147: 153
    • Crystal Structures of the Toxoplasma Gondii Hypoxanthine-Guanine Phosphoribosyltransferase Gmp and Imp Complexes: Comparison of Purine Binding Interactions with the Xmp Complex
      Heroux, A.,White, E.L.,Ross, L.J.,Borhani, D.W.
      (1999) Biochemistry 38: 14485


    Organizational Affiliation

    Drug Discovery Division, Southern Research Institute, Birmingham, Alabama 35205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
A, B
233Toxoplasma gondiiMutation(s): 1 
Gene Names: HPRT
EC: 2.4.2.22, 2.4.2.8
Find proteins for Q26997 (Toxoplasma gondii)
Go to UniProtKB:  Q26997
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
XMP
Query on XMP

Download SDF File 
Download CCD File 
A, B
XANTHOSINE-5'-MONOPHOSPHATE
5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 55.208α = 90.00
b = 112.255β = 90.00
c = 144.280γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-03-06
    Type: Data collection, Experimental preparation, Other