1DBR | pdb_00001dbr

HYPOXANTHINE GUANINE XANTHINE

• PDB DOI: https://doi.org/10.2210/pdb1DBR/pdb

• Classification: TRANSFERASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-02-13 Released: 1997-12-03 
• Deposition Author(s): Schumacher, M.A., Carter, D., Roos, D., Ullman, B., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.168 (Depositor) 

Literature

Crystal structures of Toxoplasma gondii HGXPRTase reveal the catalytic role of a long flexible loop.

Schumacher, M.A., Carter, D., Ross, D.S., Ullman, B., Brennan, R.G.

(1996) Nat Struct Biol 3: 881-887

• PubMed: 8836106 
• DOI: https://doi.org/10.1038/nsb1096-881
• Primary Citation Related Structures: 
  1DBR


• PubMed Abstract: 
  

  Crystal structures of substrate-free and XMP-soaked hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase) of the opportunistic pathogen Toxoplasma gondii have been determined to 2.4 and 2.9 A resolution, respectively. HGXPRTase displays the conserved PRTase fold. In the structure of the enzyme bound to its product, a long flexible loop (residues 115-126) is located away from the active site. Comparison to the substrate-free structure reveals a striking relocation of the loop, which is poised to cover the catalytic pocket, thus providing a mechanism by which the HG(X)PRTases shield their oxocarbonium transition states from nucleophilic attack by the bulk solvent. The conserved Ser 117-Tyr 118 dipeptide within the loop is brought to the active site, completing the ensemble of catalytic residues.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, Portland 97201-3098, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.19 kDa 
• Atom Count: 7,494 
• Modeled Residue Count: 876 
• Deposited Residue Count: 924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXANTHINE GUANINE XANTHINE PHOSPHORIBOSYLTRANSFERASE	A, B, C, D	231	Toxoplasma gondii	Mutation(s): 0  EC: 2.4.2.22 (UniProt), 2.4.2.8 (UniProt)
UniProt
Find proteins for Q26997 (Toxoplasma gondii) Explore Q26997  Go to UniProtKB:  Q26997

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.15	α = 90
b = 109.22	β = 111.8
c = 79.74	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-03 
Deposition Author(s): Schumacher, M.A., Carter, D., Roos, D., Ullman, B., Brennan, R.G.

Revision History  

• Version 1.0: 1997-12-03
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other