1BZY | pdb_00001bzy

HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1BZY/pdb

• Classification: PHOSPHORIBOSYLTRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-11-05 Released: 1999-06-22 
• Deposition Author(s): Shi, W., Li, C., Tyler, P.C., Furneaux, R.H., Grubmeyer, C., Schramm, V.L., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor) 
• R-Value Work: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor.

Shi, W., Li, C.M., Tyler, P.C., Furneaux, R.H., Grubmeyer, C., Schramm, V.L., Almo, S.C.

(1999) Nat Struct Biol 6: 588-593

• PubMed: 10360366 
• DOI: https://doi.org/10.1038/9376
• Primary Citation Related Structures: 
  1BZY


• PubMed Abstract: 
  

  The structure of human HGPRT bound to the transition-state analog immucillinGP and Mg2+-pyrophosphate has been determined to 2.0 A resolution. ImmucillinGP was designed as a stable analog with the stereoelectronic features of the transition state. Bound inhibitor at the catalytic site indicates that the oxocarbenium ion of the transition state is stabilized by neighboring-group participation from MgPPi and O5'. A short hydrogen bond forms between Asp 137 and the purine ring analog. Two Mg2+ ions sandwich the pyrophosphate and contact both hydroxyls of the ribosyl analog. The transition-state analog is shielded from bulk solvent by a catalytic loop that moves approximately 25 A to cover the active site and becomes an ordered antiparallel beta-sheet.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, 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: 100.27 kDa 
• Atom Count: 7,216 
• Modeled Residue Count: 856 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE	A, B, C, D	217	Homo sapiens	Mutation(s): 0  EC: 2.4.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for P00492 (Homo sapiens) Explore P00492  Go to UniProtKB:  P00492
PHAROS:  P00492 GTEx:  ENSG00000165704

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMU	G [auth A], K [auth B], O [auth C], S [auth D]	PHOSPHORIC ACID MONO-[5-(2-AMINO-4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXY-PYRROLIDIN-2-YLMETHYL] ESTER C11 H16 N5 O7 P IQLBECLICFDTTF-PVEDRDFWSA-N
POP	H [auth A], L [auth B], P [auth C], T [auth D]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor) 
• R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.96	α = 90
b = 102.01	β = 90
c = 144.27	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-22 
Deposition Author(s): Shi, W., Li, C., Tyler, P.C., Furneaux, R.H., Grubmeyer, C., Schramm, V.L., Almo, S.C.

Revision History  

• Version 1.0: 1999-06-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection