1D6N

TERNARY COMPLEX STRUCTURE OF HUMAN HGPRTASE, PRPP, MG2+, AND THE INHIBITOR HPP REVEALS THE INVOLVEMENT OF THE FLEXIBLE LOOP IN SUBSTRATE BINDING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Ternary complex structure of human HGPRTase, PRPP, Mg2+, and the inhibitor HPP reveals the involvement of the flexible loop in substrate binding.

Balendiran, G.K.Molina, J.A.Xu, Y.Torres-Martinez, J.Stevens, R.Focia, P.J.Eakin, A.E.Sacchettini, J.C.Craig III, S.P.

(1999) Protein Sci 8: 1023-1031

  • DOI: 10.1110/ps.8.5.1023
  • Primary Citation of Related Structures:  
    1D6N

  • PubMed Abstract: 
  • Site-directed mutagenesis was used to replace Lys68 of the human hypoxanthine phosphoribosyltransferase (HGPRTase) with alanine to exploit this less reactive form of the enzyme to gain additional insights into the structure activity relationship of HGPRTase ...

    Site-directed mutagenesis was used to replace Lys68 of the human hypoxanthine phosphoribosyltransferase (HGPRTase) with alanine to exploit this less reactive form of the enzyme to gain additional insights into the structure activity relationship of HGPRTase. Although this substitution resulted in only a minimal (one- to threefold) increase in the Km values for binding pyrophosphate or phosphoribosylpyrophosphate, the catalytic efficiencies (k(cat)/Km) of the forward and reverse reactions were more severely reduced (6- to 30-fold), and the mutant enzyme showed positive cooperativity in binding of alpha-D-5-phosphoribosyl-1-pyrophosphate (PRPP) and nucleotide. The K68A form of the human HGPRTase was cocrystallized with 7-hydroxy [4,3-d] pyrazolo pyrimidine (HPP) and Mg PRPP, and the refined structure reported. The PRPP molecule built into the [(Fo - Fc)phi(calc)] electron density shows atomic interactions between the Mg PRPP and enzyme residues in the pyrophosphate binding domain as well as in a long flexible loop (residues Leu101 to Gly111) that closes over the active site. Loop closure reveals the functional roles for the conserved SY dipeptide of the loop as well as the molecular basis for one form of gouty arthritis (S103R). In addition, the closed loop conformation provides structural information relevant to the mechanism of catalysis in human HGPRTase.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-2128, USA. balendra@reddrum.tamu.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)A, B214Homo sapiensMutation(s): 1 
Gene Names: HPRT1HPRT
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRP
Query on PRP

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
PPO
Query on PPO

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]3H-PYRAZOLO[4,3-D]PYRIMIDIN-7-OL
C5 H4 N4 O
OGCXIHWGXUQTCQ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPOKi :  31500   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.56α = 90
b = 65.85β = 90
c = 51.46γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1999-10-14 
  • Released Date: 1999-12-30 
  • Deposition Author(s): Balendiran, G.K.

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Database references
  • Version 1.5: 2018-01-31
    Changes: Database references
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary