Crystal Structure of Human APRT wild type in complex with Adenine, PRPP and Mg2+

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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This is version 1.2 of the entry. See complete history


Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase.

Huyet, J.Ozeir, M.Burgevin, M.C.Pinson, B.Chesney, F.Remy, J.M.Siddiqi, A.R.Lupoli, R.Pinon, G.Saint-Marc, C.Gibert, J.F.Morales, R.Ceballos-Picot, I.Barouki, R.Daignan-Fornier, B.Olivier-Bandini, A.Auge, F.Nioche, P.

(2018) Cell Chem Biol 25: 666-676.e4

  • DOI: https://doi.org/10.1016/j.chembiol.2018.02.011
  • Primary Citation of Related Structures:  
    6FCH, 6FCI, 6FCL, 6FD4, 6FD5, 6FD6

  • PubMed Abstract: 

    Phosphoribosyltransferases catalyze the displacement of a PRPP α-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.

  • Organizational Affiliation

    Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenine phosphoribosyltransferase
A, B, C, D
179Homo sapiensMutation(s): 0 
Gene Names: APRT
UniProt & NIH Common Fund Data Resources
Find proteins for P07741 (Homo sapiens)
Explore P07741 
Go to UniProtKB:  P07741
PHAROS:  P07741
GTEx:  ENSG00000198931 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07741
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PRP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
C5 H13 O14 P3
Query on ADE

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
C5 H5 N5
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.71α = 90.05
b = 49.79β = 93.48
c = 71.49γ = 101.91
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary