6HGR

Crystal Structure of Human APRT wild type in complex with IMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Literature

Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.

Ozeir, M.Huyet, J.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.

(2019) J Biol Chem 294: 11980-11991

  • DOI: 10.1074/jbc.RA119.009087
  • Primary Citation of Related Structures:  
    6HGP, 6HGR, 6HGQ, 6HGS

  • PubMed Abstract: 
  • The reversible adenine phosphoribosyltransferase enzyme (APRT) is essential for purine homeostasis in prokaryotes and eukaryotes. In humans, APRT (hAPRT) is the only enzyme known to produce AMP in cells from dietary adenine. APRT can also process adenine analogs, which are involved in plant development or neuronal homeostasis ...

    The reversible adenine phosphoribosyltransferase enzyme (APRT) is essential for purine homeostasis in prokaryotes and eukaryotes. In humans, APRT (hAPRT) is the only enzyme known to produce AMP in cells from dietary adenine. APRT can also process adenine analogs, which are involved in plant development or neuronal homeostasis. However, the molecular mechanism underlying substrate specificity of APRT and catalysis in both directions of the reaction remains poorly understood. Here we present the crystal structures of hAPRT complexed to three cellular nucleotide analogs (hypoxanthine, IMP, and GMP) that we compare with the phosphate-bound enzyme. We established that binding to hAPRT is substrate shape-specific in the forward reaction, whereas it is base-specific in the reverse reaction. Furthermore, a quantum mechanics/molecular mechanics (QM/MM) analysis suggests that the forward reaction is mainly a nucleophilic substitution of type 2 (S N 2) with a mix of S N 1-type molecular mechanism. Based on our structural analysis, a magnesium-assisted S N 2-type mechanism would be involved in the reverse reaction. These results provide a framework for understanding the molecular mechanism and substrate discrimination in both directions by APRTs. This knowledge can play an instrumental role in the design of inhibitors, such as antiparasitic agents, or adenine-based substrates.


    Organizational Affiliation

    Université Paris Descartes, Structural and Molecular Analysis Platform, Paris, 75006, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenine phosphoribosyltransferaseA, B178Homo sapiensMutation(s): 0 
Gene Names: APRT
EC: 2.4.2.7
UniProt & NIH Common Fund Data Resources
Find proteins for P07741 (Homo sapiens)
Explore P07741 
Go to UniProtKB:  P07741
PHAROS:  P07741
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP (Subject of Investigation/LOI)
Query on IMP

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IMP Binding MOAD:  6HGR Ki: 3.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.585α = 76.43
b = 47.625β = 69.24
c = 47.846γ = 61.29
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata 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: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references