6HGQ

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

Summary for 6HGQ

• Entry DOI: 10.2210/pdb6hgq/pdb
• Related: 6FCH 6FCI 6FCL 6FD4 6FD5 6FD6 6HPG
• Descriptor: Adenine phosphoribosyltransferase, GLYCEROL, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: rossman fold, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 80288.16

Authors

Nioche, P.,Huyet, J.,Ozeir, M. (deposition date: 2018-08-23, release date: 2019-07-31, Last modification date: 2024-01-17)

Primary citation

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.
Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
J.Biol.Chem., 294:11980-11991, 2019

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. 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 (S2) with a mix of S1-type molecular mechanism. Based on our structural analysis, a magnesium-assisted S2-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.

PubMed: 31160323
DOI: 10.1074/jbc.RA119.009087

Experimental method

X-RAY DIFFRACTION (1.9 Å)