6HGR

Crystal Structure of Human APRT wild type in complex with IMP

6HGR の概要

• エントリーDOI: 10.2210/pdb6hgr/pdb
• 関連するPDBエントリー: 6FCH 6FCI 6FCL 6FD4 6FD5 6FD6 6HGP 6HGQ
• 分子名称: Adenine phosphoribosyltransferase, INOSINIC ACID (3 entities in total)
• 機能のキーワード: rossman fold, transferase
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 39551.32

構造登録者

Nioche, P.,Huyet, J.,Ozeir, M. (登録日: 2018-08-23, 公開日: 2019-07-31, 最終更新日: 2024-01-17)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.52 Å)