Crystal structure of human nicotinic acid phosphoribosyltransferase

Ada Serena Marletta; Alberto Massarotti; Giuseppe Orsomando; Giulio Magni; Menico Rizzi; Silvia Garavaglia

doi:10.1016/j.fob.2015.05.002

Crystal structure of human nicotinic acid phosphoribosyltransferase

FEBS Open Bio. 2015 May 7:5:419-28. doi: 10.1016/j.fob.2015.05.002. eCollection 2015.

Authors

Ada Serena Marletta¹, Alberto Massarotti¹, Giuseppe Orsomando², Giulio Magni², Menico Rizzi¹, Silvia Garavaglia¹

Affiliations

¹ Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
² Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Via Ranieri 67, 60131 Ancona, Italy.

Abstract

Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss-Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent.

Keywords: FK866; NAD biosynthesis; NAD, nicotinamide adenine dinucleotide; NMN, nicotinamide mononucleotide; NMNAT, nicotinamide mononucleotide adenylyltransferase; Na, nicotinic acid; NaAD, nicotinic acid dinucleotide; NaMN, nicotinic acid mononucleotide; NaPRTase, nicotinic acid phosphoribosyltransferase; NamR, nicotinamide riboside; Nicotinic Acid; PRPP, 5-phosphoribosyl-1-pyrophosphate; Phosphoribosyltransferase; Preiss–Handler pathway; QA, quinolinic acid; Recycling NAD pathway.