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Crystal structure of human nicotinic acid phosphoribosyltransferase.

Marletta AS, Massarotti A, Orsomando G, Magni G, Rizzi M, Garavaglia S - FEBS Open Bio (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, 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.

No MeSH data available.


Related in: MedlinePlus

Metabolic pathway for NAD(P) biosynthesis in humans. NAD biosynthesis starting from four different sources of the pyridine ring, namely QA, Na, Nam and NamR, through four distinct ways. The de novo pathway (blue dotted line) allows NAD biosynthesis starting from QA derived from Trp and Na is processed to NAD through the Preiss–Handler pathway enzymes (green dotted line). Through a salvage pathway Nam and NamR can be transformed in NMN by NMPRTase and NamRKinase respectively. Finally, some of the cellular NAD can be converted into NADP by NAD kinase (EC 2.7.1.23). QAPRTase, quinolinic acid phosphoribosyltransferase (EC 2.4.2.19); NaPRTase, nicotinic acid phosphoribosyltransferase (EC 2.4.2.11); NMPRTase, nicotinamide phosphoribosyltransferase (EC 2.4.2.12); NamRKinase, nicotinamide riboside kinase (EC 2.7.1.22); NMNAT nicotinamide mononucleotide adenylyltransferase (EC 2.7.7.1); NADS, NAD synthetase (EC 6.3.5.1).
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f0005: Metabolic pathway for NAD(P) biosynthesis in humans. NAD biosynthesis starting from four different sources of the pyridine ring, namely QA, Na, Nam and NamR, through four distinct ways. The de novo pathway (blue dotted line) allows NAD biosynthesis starting from QA derived from Trp and Na is processed to NAD through the Preiss–Handler pathway enzymes (green dotted line). Through a salvage pathway Nam and NamR can be transformed in NMN by NMPRTase and NamRKinase respectively. Finally, some of the cellular NAD can be converted into NADP by NAD kinase (EC 2.7.1.23). QAPRTase, quinolinic acid phosphoribosyltransferase (EC 2.4.2.19); NaPRTase, nicotinic acid phosphoribosyltransferase (EC 2.4.2.11); NMPRTase, nicotinamide phosphoribosyltransferase (EC 2.4.2.12); NamRKinase, nicotinamide riboside kinase (EC 2.7.1.22); NMNAT nicotinamide mononucleotide adenylyltransferase (EC 2.7.7.1); NADS, NAD synthetase (EC 6.3.5.1).

Mentions: Nicotinamide adenine dinucleotide (NAD) and its phosphorylated form (NADP) are essential ubiquitous coenzymes playing fundamental roles in living cells. Beyond renown redox roles in energy metabolism, NAD(P) is also intimately involved in signaling pathways through a number of consuming reactions that underscore a wealth of physiopathological conditions [1–4]. Indeed, the NAD(P) derivatives nicotinic acid adenine dinucleotide phosphate (NaADP) and cyclic ADP-ribose (cADPR) are among the most potent intracellular calcium-mobilizing agents [4,5]. Moreover, NAD is the substrate for poly(ADP-ribosyl)ation reactions that in higher eukaryotes regulate chromatin function and gene expression, as well as for mono(ADP-ribosyl)ation modifications of target proteins in both mammalian and prokaryotic cells [4]. In all organisms, NAD can also be consumed by important regulatory enzymes, named sirtuins, that catalyze NAD-dependent deacetylation reactions of target proteins [6]. Clearly, physiological NAD depletion caused by overall NAD-consuming reactions necessitates permanent regeneration of this cofactor. Therefore NAD biosynthesis appears of therapeutically value for the treatment of pathological conditions arising from severe altering of NAD(P) homeostasis like in the case of neurological, neoplastic, and infectious disorders, as well as in the process of ageing [1,3,7–10]. Based on current knowledge, four different substrates can be used as a source of the pyridine ring in the NAD biosynthesis: quinolinic acid (QA) in the de novo pathway; nicotinic acid (Na), nicotinamide (Nam) and nicotinamide riboside (NamR) in the salvage pathways. While this latter compound is phosphorylated by action of an ATP-dependent kinase activity [11], the three other precursors, QA, Na and Nam, can be individually transferred to a phosphoribosyl pyrophosphate moiety (PRPP) by respective phosphoribosyl-transferase activities [12]. The resulting mononucleotide products, nicotinic acid mononucleotide (NaMN) and nicotinamide mononucleotide (NMN), are then converted to dinucleotide forms, i.e. nicotinic acid dinucleotide (NaAD) and NAD, by action of a single enzymatic activity represented by nicotinamide mononucleotide adenylyltransferase (NMNAT) [13,14]. NaAD is finally amidated to NAD by a NAD synthetase activity (Fig. 1) [7,12,15].


Crystal structure of human nicotinic acid phosphoribosyltransferase.

Marletta AS, Massarotti A, Orsomando G, Magni G, Rizzi M, Garavaglia S - FEBS Open Bio (2015)

Metabolic pathway for NAD(P) biosynthesis in humans. NAD biosynthesis starting from four different sources of the pyridine ring, namely QA, Na, Nam and NamR, through four distinct ways. The de novo pathway (blue dotted line) allows NAD biosynthesis starting from QA derived from Trp and Na is processed to NAD through the Preiss–Handler pathway enzymes (green dotted line). Through a salvage pathway Nam and NamR can be transformed in NMN by NMPRTase and NamRKinase respectively. Finally, some of the cellular NAD can be converted into NADP by NAD kinase (EC 2.7.1.23). QAPRTase, quinolinic acid phosphoribosyltransferase (EC 2.4.2.19); NaPRTase, nicotinic acid phosphoribosyltransferase (EC 2.4.2.11); NMPRTase, nicotinamide phosphoribosyltransferase (EC 2.4.2.12); NamRKinase, nicotinamide riboside kinase (EC 2.7.1.22); NMNAT nicotinamide mononucleotide adenylyltransferase (EC 2.7.7.1); NADS, NAD synthetase (EC 6.3.5.1).
© Copyright Policy - CC BY
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4442680&req=5

f0005: Metabolic pathway for NAD(P) biosynthesis in humans. NAD biosynthesis starting from four different sources of the pyridine ring, namely QA, Na, Nam and NamR, through four distinct ways. The de novo pathway (blue dotted line) allows NAD biosynthesis starting from QA derived from Trp and Na is processed to NAD through the Preiss–Handler pathway enzymes (green dotted line). Through a salvage pathway Nam and NamR can be transformed in NMN by NMPRTase and NamRKinase respectively. Finally, some of the cellular NAD can be converted into NADP by NAD kinase (EC 2.7.1.23). QAPRTase, quinolinic acid phosphoribosyltransferase (EC 2.4.2.19); NaPRTase, nicotinic acid phosphoribosyltransferase (EC 2.4.2.11); NMPRTase, nicotinamide phosphoribosyltransferase (EC 2.4.2.12); NamRKinase, nicotinamide riboside kinase (EC 2.7.1.22); NMNAT nicotinamide mononucleotide adenylyltransferase (EC 2.7.7.1); NADS, NAD synthetase (EC 6.3.5.1).
Mentions: Nicotinamide adenine dinucleotide (NAD) and its phosphorylated form (NADP) are essential ubiquitous coenzymes playing fundamental roles in living cells. Beyond renown redox roles in energy metabolism, NAD(P) is also intimately involved in signaling pathways through a number of consuming reactions that underscore a wealth of physiopathological conditions [1–4]. Indeed, the NAD(P) derivatives nicotinic acid adenine dinucleotide phosphate (NaADP) and cyclic ADP-ribose (cADPR) are among the most potent intracellular calcium-mobilizing agents [4,5]. Moreover, NAD is the substrate for poly(ADP-ribosyl)ation reactions that in higher eukaryotes regulate chromatin function and gene expression, as well as for mono(ADP-ribosyl)ation modifications of target proteins in both mammalian and prokaryotic cells [4]. In all organisms, NAD can also be consumed by important regulatory enzymes, named sirtuins, that catalyze NAD-dependent deacetylation reactions of target proteins [6]. Clearly, physiological NAD depletion caused by overall NAD-consuming reactions necessitates permanent regeneration of this cofactor. Therefore NAD biosynthesis appears of therapeutically value for the treatment of pathological conditions arising from severe altering of NAD(P) homeostasis like in the case of neurological, neoplastic, and infectious disorders, as well as in the process of ageing [1,3,7–10]. Based on current knowledge, four different substrates can be used as a source of the pyridine ring in the NAD biosynthesis: quinolinic acid (QA) in the de novo pathway; nicotinic acid (Na), nicotinamide (Nam) and nicotinamide riboside (NamR) in the salvage pathways. While this latter compound is phosphorylated by action of an ATP-dependent kinase activity [11], the three other precursors, QA, Na and Nam, can be individually transferred to a phosphoribosyl pyrophosphate moiety (PRPP) by respective phosphoribosyl-transferase activities [12]. The resulting mononucleotide products, nicotinic acid mononucleotide (NaMN) and nicotinamide mononucleotide (NMN), are then converted to dinucleotide forms, i.e. nicotinic acid dinucleotide (NaAD) and NAD, by action of a single enzymatic activity represented by nicotinamide mononucleotide adenylyltransferase (NMNAT) [13,14]. NaAD is finally amidated to NAD by a NAD synthetase activity (Fig. 1) [7,12,15].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, 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.

No MeSH data available.


Related in: MedlinePlus