{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL2311140001?filename=NADnet_Bcell_model_L2V4_Nov2024.xml"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Adithya Chedere"],"curationStatus":["Non-curated"],"modellingApproach":["ordinary differential equation model"],"levelVersion":["L2V4"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL2311140001"],"publication_pubmed":["39661983"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["DeboraSoncini2024   NAD Biosynthesis in Human B Lymphocytes,ODE model"],"publication_year":["2024"],"submissionId":["MODEL2311140001"],"publication_authors":["Adithya Chedere, Debora Soncini, Nagasuma Chandra, MICHELE CEA"],"first_author":["Adithya Chedere"],"publication":["39661983,\n                            Elevated levels of the nicotinamide adenine dinucleotide (NAD+)-generating enzyme nicotinamide phosphoribosyltransferase (NAMPT) are a common feature across numerous cancer types. Accordingly, we previously reported pervasive NAD+ dysregulation in Multiple Myeloma (MM) cells in association with upregulated NAMPT expression. Unfortunately, albeit being effective in preclinical models of cancer, NAMPT inhibition has proven ineffective in clinical trials due to the existence of alternative NAD+ production routes utilizing NAD+ precursors other than nicotinamide. Here, by leveraging mathematical modelling approaches integrated with transcriptome data, we defined the specific NAD+ landscape of MM cells and established that the Preiss-Handler pathway for NAD+-biosynthesis, which utilizes nicotinic acid as a precursor, supports NAD+ synthesis in MM cells via its key enzyme nicotinate phosphoribosyltransferase (NAPRT). Accordingly, we found that NAPRT confers resistance to NAD+ -depleting agents. Transcriptomic, metabolic, and bioenergetic profiling of NAPRT knock-out (KO) MM cells showed these to have weakened endogenous antioxidant defenses, increased propensity to oxidative stress, and enhanced genomic instability. Concomitant NAMPT inhibition further compounded the effects of NAPRT KO, effectively sensitizing MM cells to the chemotherapeutic drug, melphalan; NAPRT added-back fully rescues these phenotypes. Overall, our results propose comprehensive NAD+ biosynthesis inhibition, through simultaneously targeting NAMPT and NAPRT, as a promising strategy to be tested in randomized clinical trials involving transplant-eligible MM patients, especially those with more aggressive disease.. null, null.\n                            Indian Institute of Science Bangalore, Bengaluru, India.\nUniversity of Genoa, Genoa, Italy."],"submitter_mail":["adithyachedere@gmail.com"],"submitter_affiliation":["Indian Institute of Science Bangalore"],"pubmed_abstract":["Nicotinate phosphoribosyltransferase (NaPRT, EC 2.4.2.11) catalyzes the conversion of nicotinate (Na) to nicotinate mononucleotide, the first reaction of the Preiss-Handler pathway for the biosynthesis of NAD(+). Even though NaPRT activity has been described to be responsible for the ability of Na to increase NAD(+) levels in human cells more effectively than nicotinamide (Nam), so far a limited number of studies on the human NaPRT have appeared. Here, extensive characterization of a recombinant human NaPRT is reported. We determined its major kinetic parameters and assayed the influence of different compounds on its enzymatic activity. In particular, ATP showed an apparent dual stimulation/inhibition effect at low/high substrates saturation, respectively, consistent with a negative cooperativity model, whereas inorganic phosphate was found to act as an activator. Among other metabolites assayed, including nucleotides, nucleosides, and intermediates of carbohydrates metabolism, some showed inhibitory properties, i.e. CoA, several acyl-CoAs, glyceraldehyde 3-phosphate, phosphoenolpyruvate, and fructose 1,6-bisphosphate, whereas dihydroxyacetone phosphate and pyruvate exerted a stimulatory effect. Furthermore, in light of the absence of crystallographic data, we performed homology modeling to predict the protein three-dimensional structure, and molecular docking simulations to identify residues involved in the recognition and stabilization of several ligands. Most of these residues resulted universally conserved among NaPRTs, and, in this study, their importance for enzyme activity was validated through site-directed mutagenesis.","Recombinant human kynureninase (L-kynurenine hydrolase, EC 3.7.1.3) was purified to homogeneity (60-fold) from Spodoptera frugiperda (Sf9) cells infected with baculovirus containing the kynureninase gene. The purification protocol comprised ammonium sulfate precipitation and several chromatographic steps, including DEAE-Sepharose CL-6B, hydroxyapatite, strong anionic and cationic separations. The purity of the enzyme was determined by SDS/PAGE, and the molecular mass verified by MALDI-TOF MS. The monomeric molecular mass of 52.4 kDa determined was > 99.99% of the predicted molecular mass. A UV absorption spectrum of the holoenzyme resulted in a peak at 432 nm. The optimum pH was 8.25 and the enzyme displayed a strong dependence on the ionic strength of the buffer for optimum activity. This cloned enzyme was highly specific for 3-hydroxykynurenine (Km = 3.0 microm +/- 0.10) and was inhibited by L-kynurenine (Ki = 20 microm), d-kynurenine (Ki = 12 microm) and a synthetic substrate analogue D,L-3,7-dihydroxydesaminokynurenine (Ki = 100 nm). The activity/concentration profile for kynureninase from this source was sigmoidal in all instances. There appeared to be partial inhibition by substrate, and excess pyridoxal 5'-phosphate was found to be inhibitory.","The leucoyte surface antigen CD38 has been shown to be an ecto-enzyme with multiple catalytic activities. It is principally a NAD+ glycohydrolase that transforms NAD+ into ADP-ribose and nicotinamide. CD38 is also able to produce small amounts of cyclic ADP-ribose (ADP-ribosyl cyclase activity) and to hydrolyse this cyclic metabolite into ADP-ribose (cyclic ADP-ribose hydrolase activity). To classify CD38 among the enzymes that transfer the ADP-ribosyl moiety of NAD+ to a variety of acceptors, we have investigated its substrate specificity and some characteristics of its kinetic and molecular mechanisms. We find that CD38-catalysed cleavage of the nicotinamide-ribose bond results in the formation of an E.ADP-ribosyl intermediary complex, which is common to all reaction pathways; this intermediate reacts (1) with acceptors such as water (hydrolysis), methanol (methanolysis) or pyridine (transglycosidation), and (2) intramolecularly, yielding cyclic ADP-ribose with a low efficiency. This reaction scheme is also followed when using nicotinamide guanine dinucleotide as an alternative substrate; in this case, however, the cyclization process is highly favoured. The results obtained here are not compatible with the prevailing model for the mode of action of CD38, according to which this enzyme produces first cyclic ADP-ribose which is then immediately hydrolysed into ADP-ribose (i.e. sequential ADP-ribosyl cyclase and cyclic ADP-ribose hydrolase activities). We show instead that the cyclic metabolite was a reaction product of CD38 rather than an obligatory reaction intermediate during the glycohydrolase activity. Altogether our results lead to the conclusion that CD38 is an authentic 'classical' NAD(P)+ glycohydrolase (EC 3.2.2.6).","The kinetic properties of highly purified human placental cytoplasmic 5'-nucleotidase were investigated. Initial velocity studies gave Michaelis constants for AMP, IMP, and CMP of 18, 30, and 2.2 microM, respectively. The enzyme shows the following relative Vmax values: CMP greater than UMP greater than dUMP greater than GMP greater than AMP greater than dCMP greater than IMP. The activity was magnesium-dependent, and this cation binds sequentially with a Km of 14 microM for AMP and an apparent Km of 6 mM for magnesium. A large variety of purine, pyrimidine, and pyridine compounds exert an inhibitory effect on enzyme activity. IMP, GMP, and NADH produce almost 100% inhibition at 1.0 mM. Nucleoside di- and triphosphates are potent inhibitors. ATP and ADP are competitive inhibitors with respect to AMP and IMP as substrates with Ki values of 100 and 15 microM, respectively. Inorganic phosphate is a noncompetitive inhibitor with Ki values of 19 and 43 mM. Nucleosides and other compounds studied produce only a modest decrease of enzyme activity at 1 mM. Our findings suggest that the enzyme is regulated under physiological conditions by the concentrations of magnesium, nucleoside 5'-monophosphates, and nucleoside di- and triphosphates. The nucleotide pool concentration regulates the enzyme possibly by a mechanism of heterogeneous metabolic pool inhibition. These properties of human placental cytoplasmic 5'-nucleotidase may be related to the control of nucleotide degradation in vivo.","3-Hydroxyanthranilic acid 3,4-dioxygenase (EC 1.13.11.6; HADO) was purified to homogeneity from beef liver with the use of two dye columns (Cibacron Blue and Reactive Green 19) and hydroxyapatite. Two active peaks of enzyme were isolated from the hydroxyapatite column or by nondenaturing chromatofocusing of the enzyme prior to hydroxyapatite. The two active forms moved with different electrophoretic mobilities when they were subjected to nondenaturing polyacrylamide gel electrophoresis, regardless of the method of isolation. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), however, these species had apparently identical mobilities and have, therefore, close molecular mass. Analysis by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry gave them a molecular mass of 32566 and 32515 Da, respectively, for the species with apparent pI values of 5.60 and 4.98, respectively, suggesting that they differ only in the presence or absence of the iron cofactor. The N-terminal group appears to be blocked as no amino-terminal sequence was possible from direct Edman degradation. A new inactivator of the enzyme, 6-chloro-3-hydroxyanthranilic acid, was synthesized and was shown to exhibit time-dependent inactivation. A possible mechanism for inactivation is proposed.","Arylformamidase (AFMID) is the second enzyme of the kynurenine pathway metabolizing tryptophan to nicotinic acid and nicotinamide adenine dinucleotide cofactors. Inhibition of AFMID by organophosphorus insecticides in developing chicken embryos is correlated with lowered NAD levels and severe teratogenesis. The cDNA sequence previously identified for mouse liver AFMID (AF399717) (MW 34229) was cloned and expressed in Escherichia coli. Residues identified as potential catalytic triad members (S162, D247, and H279) through sequence motif and homology modeling were mutated to alanine to probe their contributions to enzyme activity. The wild-type and mutant AFMIDs were expressed as amino terminal 6 x His-tagged recombinant proteins to facilitate purification. Three chromatography steps isolated highly purified proteins for enzyme activity comparisons. Expressed AFMID showed high activity, 42+/-1 micromol/min/mg protein, for its natural substrate, N-formyl-l-kynurenine. The same K(m) (0.18--0.19 mM) was observed for expressed and native cytosolic AFMID. The single mutants (S162A, D247A, and H279A) lost essentially all (>99%) activity. The predicted catalytic triad of S162, D247, and H279 is therefore confirmed by site-directed mutagenesis.","NAD kinase (NADK, EC 2.7.1.23) is the sole NADP(+)-biosynthetic enzyme that catalyzes phosphorylation of NAD(+) to yield NADP(+) using ATP as a phosphoryl donor, and thus, plays a vital role in the cell and represents a potentially powerful antimicrobial drug target. Although methods for expression and purification of human NADK have been previously established (Lerner et al. Biochem Biophys Res Commun 288:69-74, 2001), the purification procedure could be significantly improved. In this study, we improved the method for expression and purification of human NADK in Escherichia coli and obtained a purified homogeneous enzyme only through heat treatment and single column chromatography. Using the purified human NADK, we revealed a sigmoidal kinetic behavior toward ATP and the inhibitory effects of NADPH and NADH, but not of NADP(+), on the catalytic activity of the enzyme. These inhibitory effects provide insight into the regulation of intracellular NADPH synthesis. Furthermore, these attributes may provide a clue to design a novel drug against Mycobacterium tuberculosis in which this bacterial NADK is potently inhibited by NADP(+).","The eukaryotic nicotinamide riboside kinase (Nrk) pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+) by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.","The ADP-ribosyl moiety of NAD+ is consumed in reactions catalyzed by three classes of enzymes: poly(ADP-ribose) polymerase, protein mono(ADP-ribosyl)transferases, and NAD+ glycohydrolases. In this study, we have evaluated the selectivity of compounds originally identified as inhibitors of poly(ADP-ribose) polymerase on members of the three classes of enzymes. The 50% inhibitory concentration (IC50) of more than 20 compounds was determined in vitro for both poly(ADP-ribose) polymerase and mono(ADP-ribosyl)transferase A in an assay containing 300 microM NAD+. Of the compounds tested, benzamide was the most potent inhibitor of poly(ADP-ribose) polymerase with an IC50 of 3.3 microM. The IC50 for benzamide for mono(ADP-ribosyl)transferase A was 4.1 mM, and similar values were observed for four additional cellular mono(ADP-ribosyl)transferases. The IC50 for NAD+ glycohydrolase for benzamide was approximately 40 mM. For seven of the best inhibitors, inhibition of poly(ADP-ribose) polymerase in intact C3H1OT1/2 cells was studied as a function of the inhibitor concentration of the culture medium, and the concentration for 50% inhibition (culture medium IC50) was determined. Culture medium IC50 values for benzamide and its derivatives were very similar to in vitro IC50 values. For other inhibitors, such as nicotinamide, 5-methyl-nicotinamide, and 5-bromodeoxyuridine, culture medium IC50 values were 3-5-fold higher than in vitro IC50 values. These results suggest that micromolar levels of the benzamides in the culture medium should allow selective inhibition of poly(ADP-ribose) metabolism in intact cells. Furthermore, comparative quantitative inhibition studies should prove useful for assigning the biological effects of these inhibitors as an effect on either poly(ADP-ribose) or mono(ADP-ribose) metabolism.","Human nicotinamide phosphoribosyltransferase (NAMPT, EC 2.4.2.12) catalyzes the reversible synthesis of nicotinamide mononucleotide (NMN) and inorganic pyrophosphate (PP i) from nicotinamide (NAM) and alpha- d-5-phosphoribosyl-1-pyrophosphate (PRPP). NAMPT, by capturing the energy provided by its facultative ATPase activity, allows the production of NMN at product:substrate ratios thermodynamically forbidden in the absence of ATP. With ATP hydrolysis coupled to NMN synthesis, the catalytic efficiency of the system is improved 1100-fold, substrate affinity dramatically increases ( K m (NAM) from 855 to 5 nM), and the K eq shifts -2.1 kcal/mol toward NMN formation. ADP-ATP isotopic exchange experiments support the formation of a high-energy phosphorylated intermediate (phospho-H247) as the mechanism for altered catalytic efficiency during ATP hydrolysis. NAMPT captures only a small portion of the energy generated by ATP hydrolysis to shift the dynamic chemical equilibrium. Although the weak energetic coupling of ATP hydrolysis appears to be a nonoptimized enzymatic function, closer analysis of this remarkable protein reveals an enzyme designed to capture NAM with high efficiency at the expense of ATP hydrolysis. NMN is a rate-limiting precursor for recycling to the essential regulatory cofactor, nicotinamide adenine dinucleotide (NAD (+)). NMN synthesis by NAMPT is powerfully inhibited by both NAD (+) ( K i = 0.14 muM) and NADH ( K i = 0.22 muM), an apparent regulatory feedback mechanism.","The human NUDT12 Nudix hydrolase has been expressed in insect cells from a baculovirus vector as a His-tagged recombinant protein. In vitro, it efficiently hydrolyses NAD(P)H to NMNH and AMP (2',5'-ADP), and diadenosine diphosphate to AMP. It also has activity towards NAD(P)(+), ADP-ribose and diadenosine triphosphate. K (m) values for NADH, NADPH and NAD(+) are 11, 16 and 190 microM and k (cat) values are 11, 16 and 10.5 s(-1) respectively. Thus, like other NADH diphosphatases of the Nudix family, NUDT12 has a marked substrate preference for the reduced nicotinamide nucleotides. Optimal activity was supported by 50 microM Mn(2+) ions in vitro, with 3-fold lower activity at 0.4 mM Mg(2+). Expression of NUDT12 as a C-terminal fusion to green fluorescent protein revealed that it was targeted to peroxisomes by the C-terminal tripeptide PNL acting as a novel type 1 peroxisomal targeting signal. Deletion of PNL resulted in diffuse cellular fluorescence. In addition, C-terminal, but not N-terminal, fusions with or without the PNL signal accumulated in large, unidentified cytoplasmic structures. NUDT12 may act to regulate the concentration of peroxisomal nicotinamide nucleotide cofactors required for oxidative metabolism in this organelle.","Human indoleamine 2,3-dioxygenase (hIDO) is an intracellular heme-containing enzyme, which catalyzes the initial and rate-determining step of L-tryptophan (L-Trp) metabolism via the kynurenine pathway. Due to its immunosuppressive function, hIDO has been recognized as an important drug target for cancer. Here we report evidence supporting the presence of an inhibitory substrate binding site (S(i)) in hIDO that is capable of binding molecules with a wide variety of structures, including substrates (L-Trp and 1-methyl-L-tryptophan), an effector (3-indole ethanol), and an uncompetitive inhibitor (Mitomycin C). The data offer useful guidelines for future development of more potent hIDO inhibitors; they also call for the re-evaluation of the action mechanism of Mitomycin C (MtoC), a widely used antitumor chemotherapeutic agent.","Kynurenine 3-monooxygenase (KMO) is an NADPH-dependent flavoprotein hydroxylase that catalyzes the conversion of l-Kynurenine (L-Kyn) to 3-hydroxykynurenine (3OHKyn). The reaction is central to the tryptophan degradative pathway and takes place within microglial cells defining cellular concentrations of the N-methyl-d-aspatate (NMDA) receptor agonist quinolinate and antagonist kynurenate. The influence over the cellular concentrations of these NMDA receptor effectors makes KMO an attractive target for the treatment of ischemic stroke. Pseudomonas fluorescens str 17400, expresses five activities of tryptophan catabolism including that of KMO. The KMO gene from P. fluorescens was cloned into the pET-17b plasmid using incorporated NdeI and XhoI restriction sites. This construct yielded PfKMO to 20% of total cell protein after 12h of expression at 22 degrees C without induction by isopropyl-beta-thiogalactopyranoside (IPTG). The enzyme could be readily purified using ammonium sulfate fractionation and ion exchange chromatography, resulting in pure KMO with a turnover number of 5.0 s(-1). PfKMO activity was dependent on the reduction state of the enzyme. Preparation and storage benefited from the presence of a reductant such as dithiothreitol or beta-mercaptoethanol. The loss of activity was found to be directly related to the oxidation of thiols as measured by dinitrothiobenzoate assay. Steady-state assays monitoring the consumption of dioxygen were used to measure apparent kinetic parameters and ligand perturbation of flavin fluorescence was used to determine a Kd value for both L-Kyn and the inhibitor m-nitrobenzoylalanine. PfKMO is offered as prototypical bacterial form of the enzyme to serve as a viable platform on which to base future KMO studies.","Initial-rate and product inhibition studies revealed distinctive ordered ternary complex kinetic mechanisms, substrate specificities, and metal ion preferences for the three isozymes of human nicotinamide mononucleotide adenylyl-transferase (NMNAT, EC 2.7.7.1). ATP binds before NMN with nuclear isozyme NMNAT1 and Golgi apparatus NMNAT2, but the opposite order is observed with the mitochondrial isozyme NMNAT3. Only the latter utilizes ITP efficiently in place of ATP, and while NMNH conversion to NADH by NMNAT1 and NMNAT3 occurs at similar rates, conversion by NMNAT2 is much slower. These isozymes can also be discriminated by their action on tiazofurin monophosphate (TrMP), a metabolite of the antineoplastic prodrug tiazofurin. Our finding that TrMP is only a substrate with NMNAT1 and NMNAT3 reveals for the first time an organelle selectivity in the metabolism of this important drug. In search of additional ways to discriminate these isozymes, we synthesized and tested the P1-(nicotinamide/nicotinate-riboside-5')-Pn-(adenosine-5') dinucleotides Np3AD, Np4AD, and Nap4AD. In addition to being highly effective inhibitors, these multisubstrate geometric inhibitors gave inhibition patterns that are consistent with the aforementioned isozyme differences in substrate binding order. Distinctive differences in their substrate specificity and metal ion selectivity also permitted us to quantify individual isozyme contributions to NAD+ formation in human cell extracts.","The structures of beta-methylenethiazole-4-carboxamide adenine dinucleotide (TAD), NAD(+), and NADH as bound to ecto-ADP-ribosyltransferase 2.2 from rat and to its mutants E189I and E189A, respectively, have been established. The positions and conformations of NAD(+) and its analogues agree in general with those in other ADP-ribosyltransferases. The kinetic constants for NAD(+) hydrolysis were determined by RP-HPLC. The specific activity amounts to 26 units/mg, which is 6000-fold higher than a previously reported rate and 500-fold higher than the hydrolysis rates of other ADP-ribosyltransferases, confirming that hydrolysis is the major function of this enzyme. On the basis of structures and mutant activities, a catalytic mechanism is proposed. The known auto-ADP-ribosylation of the enzyme at the suggested position R184 is supported by one of the crystal structures where the nucleophile position is occupied by an Neta atom of this arginine which in turn is backed up by the base E159.","KAT (kynurenine aminotransferase) II is a primary enzyme in the brain for catalysing the transamination of kynurenine to KYNA (kynurenic acid). KYNA is the only known endogenous antagonist of the N-methyl-D-aspartate receptor. The enzyme also catalyses the transamination of aminoadipate to alpha-oxoadipate; therefore it was initially named AADAT (aminoadipate aminotransferase). As an endotoxin, aminoadipate influences various elements of glutamatergic neurotransmission and kills primary astrocytes in the brain. A number of studies dealing with the biochemical and functional characteristics of this enzyme exist in the literature, but a systematic assessment of KAT II addressing its substrate profile and kinetic properties has not been performed. The present study examines the biochemical and structural characterization of a human KAT II/AADAT. Substrate screening of human KAT II revealed that the enzyme has a very broad substrate specificity, is capable of catalysing the transamination of 16 out of 24 tested amino acids and could utilize all 16 tested alpha-oxo acids as amino-group acceptors. Kinetic analysis of human KAT II demonstrated its catalytic efficiency for individual amino-group donors and acceptors, providing information as to its preferred substrate affinity. Structural analysis of the human KAT II complex with alpha-oxoglutaric acid revealed a conformational change of an N-terminal fraction, residues 15-33, that is able to adapt to different substrate sizes, which provides a structural basis for its broad substrate specificity.","DNA damage induced in higher eukaryotes by alkylating agents, oxidants or ionising radiation triggers the synthesis of protein-conjugated poly(ADP-ribose) catalysed by poly(ADP-ribose) polymerase-1 (PARP-1). Previously, cellular poly(ADP-ribosyl)ation capacity has been shown to correlate positively with the life span of mammalian species [Proc. Natl. Acad. Sci. USA 89 (1992) 11,759-11,763]. Here, we have tested whether this correlation results from differences in kinetic parameters of the enzymatic activity of PARP-1. We therefore compared recombinant enzymes, expressed in a baculovirus system, from rat and man as two mammalian species with extremely divergent life span. In standard activity assays performed in the presence of histones as poly(ADP-ribose) acceptors both enzymes showed saturation kinetics with [NAD(+)]. The kinetic parameters (k(cat), k(m) and k(cat)/k(m)) of the two enzymes were not significantly different. However, in assays assessing the auto-poly(ADP-ribosyl)ation reaction, both enzymes displayed second-order kinetics with respect to [PARP-1], and up to two-fold higher specific activity was observed for human versus rat PARP-1. We conclude that the correlation of poly(ADP-ribosyl)ation capacity with life span is not reflected in the kinetic parameters, but that subtle differences in primary structure of PARP-1 from mammalian species of different longevity may control the extent of the automodification reaction.","NAD synthetase catalyzes the final step in the biosynthesis of NAD. In the present study, we obtained cDNAs for two types of human NAD synthetase (referred as NADsyn1 and NADsyn2). Structural analysis revealed in both NADsyn1 and NADsyn2 a domain required for NAD synthesis from ammonia and in only NADsyn1 an additional carbon-nitrogen hydrolase domain shared with enzymes of the nitrilase family that cleave nitriles as well as amides to produce the corresponding acids and ammonia. Consistent with the domain structures, biochemical assays indicated (i) that both NADsyn1 and NADsyn2 have NAD synthetase activity, (ii) that NADsyn1 uses glutamine as well as ammonia as an amide donor, whereas NADsyn2 catalyzes only ammonia-dependent NAD synthesis, and (iii) that mutant NADsyn1 in which Cys-175 corresponding to the catalytic cysteine residue in nitrilases was replaced with Ser does not use glutamine. Kinetic studies suggested that glutamine and ammonia serve as physiological amide donors for NADsyn1 and NADsyn2, respectively. Both synthetases exerted catalytic activity in a multimeric form. In the mouse, NADsyn1 was seen to be abundantly expressed in the small intestine, liver, kidney, and testis but very weakly in the skeletal muscle and heart. In contrast, expression of NADsyn2 was observed in all tissues tested. Therefore, we conclude that humans have two types of NAD synthetase exhibiting different amide donor specificity and tissue distributions. The ammonia-dependent synthetase has not been found in eucaryotes until this study. Our results also indicate that the carbon-nitrogen hydrolase domain is the functional domain of NAD synthetase to make use of glutamine as an amide donor in NAD synthesis. Thus, glutamine-dependent NAD synthetase may be classified as a possible glutamine amidase in the nitrilase family. Our molecular identification of NAD synthetases may prove useful to learn more of mechanisms regulating cellular NAD metabolism.","4-Nitrophenyl and 2-napthyl monoesters of phenylphosphonic acid have been synthesized, and an enzyme catalyzing their hydrolysis was resolved from alkaline phosphatase of a commerical calf intestinal alkaline phosphatase preparation by extensive ion-exchange chromatography, chromatography on L-phenylalanyl-Sepharose with a decreasing gradient of (NH4) 2SO4, and gel filtration. Detergent-solubilized enzyme from fresh bovine intestine was purified after (NH4)2SO4 fractionation by the same technique. The purified enzyme is homogeneous by polyacrylamide gel electrophoresis and sedimentation equilibrium centrifugation. It has a molecular weight of 108,000, contains approximately 21% carbohydrate, and has an amino acid composition considerably different from that reported from alkaline phosphatase from the same tissue. The homogeneous intestinal enzyme, an efficient catalyst of phosphonate ester hydoolysis but not of phosphate monoester hydrolysis, was identified as a 5'-nucleotide phosphodiesterase by its ability to hydrolyze 4-nitrophenyl esters of 5'-TMP but not of 3'-TMP. Also consistent with this identification was the ability of the enzyme to hydrolyze 5'-ATP to 5'-AMP and PPi, NAD+ to 5'-AMP and NMN, TpT to 5'-TMP and thymidine, pApApApA to 5'-AMP, and only the single-stranded portion of tRNA from the 3'-OH end. Snake venom 5'-nucleotide phosphodiesterase also hydrolyzes phosphonate esters, but 3'-nucleotide phosphodiesterase of spleen and cyclic 3',5'-AMP phosphodiesterase do not. Thus, types of phosphodiesterases can be conveniently distinguished by their ability to hydrolyze phosphonate esters. As substrates for 5'-nucleotide phosphodiesterases, phosphonate esters are preferable to the more conventional esters of nucleotides and bis(4-nitrophenyl) phosphate because of their superior stability and ease of synthesis. Furthermore, the rate of hydrolysis of phosphonate esters under saturating conditions is greater than that of the conventional substrates. At substrate concentrations of 1 mM the rates of hydrolysis of phosphonate esters and of nucleotide esters are comparable and both superior to that of bis(4-nitrophenyl) phosphate.","An Arg-specific mono(ADP-ribosyl)transferase activity on the surface of human polymorphonuclear neutrophil leucocytes (PMNs) was confirmed by the use of diethylamino-(benzylidineamino)guanidine (DEA-BAG) as an ADP-ribose acceptor. Two separate HPLC systems were used to separate ADP-ribosyl-DEA-BAG from reaction mixtures, and its presence was confirmed by electrospray mass spectrometry. ADP-ribosyl-DEA-BAG was produced in the presence of PMNs, but not in their absence. Incubation of DEA-BAG with ADP-ribose (0.1-10 mM) did not yield ADP-ribosyl-DEA-BAG, which indicates that ADP-ribosyl-DEA-BAG formed in the presence of PMNs was not simply a product of a reaction between DEA-BAG and free ADP-ribose, due possibly to the hydrolysis of NAD+ by an NAD+ glycohydrolase. The assay of mono(ADP-ribosyl)transferase with agmatine as a substrate was modified for intact PMNs, and the activity was found to be approx. 50-fold lower than that in rabbit cardiac membranes. The Km of the enzyme for NAD+ was 100.1 30.4 microM and the Vmax 1.4 0.2 pmol of ADP-ribosylagmatine/h per 10(6) cells. The enzyme is likely to be linked to the cell surface via a glycosylphosphatidylinositol anchor, since incubation of intact PMNs with phosphoinositol-specific phospholipase C (PI-PLC) led to a 98% decrease in mono(ADP-ribosyl)transferase activity in the cells. Cell surface proteins were labelled after exposure of intact PMNs to [32P]NAD+. Their molecular masses were 79, 67, 46, 36 and 26 kDa. The time course for labelling was non-linear under these conditions over a period of 4 h. The labelled products were identified as mono(ADP-ribosyl)ated proteins by hydrolysis with snake venom phosphodiesterase to yield 5'-AMP.","Quinolinate phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) catalyzes the formation of nicotinate mononucleotide, carbon dioxide, and pyrophosphate from 5-phosphoribosyl 1-pyrophosphate (PRPP) and quinolinic acid (QA, pyridine 2,3-dicarboxylic acid). The enzyme is the only type II PRTase whose X-ray structure is known. Here we determined the kinetic mechanism of the enzyme from Salmonella typhimurium. Equilibrium binding studies show that PRPP and QA each form binary complexes with the enzyme, with K(D) values (53 and 21 microM, respectively) similar to their K(M) values (30 and 25 microM, respectively). Although neither PP(i) nor NAMN products bound well to the enzyme, 130-fold tighter binding of PP(i) (K(D) = 75 microM) and NAMN (K(D) = 6 microM) in a ternary complex was observed. Phthalic acid (K(D) = 21 microM) and PRPP each caused a 2.5-fold tightening of the other's binding. Isotope trapping experiments indicated that the E.QA complex is catalytically competent, whereas the E.PRPP complex could not be trapped. Pre-steady-state kinetics gave a linear rate of NAMN formation, indicating that on-enzyme phosphoribosyl transfer chemistry is rate-determining. Isotope trapping from the steady state revealed that nearly all QA and about one-third of PRPP in ternary enzyme.QA.PRPP complexes could be trapped as the product. Substrate inhibition by PRPP was observed. These data demonstrate a predominantly ordered kinetic mechanism in which productive binding of quinolinic acid precedes that of PRPP. An E.PRPP complex exists as a nonproductive side branch.","The biosynthesis of quinolinate 3, the precursor to the pyridine ring of NAD, is still poorly understood. Two pathways have been identified, one involving the direct formation of quinolinic acid from aspartate and dihydroxyacetone phosphate, the other requiring a five-step degradation of tryptophan. The final step in this degradation is catalyzed by the non-heme Fe(II)-dependent enzyme 3-hydroxyanthranilate-3,4-dioxygenase (HAD). This enzyme catalyzes the oxidative ring opening of 3-hydroxyanthranilate (1) to 2-amino-3-carboxymuconic semialdehyde (ACMS, 2) which then cyclizes to quinolinate (3). In this communication, we demonstrate the following: (1) cyclization of ACMS to 3 is not HAD catalyzed, (2) the most stable form of ACMS in solution is an all trans isomer which undergoes facile cis to trans isomerization about the C2-C3 and C4-C5 double bonds via transient formation of its enol tautomer (6), (3) a model study on the ring opening of N,N-dimethylcarbamoylpyridinium with hydroxide and methoxide suggests that the cyclization of ACMS occurs by an electrocyclization reaction of its enol tautomer 6. Thus, the biosynthesis of quinolinic acid, by the tryptophan pathway, is likely to be a member of a growing family of natural products whose biosynthesis involves a pericyclic reaction.","The family of heme dioxygenases, as exemplified by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase, catalyzes the oxidative cleavage of L-tryptophan to N-formylkynurenine. Here, we describe a bacterial expression system for human tryptophan 2,3-dioxygenase (rhTDO) together with spectroscopic, kinetic, and redox analyses. We find unexpected differences between human tryptophan 2,3-dioxygenase and human indoleamine 2,3-dioxygenase [Chauhan et al. (2008) Biochemistry 47, 4761-4769 ]. Thus, in contrast to indoleamine 2,3-dioxygenase, the catalytic ferrous-oxy complex of rhTDO is not observed, nor does the enzyme discriminate against substrate binding to the ferric derivative. In addition, we show that the rhTDO is also catalytically active in the ferric form. These new findings illustrate that significant mechanistic differences exist across the heme dioxygenase family, and the data are discussed within this broader framework.","A subunit of choleragen and an erythrocyte ADP-ribosyltransferase catalyze the transfer of ADP-ribose from NAD to proteins and low molecular weight guanidino compounds such as arginine. These enzymes also catalyze the hydrolysis of NAD to nicotinamide and ADP-ribose. The kinetic mechanism for both transferases was investigated in the presence and absence of the product inhibitor nicotinamide by using agmatine as the acceptor molecule. To obtain accurate estimates of kinetic parameters, the transferase and glycohydrolase reactions were monitored simultaneously by using [adenine-2,8-3H]NAD and [carbonyl-14C]NAD as tracer compounds. Under optimal conditions for the transferase assay, NAD hydrolysis occurred at less than 5% of the Vmax for ADP-ribosylation; at subsaturating agmatine concentrations, the ratio of NAD hydrolysis to ADP-ribosylation was significantly higher. Binding of either NAD or agmatine resulted in a greater than 70% decrease in affinity for the second substrate. All data were consistent with a rapid equilibrium random sequential mechanism for both enzymes.","To probe the catalytic mechanism of human purine nucleoside phosphorylase (PNP), 13 active-site mutants were constructed and characterized by steady-state kinetics. In addition, microtiter plate assays were developed for both the phosphorolytic and synthetic reactions and used to determine the kinetic parameters of each mutant. Mutations in the purine binding site exhibited the largest effects on enzymatic activity with the Asn243Ala mutant resulting in a 1000-fold decrease in the kcat for inosine phosphorolysis. This result in combination with the crystallographic location of the Asn243 side chain suggested a potential transition state (TS) structure involving hydrogen bond donation by the carboxamido group of Asn243 to N7 of the purine base. Analogous to the oxyanion hole of serine proteases, this hydrogen bond was predicted to aid catalysis by preferentially stabilizing the TS as a consequence of the increase in negative charge on N7 that occurs during glycosidic bond cleavage and the associated increase in the N7-Asn243 hydrogen bond strength. Two residues in the phosphate binding site, namely His86 and Glu89, were also predicted to be catalytically important based on their alignment with phosphate in the X-ray structure and the 10-25-fold reduction in catalytic activity for the His86Ala and Glu89Ala mutants. In contrast, catalytic efficiencies for the Tyr88Phe and Lys244Ala mutants were comparable with wild-type, indicating that the hydrogen bonds predicted in the initial X-ray structure of PNP [Ealick, S. E., et al. (1990) J. Biol. Chem. 265, 1812-1820] were not essential for catalysis. These results provided the foundation for studies reported in the ensuing two manuscripts focused on the PNP catalytic mechanism [Erion, M. D., et al. (1997) Biochemistry 36, 11735-11748] and the use of mutagenesis to reverse the PNP substrate specificity from 6-oxopurines to 6-aminopurines [Stoeckler, J. D., et al. (1997) Biochemistry 36, 11749-11756].","<h4>Abstract</h4>Elevated levels of the NAD+-generating enzyme nicotinamide phosphoribosyltransferase (NAMPT) are a common feature across numerous cancer types. Accordingly, we previously reported pervasive NAD+ dysregulation in multiple myeloma (MM) cells in association with upregulated NAMPT expression. Unfortunately, albeit being effective in preclinical models of cancer, NAMPT inhibition has proven ineffective in clinical trials because of the existence of alternative NAD+ production routes using NAD+ precursors other than nicotinamide. Here, by leveraging mathematical modeling approaches integrated with transcriptome data, we defined the specific NAD+ landscape of MM cells and established that the Preiss-Handler pathway for NAD+ biosynthesis, which uses nicotinic acid as a precursor, supports NAD+ synthesis in MM cells via its key enzyme nicotinate phosphoribosyltransferase (NAPRT). Accordingly, we found that NAPRT confers resistance to NAD+-depleting agents. Transcriptomic, metabolic, and bioenergetic profiling of NAPRT-knockout (KO) MM cells showed these to have weakened endogenous antioxidant defenses, increased propensity to oxidative stress, and enhanced genomic instability. Concomitant NAMPT inhibition further compounded the effects of NAPRT-KO, effectively sensitizing MM cells to the chemotherapeutic drug, melphalan; NAPRT added-back fully rescues these phenotypes. Overall, our results propose comprehensive NAD+ biosynthesis inhibition, through simultaneously targeting NAMPT and NAPRT, as a promising strategy to be tested in randomized clinical trials involving transplant-eligible patients with MM, especially those with more aggressive disease."],"pubmed_title":["Hydrolysis of phosphonate esters catalyzed by 5'-nucleotide phosphodiesterase.","Inhibitory substrate binding site of human indoleamine 2,3-dioxygenase.","Purine nucleoside phosphorylase. 1. Structure-function studies.","Kinetic mechanisms of two NAD:arginine ADP-ribosyltransferases: the soluble, salt-stimulated transferase from turkey erythrocytes and choleragen, a toxin from Vibrio cholerae.","Initial-rate kinetics of human NMN-adenylyltransferases: substrate and metal ion specificity, inhibition by products and multisubstrate analogues, and isozyme contributions to NAD+ biosynthesis.","Kynurenine formamidase. Purification and characterization of the adult chicken liver enzyme and immunochemical analyses of the enzyme of developing chicks.","Heterologous expression and purification of kynurenine-3-monooxygenase from Pseudomonas fluorescens strain 17400.","Purification and inactivation of 3-hydroxyanthranilic acid 3,4-dioxygenase from beef liver.","Mammalian NADH diphosphatases of the Nudix family: cloning and characterization of the human peroxisomal NUDT12 protein.","Nicotinamide riboside kinase structures reveal new pathways to NAD+.","Cloning, expression, and catalytic triad of recombinant arylformamidase.","Quantitative studies of inhibitors of ADP-ribosylation in vitro and in vivo.","A kinetic, spectroscopic, and redox study of human tryptophan 2,3-dioxygenase.","The oxygenated form of L-tryptophan 2,3-dioxygenase as reaction intermediate.","The pyridine ring of NAD is formed by a nonenzymatic pericyclic reaction.","Weak coupling of ATP hydrolysis to the chemical equilibrium of human nicotinamide phosphoribosyltransferase.","NADPH regulates human NAD kinase, a NADP⁺-biosynthetic enzyme.","Characterization of human nicotinate phosphoribosyltransferase: Kinetic studies, structure prediction and functional analysis by site-directed mutagenesis.","Human placental cytoplasmic 5'-nucleotidase. Kinetic properties and inhibition.","Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.","Purification and biochemical characterization of some of the properties of recombinant human kynureninase.","Quinolinate phosphoribosyltransferase: kinetic mechanism for a type II PRTase.","Human CD38 is an authentic NAD(P)+ glycohydrolase.","Substrate specificity and structure of human aminoadipate aminotransferase/kynurenine aminotransferase II.","NAD+ metabolism restriction boosts high-dose melphalan efficacy in patients with multiple myeloma.","Substrate binding and catalysis of ecto-ADP-ribosyltransferase 2.2 from rat.","Arginine-specific mono(ADP-ribosyl)transferase activity on the surface of human polymorphonuclear neutrophil leucocytes.","Comparative characterisation of poly(ADP-ribose) polymerase-1 from two mammalian species with different life span."],"pubmed_authors":["Pabarcus Michael K MK, Casida John E JE","Berthelier V V, Tixier J M JM, Muller-Steffner H H, Schuber F F, Deterre P P","Han Qian Q, Cai Tao T, Tagle Danilo A DA, Robinson Howard H, Li Jianyong J","Sorci Leonardo L, Cimadamore Flavio F, Scotti Stefania S, Petrelli Riccardo R, Cappellacci Loredana L, Franchetti Palmarisa P, Orsomando Giuseppe G, Magni Giulio G","Donnelly L E LE, Rendell N B NB, Murray S S, Allport J R JR, Lo G G, Kefalas P P, Taylor G W GW, MacDermot J J","Tempel Wolfram W, Rabeh Wael M WM, Bogan Katrina L KL, Belenky Peter P, Wojcik Marzena M, Seidle Heather F HF, Nedyalkova Lyudmila L, Yang Tianle T, Sauve Anthony A AA, Park Hee-Won HW, Brenner Charles C","Beneke S S, Alvarez-Gonzalez R R, Bürkle A A","Erion M D MD, Takabayashi K K, Smith H B HB, Kessi J J, Wagner S S, Hönger S S, Shames S L SL, Ealick S E SE","Soncini Debora D, Becherini Pamela P, Ladisa Francesco F, Ravera Silvia S, Chedere Adithya A, Gelli Elisa E, Giorgetti Giulia G, Martinuzzi Claudia C, Piacente Francesco F, Mastracci Luca L, Veneziano Claudia C, Santamaria Gianluca G, Monacelli Fiammetta F, Ghanem Moustafa S MS, Cagnetta Antonia A, Guolo Fabio F, Garibotto Matteo M, Aquino Sara S, Passalaqua Mario M, Bruzzone Santina S, Bellotti Axel A, Duchosal Michel A MA, Nahimana Aimable A, Angelucci Emanuele E, Nagasuma Chandra C, Nencioni Alessio A, Lemoli Roberto Massimo RM, Cea Michele M","Crozier Karen R KR, Moran Graham R GR","Kelly S J SJ, Dardinger D E DE, Butler L G LG","Burgos Emmanuel S ES, Schramm Vern L VL","Rankin P W PW, Jacobson E L EL, Benjamin R C RC, Moss J J, Jacobson M K MK","Abdelraheim Salama R SR, Spiller David G DG, McLennan Alexander G AG","Galassi Lucia L, Di Stefano Michele M, Brunetti Lucia L, Orsomando Giuseppe G, Amici Adolfo A, Ruggieri Silverio S, Magni Giulio G","Ishimura Y Y, Nozaki M M, Hayaishi O O","Ohashi Kazuto K, Kawai Shigeyuki S, Koshimizu Mari M, Murata Kousaku K","Osborne J C JC, Stanley S J SJ, Moss J J","Walsh Harold A HA, Botting Nigel P NP","Bailey C G CG, Wagner C C","Lu Changyuan C, Lin Yu Y, Yeh Syun-Ru SR","Nandi Dhirendra D, Lightcap Eric S ES, Koo Yumee Kim YK, Lu Xingliang X, Quancard Jean J, Silverman Richard B RB","Cao Hong H, Pietrak Beth L BL, Grubmeyer Charles C","Hara Nobumasa N, Yamada Kazuo K, Terashima Masaharu M, Osago Harumi H, Shimoyama Makoto M, Tsuchiya Mikako M","Ritter Holger H, Koch-Nolte Friedrich F, Marquez Victor E VE, Schulz Georg E GE","Basran Jaswir J, Rafice Sara A SA, Chauhan Nishma N, Efimov Igor I, Cheesman Myles R MR, Ghamsari Lila L, Raven Emma Lloyd EL","Madrid-Marina V V, Fox I H IH","Colabroy Keri L KL, Begley Tadhg P TP"],"name_synonyms":["Coenzyme I, DPN, Adenine Dinucleotide, single-organism biosynthetic process, Dihydronicotinamide Adenine Dinucleotide, Dinucleotide, Nadide, human being, bioformation, Man (Taxonomy), Adenosine 5'-(trihydrogen diphosphate), anabolism, Modern, NADH, Lymphoid Cells., Diphosphopyridine Nucleotide, Dihydronicotinamide Adenine, P'-5'-ester with 3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium, human, Cell, Diphosphopyridine, Nicotinamide-Adenine Dinucleotide, Human, Dihydronicotinamide, Homo sapiens, Nicotinamide Adenine Dinucleotide, Nicotinamide-Adenine, Modern Man, Cells, Lymphoid, Lymphoid Cell, Nucleotide, Man, Lymphocyte, inner salt, multicellular organismal biosynthetic process"],"pubmed_abstract_synonyms":["sodium salt, nicotinamidum, Striadyne, F14G24.15, 2410041A17Rik, strontium fructose-1, Metabolic Concepts, Nicocap, F14G24_15, Visible Light, fs(1)M34, Nucleoside, DmelCG6383, DmelCG12051, 2-Propanone, Nicobion, NAPRTase, Niacin Iron (2+) Salt, 10.5, B3, HEL-176, CG4601, Niacin Ammonium Salt, Analog, Analysis, Metabolism Concept, 10.9, calcium (1:2) salt, 3-Phosphoglyceraldehyde, Molecular Docking Analyses, A, C, F, cyt5C, Lithium, beta-pyridinecarboxamide, 2-(18)O-labeled, DHO, catabolism, Molecular, anabolism, crumb, CG18572, V, metabolic process resulting in cell growth, ATNAM, D17Mit170, Enduracin, Niacin Potassium Salt, tetrapotassium salt, CrATP, Cr(H2O)4 ATP, Nicotinsaeureamid, Oligonucleotide-Directed Mutagenesis, ACT, Niacin Manganese (2+) Salt, Act, 2-oxopropanoic acid, Nucleotide, Inorganic, ATPsyn-&bgr, Ligand, Radiation, ATPsyn-b, Actin/BAP47, UNQ391/PRO726, CTE-II, AACT, metabolism resulting in cell growth, Aptitudes, CTE-IIa, act, Ach1, hBACH, ACH1, Light, Docking, Tl3, Tl2, act42A, GIG25, LIGHT, Tosylate, niacin, Su(b), AFFX-Dros-ACTIN_M_r_at, GIG24, Magnesium Salt, actin, secretion, Hemihydrate, LACH, Niacin Cobalt (2+) Salt, nucleotides, congenital myopathy cleft palate and malignant hyperthermia, Acid, Vitamin B3, DmelCG4027, HVEML, Niacin Lithium Salt, Tartrate, disodium salt, 3-pyridinecarboxamide, human, Sodium Salt, actin5C, nicotinic amide, eve2, Molecular Docking, BACH, PEP, Sr-FDP, NAM, Oligonucleotide-Directed Mutageneses, m-(aminocarbonyl)pyridine, CG2328, Crbs, l(1)Ab, Act5c, 2-Propenoic acid, Magnesium Adenosine Triphosphate, conformation, Processes, Niacin Aluminum Salt, ATP-MgCl2, ACT5C, secondary metabolites, IB, Metabolic Processes, protein-containing complex, Bach, Vitamin B 3, Adenylpyrophosphate, Human, pyridine-3-carboxylic acid amide, Ly113, Site-Directed Mutagenesis, Crumbs, Oligonucleotide Directed, 1-hydroxy-3-(phosphonooxy)-, Gene Products, nucleosides, Cell growth-inhibiting gene 24|25 protein, CoA, Mutagenesis, nicotinic acid mononucleotide, even, Man, Nico 400, nicotinic acid phosphoribosyltransferase, CT19912, 0509/20, Niacin Tosylate, fructose 1, Site-Specific, BRWS2, Papulex, beta-ATPase, Metabolic Concept, COA, nicotine acid amide, Dihydroxyacetone 3-Phosphate, fs(1)829, anon-EST:fe2D2, Abilities, S cerevisiae, ATPasebeta, MnATP, ATPase beta, DmelCG18572, coa, T11, TR2, Act-5C, ATPB, nicotinamida, 42A, nicotinamide, niamide, CPS, cou, degradation, Proteins, dJ393D12.2, ion(1-), 2-(phosphonooxy)-, CD258, Cell, Concept, ATP-syn-B, Site-Directed Mutageneses, tetrasodium salt, Lr, native protein, CoASH, ANAC018, beta-actin, 3-carbamoylpyridine, M32055, Mutageneses, 9130210N20Rik, Wampocap, CRB, Crb, Act42, Eve, EVE, metabolism, Metabolic Phenomenon, strontium fructose 1, congenital myopathy - cleft palate - malignant hyperthermia, Inorganic Phosphate, multicellular organism metabolic process, Nico-400, 3-Phosphate, Nikotinamid, HVEM-L, PYR1, metabolite, Gene Proteins, NAPRTase 1, myopathy, NAPRTase 2, 2-PHOSPHOENOLPYRUVIC ACID, Photoradiations, Talent, Bra, DRORUD, BAP47, ACTSG, General activity, Bap47, Molecular Docking Analysis, Calcium Salt, Anabolism, biochemical pathways, Metabolic Process, Activity, 3-Pyridinecarboxamide, Adenosine Triphosphate, ACTG, ACTE, protein, csp2, Act5, l(1)G0420, primary metabolites, congenital, Dihydroxyacetone 3 Phosphate, Niacin, Niacin Sodium Salt, Concepts, vitamin B3, protein aggregate, Phenomenon, Arabidopsis NAC domain containing protein 18, Docking Analysis, multicellular organismal biosynthetic process, (alpha-D)-isomer, 3-Pyridinecarboxylic acid, single-organism biosynthetic process, Chromium Adenosine Triphosphate, me75, Orthophosphate, Man (Taxonomy), enzymes, DmelCG2328, Niacin Hydrochloride, Nicolar, barium (1:2) salt, E coli, Phosphate, Nucleoside Analogs, 3 Pyridinecarboxamide, Nicotinamid, T1, Niacin Calcium Salt, Niacinamide, reaction, TNFSF14, ATPsyn b, Glyceraldehyde 3 Phosphate, act 42A, 6-diphosphate, monohydrate, Ac5C, CG4027, biotransformation, (beta-D)-isomer, with cleft palate and malignant hyperthermia, Catabolism, ATP, Niacin Tartrate, Chromium Ammonium Salt, Aluminum Salt, NPT1 protein, l(1)G0330, CG6383, Process, Pyruvic, Modern, 3-Pyridinecarboxylic Acid, LACH1, niacin ribonucleotidase, Ability, Nicotinate phosphoribosyltransferase 1, Nicotinate phosphoribosyltransferase 2, Alpha-1-antichymotrypsin His-Pro-less, nicotinic acid amide, NO APICAL MERISTEM, Manganese Salt, DFNA26, VI, Nico400, 6-diphosphate magnesium salt, Naprt1, GAT, DFNA20, 2-(phosphonooxy)-2-propenoic acid, CG11154, Phosphates, Visible Radiations, 20.35, Visible Radiation, Vitamin, NAC DOMAIN PROTEIN NAM, Nicamin, l(1)G0117, Analogs, Actin, beta-actin/Bap47, monosodium salt, l(1)G0486, Lithium Nicotinate, pncB protein, CaATP, l(1)G0245, l(1)G0009, Pyruvate, ACTL3, Lach1, metabolites, Nicobid, MgATP, Vitamin PP, Molecular Docking Simulations, Site Specific Mutagenesis, l(3)S050920, 14.10, Dihydroxyacetone, Site Directed, Nikotinsaeureamid, Site-Specific Mutagenesis, l(1)G0010, human being, bioformation, a nucleoside, Enduramide, 3 Phosphoglyceraldehyde, CG12051, Gene, far, Site Directed Mutagenesis, NARS2, Serpin A3, Potassium Salt, l(1)G0025, Homo sapiens, Induracin, Metabolism, ATP-synbeta, Low, Nicotinamide, Metabolism Phenomena, PHOSPHOENOLPYRUVATE, Nicotinsäureamid Jenapharm, study, act5C, DmelCG11154, 1384/04, ATP MgCl2, Inorganic Phosphates, Visible, Act42a, Chromium Salt, 1700027G07Rik, (L)-isomer, Molecular Dockings, Nicotinic acid mononucleotide pyrophosphorylase, Cte-II, l(3)j1B5, l(1)G0177, Site-Specific Mutageneses, nicotinic acid ribonucleotide, nicotine amide, Niacin Copper (2+) Salt, 2-oxopropanoate, protein complex, Magnesium Chloride, Nucleoside Analog, Docking Simulation, enzyme activity, Adenosine 5'-(tetrahydrogen triphosphate), 6-bisphosphate, l(3)07207, Metabolic Phenomena, Carbohydrates, Metabolism Concepts, Atriphos, ML-1, CAD, Nicotinic acid mononucleotide glycohydrolase, Protein, Phenomena, Hydrochloride, Nicotinic Acid, Oligonucleotide-Directed, Niacin Magnesium Salt, ACTA3, fructose-1, l(3)S058104, Site-Directed., Jenapharm, 2-hydroxy-3-(phosphonooxy)-, Propanal, trisodium salt, Radiations, l(1)G0079, Manganese Adenosine Triphosphate, Oligonucleotide Directed Mutagenesis, biodegradation, Metabolic, 3 Pyridinecarboxylic Acid, VSCM, Photoradiation, act 5C, Site Specific, l(2)46Ce, Talents, B 3, Carbohydrate, nicotylamide, l(2)46Cg, LTg, l(2)46CFj, Protein Gene Products, l(2)46CFh, Nicotinsäureamid, Nicotinate, l(2)46CFp, Modern Man, ATPIB, calcium salt, Niacin Zinc Salt, Simulation, E(eve), NAC-REGULATED SEED MORPHOLOGY 2, l(2)46CFg, Actin5C"],"description_synonyms":["Plasma-Cell Myelomas, reduced NAD biosynthesis, Plasma-cell myeloma, oxidized nicotinamide adenine dinucleotide biosynthesis, Disease, human being, Myelomas, Biocatalysts, Myeloma, Multiple myeloma (disorder), Kahler's disease, Modern, Cell Myelomas, secondary metabolites, enzyme activity, Myeloma Multiple, Myeloma-Multiples, Client, Myeloma-Multiple, Cell, Multiple Myeloma, Human, MM, Al amyloidosis, NAD (oxidized) biosynthesis, multiple myeloma, NAD anabolism, Kahler, Multiple Myelomas, primary metabolites, Homo sapiens, NAD formation, [M]Plasma cell myeloma, Myelomatoses, NOS, Myelomatosis, NAD (reduced) biosynthetic process, oxidized NAD biosynthesis, Man, MULT MYELM W/O REMISSION, morphology (morphologic abnormality), Plasma-Cell, Plasma-Cell Myeloma, Plasmacytic myeloma, reduced nicotinamide adenine dinucleotide biosynthetic process, systemic, Plasma, nicotinamide adenine dinucleotide biosynthetic process, amyloidosis, no ICD-O subtype (morphologic abnormality)., Multiple myeloma, Man (Taxonomy), enzymes, NADH biosynthetic process, NAD synthesis, Plasma Cell Myelomas, metabolite, myeloma, Kahler Disease, NAD biosynthesis, oxidized NAD biosynthetic process, patient, human, Multiple myeloma without mention of remission, NAD (oxidized) biosynthetic process, Multiple, oxidized nicotinamide adenine dinucleotide biosynthetic process, NADH biosynthesis, reduced NAD biosynthetic process, Enzyme, no ICD-O subtype, Cell Myeloma, multiple, Patient, Plasma Cell Myeloma, NAD (reduced) biosynthesis, Clients, Modern Man, metabolites, Biocatalyst, nicotinamide adenine dinucleotide biosynthesis, reduced nicotinamide adenine dinucleotide biosynthesis, Multiple myeloma (clinical), Plasma Cell, myeloma - multiple"],"pubmed_title_synonyms":["Phosphoric Diester, Phosphodiesterase., esters, Phosphonates, Esters, Phosphonic Acid, Acid Esters, Ester, endonuclease VIII activity, inositol or phosphatidylinositol phosphodiesterase activity, Phosphonic, Phosphonic Acid Esters, Nucleotide, Hydrolases, phosphodiesterase, inositol/phosphatidylinositol phosphodiesterase activity, Phosphodiesterases, Phosphonate, nucleotides"],"additional_accession":[]},"is_claimable":false,"name":"DeboraSoncini2024 - NAD_Biosynthesis_in Human_B_Lymphocytes,ODE model","description":"\n      \n        This SBML file was created to capture NAD biosynthesis in human B-cells. This model contains 27 reactions with 42 enzymes, 31 metabolites and 157 parameters. This model is used further for generating patient-specific model for multiple myeloma. \n      \n    ","dates":{"last_modification":"2024-12-13","publication":"2024-12-13","submission":"2023-11-14"},"accession":"MODEL2311140001","cross_references":{"kegg__reaction":["R01960","R02668","R02665","R03348","R03005","R01724","R00257","R00189","R00104","R00102","R10631","R04176","R10634","R00555","R02294","R01271","R02323","R02324","R00103","R00137","R12688","R12693","R04293","R00678","R01959"],"pubmed":["39661983","15935693","16973376","11985583","12672479","11876660","17402747","21742010","12547821","21526340","9494110","11121685","2538435","8615841","3935159","12939142","9305962","18823127","3001058","17914902","170964","12790796","18620547","15656614","18370401","5470825","19737010","4135584"],"chebi":["CHEBI:16828","CHEBI:17380","CHEBI:16474","CHEBI:36559","CHEBI:16675","CHEBI:15763","CHEBI:17111","CHEBI:18361","CHEBI:18304","CHEBI:15846","CHEBI:16171","CHEBI:15422","CHEBI:16134","CHEBI:18050","CHEBI:18009","CHEBI:17154","CHEBI:16960","CHEBI:16946","CHEBI:15927","CHEBI:16300","CHEBI:32544","CHEBI:30249","CHEBI:15379","CHEBI:16027","CHEBI:16761","CHEBI:16467","CHEBI:18367","CHEBI:18344","CHEBI:71201","CHEBI:995"],"biomodels__db":["MODEL2311140001"],"kegg__compound":["C00078","C03227","C00005","C00632","C03722","C01185","C00119","C00013","C00857","C00003","C00455","C00002","C00014","C00064","C00006","C00153","C00301","C20742","C00328","C03150","C00620","C00253","C02700","C00007","C00020","C00008","C00062","C00009","C01717","C02470","C04409"],"pubchem__substance":["3378","6099","3307","3905","6487","4411","3419","3315","4114","3305","3741","3304","3316","3364","3308","3453","3595","254741210","3622","6038","3894","3552","5664","3309","3322","3310","3362","3311","4854","5485","7044"],"doi":["10.1016/0020-711X(75)90023-3","10.1182/bloodadvances.2024013425"]}}