Figure 3.1 The major pathways of de novo biosynthesis of purine, pyrimidine and pyridine nucleotides. Detailed pathways are shown in Part II, III, and IV, respectively. (a) Purine ribonucleotide biosynthesis: abbreviations of metabolites are as follows: PRPP, 5-phosphoribosyl-1-pyrophosphate; PRA, 5-phosphoribosyl amine; GAR, glycineamide ribonucleotide; FGAR, formylglycineamide ribonucleotide; FGRAM, formylglycine amidine ribonucleotide; AIR, 5-aminoimidazole ribonucleotide; CAIR, 5-aminoimidazole 4-carboxylate ribonucleotide; SCAIR, 5-aminoimidazole-4-N-succinocarboxyamide ribonucleotide; AICAR, 5-aminoimidazole-4-carboxyamide ribonucleotide; FAICAR, 5-formamidoimidazole-4-carboxyamide ribonucleotide; SAMP, adenylosuccinate; XMP, xanthosine-5′-monophosphate. The participated enzymes are (1) PRPP amidotransferase (2.4.2.14); (2) GAR synthetase (6.3.4.13); (3) GAR formyl transferase (2.1.2.2); (4) FGAM synthetase (6.3.5.3); (5) AIR synthetase (6.3.3.1); (6) AIR carboxylase (4.1.1.21); (7) SAICAR synthetase (6.3.2.6); (8) adenylosuccinate lyase (4.3.2.2); (9) AICAR formyl transferase (2.1.2.3); (10) IMP cyclohydrolase (3.5.4.10); (11) SAMP synthetase (6.3.4.4); (12) adenylosuccinate lyase (4.3.2.2), the same enzyme for step 8; (13) IMP dehydrogenase (1.1.1.205); (14) GMP synthetase (6.3.5.2). (b) Pyrimidine ribonucleotide biosynthesis: CP, carbamoyl phosphate; CA, carbamoyl aspartate; DHO, dihydroorotate; OA, orotate; OMP, orotidine-5′-monophosphate. Enzymes: (1) aspartate transcarbamoylase (2.1.3.2); (2) dihydroorotase (3.5.2.3); (3) dihydroorotate dehydrogenase (1.3.99.11); (4)–(5) UMP synthase (orotate phosphoribosyltransferase [2.4.2.10] plus orotidine-5′-phosphate decarboxylase [4.1.1.23]). (C) Pyridine ribonucleotide biosynthesis: Asp, aspartate; ISA, α-iminosuccinate; QA, quinolinate; NaMN, nicotinate mononucleotide; NaAD; nicotinate adenine dinucleotide. Enzymes: (1) L-aspartate oxidase (1.4.3.16); (2) quinolinate synthase (2.5.1.72); (3) quinolinate phosphoribosyltransferase (decarboxylating) (2.4.2.19); (4) nicotinate mononucleotide adenylyltransferase (2.7.7.18); (5) NAD synthase (6.3.5.1).
Compared to purine biosynthesis, the pyrimidine biosynthetic pathway (aka the orotate pathway), namely the formation of uridine monophosphate (UMP) from carbamoyl phosphate, is more straight forward. The pathway consists of six reactions and the precursors are carbamoyl phosphate, aspartate, and PRPP (Figure 3.1b). Pyrimidine nucleotide biosynthesis, which is the same in plants as other organisms, is evolutionarily conserved in all species examined to date. Since nitrogen in carbamoyl phosphate is synthesized from glutamine, the nitrogen atoms of positions 1 and 3 of pyrimidine ring are derived from aspartate and glutamine, respectively. The carbon atoms at position 2 and positions 4–6 of the ring originate from carbon dioxide and aspartate (see Part III).
Pyridine nucleotides (nicotinamide adenine dinucleotide [NAD] and nicotinamide adenine dinucleotide phosphate [NADP]) consist of two mononucleotides, namely AMP and nicotinamide mononucleotide (NMN). Since the AMP moiety is a product of purine biosynthesis, in a narrow sense, pyridine nucleotide synthesis results in the formation of nicotinate monophosphate (NaMN). Two distinct pathways called the ‘aspartate pathway’ and the ‘kynurenine pathway’ occur in different organisms. The aspartate pathway, in which aspartate, glutamine, glyceraldehyde-3-phosphate and PRPP are used as precursors, operates in plants (Figure 3.1c). This route is also found in most bacteria, including Escherichia coli. In contrast, mammals, fungi, and some bacteria produce NAD by the kynurenine pathway. The steps leading from quinolinate to NAD are conserved among prokaryotes and eukaryotes. Further details of these biosynthetic pathways are covered in Part IV.
3.3 Interconversion of Nucleoside Monophosphates, Nucleoside Diphosphates, and Triphosphates
As illustrated in Figure 3.1, products of de novo biosynthesis pathways of purine, pyrimidine, and pyridine nucleotides are AMP and GMP, UMP and NaMN. Purine and pyrimidine ribonucleoside monophosphates are converted to ribonucleoside diphosphates and triphosphates as well as deoxyribonucleotides. These processes are common to both purine and pyrimidine nucleotides. The ribonucleoside mono- (NMP), di- (NDP) and triphosphates (NTP) are interconverted (see Figure 3.5), coupled with the various reactions shown in Sections 3.3.1, 3.3.2 and 3.4.
3.3.1 Nucleoside-Monophosphate Kinase
Nucleoside monophosphates are converted to nucleoside diphosphates by nucleoside-monophosphate kinase (EC 2.7.4.4) which catalyses reaction 1 as shown in Table 3.1. The substrate specificity of this enzyme is broad; many nucleoside monophosphates can act as acceptors and other nucleoside triphosphates can also serve as phosphate donors instead of ATP. However, the cellular concentration of ATP is usually much higher than that of other nucleoside triphosphates (Table 2.1), so ATP is the principal phosphate donor.
Table 3.1 Enzymes involved in the conversion of nucleoside mono-, di- and triphosphate in plants.
| Enzymes | EC | Reaction | References | |
| 1 | Nucleoside-monophosphate kinase | 2.7.4.4 | ATP + Nucleoside monophosphate → ADP + Nucleoside diphosphate | Noda (1962) |
| 2 | Nucleoside-diphosphate kinase | 2.7.4.6 | ADP + Nucleoside triphosphate → ATP + Nucleoside diphosphate | Dorion and Rivoal (2015) |
| 3 | Adenylate kinase (= Myokinase) | 2.7.4.3 | AMP + ATP → 2 ADP | Johansson et al. (2008) |
| 4 | Guanylate kinase | 2.7.4.8 | GMP + ATP → GDP + ADP | Nomura et al. (2014) |
| 5 | UMP/CMP kinase (= Cytidylate kinase) | 2.7.4.14 | CMP + ATP → CDP + ADP UMP + ATP → UDP + ADP | Zhou et al. (1998) |
| 6 | ATP synthase (H+-transporting two-sector ATPase) | 3.6.3.14 | ADP + Pi + H+out → ATP + H2O + H+in | Li et al. (2012) |
| 7 | Phosphoglycerate kinase | 2.7.2.3 | ||