Plant Nucleotide Metabolism. Hiroshi Ashihara
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such as nicotinamide mononucleotide (NMN), are called nucleotides only by extension and analogy, and nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are referred to as dinucleotides. Flavin mononucleotide (FMN) is a step further removed, as it contains ribitol, a pentose alcohol formed by the reduction of ribose, instead of ribose, while flavin adenine dinucleotide (FAD) similarly extends the meaning of dinucleotide. N-Glycosides such as orotidine 5′-monophosphate (OMP) and adenylosuccinate (SAMP) are called nucleotides through their close relationship to the ‘true’ nucleotides. The terms ribonucleoside and ribonucleotide are used in preference to riboside and ribotides. The IUPAC-IUB Combined Commission on Biochemical Nomenclature has abbreviations and symbols for nucleotides and related compounds. However, as argued by Henderson and Paterson (1973), while they are appropriate for polynucleotides, the distinction between bases and nucleosides is not always immediately obvious, and this has limited their use. The abbreviations used here are more intuitive and better suited to the portrayal of reaction schemes in which the addition or removal of substituent groups occurs.
In Table 1.1, the abbreviations for the major nucleotides, ribo- and deoxyribonucleotides and nucleobases are presented. For readers convenience, the styles used both in this book (style #1) and those recommended by IUPAC (style #2) are shown.
Table 1.1 Nomenclature and abbreviations of purine and pyridine ribo- and deoxyribonucleotides and related compounds.
| Ribonucleotides | Ribonucleosides | #1 | #2 | Nucleobases | #1 | #2 | |
| Adenosine-5′-monophosphate | AMP | Adenosine | AR | Ado | Adenine | A | Ade |
| Guanosine-5′-monophosphate | GMP | Guanosine | GR | Guo | Guanine | G | Gua |
| Inosine-5′-monophosphate | IMP | Inosine | IR | Ino | Hypoxanthine | H | Hyp |
| Xanthosine-5′-monophosphate | XMP | Xanthosine | XR | Xao | Xanthine | X | Xan |
| Uridine-5′-monophosphate | UMP | Uridine | UR | Urd | Uracil | U | Ura |
| Cytidine-5′-monophosphate | CMP | Cytidine | CR | Cyd | Cytosine | C | Cyt |
| Orotidine-5′-monophosphate | OMP | Orotidine | OR | Ord | Orotic acid | O | Oro |
| Deoxyribonucleotides | Deoxyribonucleosides | #1 | #2 | Nucleobases | #1 | #2 | |
| Deoxyadenosine-5′-monophosphate | dAMP | Deoxyadenosine | AdR | dAdo | Adenine | A | Ade |
| Deoxyguanosine-5′-monophosphate | dGMP | Deoxyguanosine | GdR | dGuo | Guanine | G | Gua |
| Deoxyuridine-5′-monophosphate | dUMP | Deoxyuridine | UdR | dUrd | Uracil | U | Ura |
| Deoxycytidine-5′-monophosphate | dCMP | Deoxycytidine | CdR | dCyd | Cytosine | C | Cyt |
| Thymidine-5′-monophosphate | dTMP | Thymidine | TdR | dThd | Thymine | T | Thy |
Two types of symbols are used for nucleoside and nucleobases. Style #1: recommended in Nucleotide Metabolism (Henderson and Paterson 1973). Style #2: recommended by the IUPAC-IUB Commission on Biochemical Nomenclature (1970). In this book, style #1 is adopted.
Abbreviations for ribonucleosides and 2-deoxyribonucleosides are derived from those used for the bases plus those for the ribosyl or 2′-deoxyribosyl groups. Thus AR stands for adenosine and AdR is the abbreviation for deoxyadenosine. In the case of inosine, (hypoxanthine + ribose) HR may be possible, but IR is often used. The latter is used in this text.
For nucleotides, the traditional abbreviations based on the term ‘nucleoside monophosphate’ are used. Thus AMP stands for adenosine monophosphate (adenylate), UMP for uridine monophosphate (uridylate), and NMP for any ribonucleoside monophosphate. Similarly, dAMP stands for deoxyadenosine monophosphate (deoxyadenylate), dUMP for deoxyuridine monophosphate (deoxyuridylate), and dNMP for any deoxyribonucleoside monophosphate. Thymidine monophosphate (thymidylate) often does not have the ‘deoxy’ prefix in its name, because thymidine is thymine deoxyriboside. However, the symbol including