Basic Metabolism (基礎代謝)
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(The following description is translated from an article written by Arita in "Encyclopedia of Bioinformatics" under the publisher's permission, Kyoritsu Co. Ltd.)
Metabolism is the total body of physicochemical reactions inside living systems. It can be functionally divided into two groups: the basic (or primary) metabolism essential for maintenance of life systems, and the non-essential secondary metabolism. Basic metabolites therefore include bases, amino acids, sugars, and fatty acids (building blocks of DNA, protein, carbohydrate, and fat, respectively). Also included are lignin and cellulose which are essential for plant growth. On the other hand, the secondary metabolism provides species-specific functions. It includes medicinal metabolites such as antibiotics and crude drugs.
Design of Basic Metabolite ID numbers ID番号の設計
- a ... Structure type (Table 1)
- b ... degree of unsaturation (Table 2)
- c ... position of n－z (n minus z; also ω－z or omega-z) nomenclature (Table 3)
- d ... structure type (Table 4)
- e ... serial number
Systematic Name of Enzymes (酵素のシステム名)
EC (Enzyme Commission) number is assigned according to the type of reaction catalysed (EC level 1) and the type(s) of the substrate(s). Since reactions are written for the purpose of classification, the direction does not reflect the actually demonstrated catalysis. The systematic name always reflects the first enzyme-catalysed step, and subsequent transformations are written in parentheses, e.g. acetyl-CoA:glyoxylate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (EC 188.8.131.52).
- In this class, a substrate is oxidized as hydrogen donor. The systematic name is donor:acceptor oxidoreductase. The common name is usually dehydrogenase, reductase (when reverse reaction is demonstrated), or oxydase (only when O2 is the acceptor).
- In this class, a chemical 'group' is transferred from a 'donor' to an 'acceptor'. The systematic name is donor:acceptor grouptransferase. The common name is usually acceptor grouptransferase, donor grouptransferase, or phosphorylase (when phosphate is an acceptor). Transaminase is formally considered as the combination of oxidative deamination of the donor followed by reductive amination of the acceptor, but is classified in this class (EC 2.6.1).
- In this class, hydrolytic cleavage of C-O, C-N, C-C and some other bonds occurs. The systematic name is hydrolase. The common name is usually the substrate name with -ase. Hydrolase is formally considered as tranfer of a specific group to water as acceptor. The names of peptide hydrolases (proteinase) is based on their 'esterolytic' action.
- In this class, C-C, C-O, C-N, and other bonds are cleaved by elimination, leaving double bonds or rings. The systematic name is substrate group-lyase. Major common names are decarboxylase, aldolase, and dehydratase. When reverse reaction is demonstrated, synthase (not synthetase) may be used. Pyridoxal-phosphate enzymes usually replace the eliminated substituent by some other group, and therefore, may be formally considered as alkyl-transferase.
- In this class, geometry or structure is changed within one molecule. Common names include racemase, epimerase, (cis-trans-)isomerase, tautomerase, mutase or cycloisomerase.
- In this class, two substrates are joined with the hydrolysis of ATP. The systematic name is X:Y ligase (ADP-forming). An obsolete common name is synthetase (not synthase in EC4).
Systematic Name of Metabolites (代謝物のシステム名)
This category has the following 8 subcategories, out of 8 total.