Category:BM

Revision as of 12:05, 9 March 2009

Basic Metabolism (基礎代謝)

Class Overview

(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

Table 1. Classification of Basic Metabolites

1st Class
BMIO: Inorganics 無機物 metals, phosphates etc. 金属、燐酸等	BMAA: Amino acids アミノ酸 proper amino acids	BMAX: Amino acid derivatives アミノ酸誘導体 peptides etc. 修飾物、ペプチド等
2nd Class BMIOMT Metals and halogens BMIONT Nitrogen compounds BMIOOX Oxidized elements BMIOPP phosphates BMIOSF sulfates	2nd Class BMAASn Straight chain BMAABn Branched chain	2nd Class BMAXSn Straight chain BMAXBn Branched chain BMAXDP Dipeptide BMAXTP Tripeptide
BMAC: Amino-cyclic 環をもつアミノ酸 Trp, Pro, His etc.	BMMC: Mono-cyclic 単環 benzene, pyrimidine etc. ベンゼン、ピリミジン環	BMCC: Conjugated cyclic 複合環 purine, porphyrin etc. プリン、ポルフィリン環
2nd Class BMACBZ with benzene BMACID with indole BMACIZ with imidazole BMACPL with pyrrolidine	2nd Class BMMCBZ Benzene BMMCPY Pyrimidine BMMCPD Pyridine BMMCIZ Imidazole BMMCQN Quinone BMMCPL Pyrrolidine BMMCTZ Thiazole BMMCLA Lactone BMMCAC Aliphatic cycle BMMCHC Hetero cycle BMMCVA Retinol BMMCAS Assembled cycle	2nd Class BMCCPU Purine BMCCPT Pteridine BMCCPP Porphyrin BMCCID Indole BMCCQI Quinoline BMCCNP Naphthalen BMCCCC Other condensed cycle BMCCBR Bridged cycle BMCCVE Tocopherol
BMFY: Fat acyl アシル Tree-shaped 樹状のもの	BMSU: Sugar 炭水化物 100px mono, disaccharide 単糖、二糖	BMXX: Others その他
2nd Class BMFYSn Straight chain BMFYBn Branched chain	2nd Class BMSUM4 Monosaccharide (C4) 70px BMSUM5 Monosaccharide (C5) 70px BMSUM6 Monosaccharide (C6) 70px BMSUM7 Monosaccharide (C >7 ) 70px	2nd Class BMXXSx Straight BMXXBx Branched

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 2.3.3.9).

EC class 1 Oxidoreductase (酸化還元酵素)

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).

EC class 2 Tranferase (転移酵素)

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).

EC class 3 Hydrolase (加水分解酵素)

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.

EC class 4 Lyase (除去付加酵素)

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.

EC class 5 Isomerase (異性化酵素)

In this class, geometry or structure is changed within one molecule. Common names include racemase, epimerase, (cis-trans-)isomerase, tautomerase, mutase or cycloisomerase.

EC class 6 Ligase (合成酵素)

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)

準備中