E.C. nomenclature

An overview of databases yields the number of publicly accessible genomes 112 finished microbial and two eukaryotic genomes with over 300 overall in progress (as of April 2003). The number of enzymes with E.C. nomenclature is 4159 according to the ExPASy website and 3225 according to Brenda databases the number of accessible 3D structures totals 20 946, 18 872 of which are proteins. 

Of the 14500 entries currently in PDB, there are roughly 7200 enzyme structures. The Enzymes Structures Database, maintained by University College, University of London, focuses on this portion of PDB and offers links between the E.C. nomenclature of the IUBMB and the corresponding PDB entries. 

After ECE the E C nomenclature breaks down ECE can mean several different things (and one cannot be sure what an ECECCE" mechanism refers to ). At this point the mechanism needs to be further defined—for instance, by a reaction sequence or schematic drawing that indicates all possible chemical and electrochemical events considered. 

Nomenclature Committee oflUBMB (NC-1UBMB) (those additional to JCBN) A. Bairoch (Switzerland), H. Berman (USA), H. Bielka (Germany), C.R. Cantor (USA), W. Saenger (Germany), N. Sharon (Israel), E. van Lenten (USA), E.C. Webb (Australia). 

The E/Z nomenclature is here extended to apply not only to the C=C double bond but also to the bond linking the C=C and C=Q groups, which has some double bond character. 

The trivial name oxidoreductase is often used for enzymes that catalyze this reaction, but the systematic Enzyme Nomenclature includes them in the hydrolyase group (E.C. 4.2.1) and not in the oxidoreductase one. 

The three isomers are cis/trans isomers with respect to the substituents -phenyl and -0-0 at C-4, and -OC2H5, = 0 at the P atom. For convenience, we use the E/Z nomenclature recommended for ethylene diastereoisomer assignment. If we replace the plane in ethylenes through the sp and sp atoms by a plane vertical to the phosphacyclohexadiene (2,4) ring (thought of in first approximation as planar) through C—4 and the phosphorus atom, we have to denote the isomer with -0—0 at C—4 and = O at P on the same side of this plane as Z , and that with -0-0 at C—4 and -OC2H5 at P on different sides as E diasteroisomer. 

Table I is a list of all the enzymes that will be mentioned in this article. Neither the E.C. number nor the nomenclature name is convenient for repeated use in a discussion. Therefore, for the running text, we shall use mostly the time-established trivial names. We shall use 1 to 3-letter symbols in the Tables. For these, we have followed common practice as much as possible, but we had to innovate in some cases in order to avoid confusion.

An alternative mechanism for the oxidation of phenolic compounds is enzyme-catalyzed oxidation. Several classes of enzymes can catalyze this reaction. According to the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), these enzymes are part of the E C. 1 class of oxidoreductases (see the Internet web site http //www.chem.qmul.ac.uk/iubmb/enzyme/ECl). The three main classes of enzymes that catalyze the oxidation of phenolic compounds are the oxidoreductases that use oxygen as electron acceptor (E.C. 1.10.3), the peroxidases (E.C. 1.11.1), and monophenol monooxygenase (E.C. 

E. C. Webb, Enzyme Nomenclature, Academic Press, San Diego. CA. 

NC-IUBMN, In Webb, E. C. Editor. Enzyme Nomenclature 1992. ed. San Diego, California Academic Press, Inc. (1992). 

Deprotonation of a-alkylated acetic acid esters (e.g., the propionic acid ester of Figure 10.13) with LDA at —78°C selectively yields the -enolatcs.Thc quotation marks indicate that this application of the term is based on an extension of the E/Z-nomenclature here, the Cahn-Ingold-Prelog priority of the O I, i1 substituent is considered to be higher than the priority of the OR group. The deprotonation of the ester shown in Figure 10.13 occurs via the strain-free transition state A. The alternative transition state B is destabilized by a 1,3-diaxial interaction. 

E. C. Webb, Enzyme Nomenclature 1992, Academic Press, New York (1992). http // wvrw.chem.qnnir.ac.uk / iubmb / enzyme /... 

Beware The terms cis and trans do not always translate directly into Zand E, Consider the preparation of an enamine from cyclohexanone, which forms a double bond that you d probably call c/s (it s in a ring). But applying the rigorous rules laid down for E/Z nomenclature (p. 000), it is E. As for the useful terms syn and ant/(Chapter 16), there are no rigid rules for deciding whether a double bond is c/s or trans. 

Since this is in part an historical sketch, mention is made here of the interesting nomenclature suggestions of E. C. Franklin (10) for his liquid-ammonia work. We are accustomed to a so-called water world as far as chemical nomenclature and almost everything else are concerned. Franklin built up a corresponding nomenclature based on a liquid-ammonia world. 

For more details on fluorocarbon nomenclature R. E. Banks, Nomenclature in Houben-Weyl Organo-Fluorine Compounds (B. Baasner, H. Hagemann, J. C. Tatlow eds.), Vol. E 10a, Georg Thieme Verlag, Stuttgart, 2000, pp. 12-17. 

One special application comes when silyl enol ethers of allylic esters provide the starting material this is known as the Claisen-Ireland reaction. Esters normally form E-enolates 181 with LDA at low temperature. Because the E/Z nomenclature depends on the hierarchy of the substituents it is particularly ridiculous when applied to enol derivatives of esters. A lithium enolate (Li < C) would have the opposite stereochemical label from a silyl enol ether (Si > C) so a uniform scheme is adopted whereby the metal - O bond always has priority over the other. The mechanism 180 may remind you of the reasons for this - they are discussed in more detail in chapter 4. 

Webb, E. C. 1984. Enzyme nomenclature 1984 Recommendations of the nomenclature committee of the international union of biochemistry on the nomenclature and classification of enzyme-catalyzed reactions. Orlando, FL Academic Press. 

The first proposed nomenclature suggested that isomers should be called cis when W and Y are on the same side of the double bond and trans when they are on the opposite side (Fig. 1.2), provided W X and Y Z. However, this nomenclature was limited to the particular case where W and Y are identical. The more recent nomenclature of Cahn-Ingold-Prelog, based on the German Zusammen (Z) and Entgegen (E) notation, was extended to systems where W and Y are different substituents (Fig. 1.2). There is no direct relation between the two nomenclatures since they depend on the nature of substituents and so the Z isomer is not necessarily cis. Moreover, the order of priority is determined by the atomic number of each atom connected to the C=C double bond [1]. Although the E/Z nomenclature may also be applied to compounds B/B and C/C, these are considered as conformational isomers, whereas compounds A/A are configurational isomers. 

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