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Newsletter 1988
ARCHIVES
OF BIOCHEMISTRY
Vol. 260, No. 2, February
AND
BIOPHYSICS
1, pp. 851-854,1988
NOMENCLATURE
ANNOUNCEMENT
Newsletter
1988
Nomenclature Committee of IUB (NC-IUB) and IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) NC-IUB and JCBN hope that their Newsletters, designed to inform scientists about the work of the committees, may help the biochemical community. They are intended to call attention to features of recommendations that are recently published or that are in press. Comments on any item in this Newsletter, or any other aspect of biochemical nomenclature, may be sent to any member of the nomenclature committees, or to their secretary, Dr. A. CornishBowden, CNRS-CBM, 31 chemin Joseph-Aiguier, B. P. 71,13402 Marseille, France. There was no Newsletter in 1987. The most recent was therefore the 1986 Newsletter, which was published in Arch. B&hem. Biophys. 244,393-395 (1986); B&hem. Int. 12, following p. 180 (1986); B&hem. .I. 233, I-III (1986); Biol. Chem. Hqwpt-Seyler 367, l-4 (1986); Biosci Rep. 6,121-125 (1986); Eur. J. Biochem 154,485-487 (1986). An abridged version containing JCBN but not NC-IUB material appeared in Chem. Int. 8, No. 4,30-31 (1986). MEMBERSHIP The current membership of NC-IUB and JCBN is as follows: Dr. H. B. F. Dixon (Chairman of NC-IUB and JCBN, UK); Dr. J. R. Bull (JCBN, South Africa); Dr. C. R. Cantor (NC-IUB, U.S.A.); Dr. A. CornishBowden (JCBN: Secretary to both committees; France); Dr C. Liebecq (NC-IUB and JCBN; as representative of the IUB Committee of Editors of Biochemical Journals; Belgium); Dr. J. Reedijk (JCBN; the Netherlands); Dr. N. Sharon (NC-IUB; Israel); Dr. P. Venetianer (NC-IUB and JCBN; Hungary); Dr. J. F. G. Vliegenthart (NC-IUB and JCBN; the Netherlands). In addition the following are associate members: Dr. P. Karlson (NC-IUB; Federal Republic of Germany); Dr. K. Loening (NC-IUB, USA); Dr. G. P. Moss (JCBN; UK); Dr. E. J. Van Lenten (NCIUB, U.S.A.); Dr. E. C. Webb (NC-IUB; Australia). Dr. K. Loening (U.S.A.) retired from JCBN at the end of 1985, and Dr. G. P. Moss retired from JCBN at the end of 1986. Dr. J. R. Bull was appointed by IUPAC to fill one of the vacancies created.
ENZYME
NOMENCLATURE
Supplement 1 to the 1984 edition of Enzyme Ne menclature was published in Eur. J. B&hem. 157, l-26 (1986). It contains 107 entries for new enzymes that came to light after the 1984 edition was finalized at the end of November 1983. It also contains 55 revised entries for enzymes already listed. Work on a second supplement is progressing and NC-IUB hopes that this will be ready for publication toward the end of 1988. NC-IUB plans to issue further supplements as appropriate during the years until the next edition is published so as to keep Enzyme Nomenclature up to date. The 1984 edition was published for IUB by Academic Press Inc., Orlando, Florida, U.S.A. It is still available in both hardback (ISBN O-12-227162-9) at U.S. $45.00 and paperback (ISBN O-12-227163-7) at U.S. $19.50 NC-IUB is heavily dependent on information supplied by biochemists around the world for preparing new entries and modifying old ones. We take this opportunity to repeat our standing invitation to send comments on Enzyme Nomenclature to Emeritus Professor E. C. Webb, l/221 King’s Road, Mundingburra, Townsville, Queensland, Australia 4812, or to any member of NC-IUB or JCBN. A report form for this purpose, which is not copyright and may be freely copied, may be found inside the back cover of Enzyme Nomenclature. (The address shown at the bottom of this form has, however, been superseded by the one given here.) As noted in the 1986 Newsletter, it did not prove practicable to include a complete list of site-specific methyltransferases and deoxyriboncleases (“restriction enzymes”) in the 1984 edition of Enzyme Nomenclature. Such lists have, however, been prepared by Roberts (1) and by Kessler and Holtke (2). These lists are updated annually. BIOCHEMICAL NOMENCLATURE RELATED DOCUMENTS
AND
A new edition of the Compendium Biochemical Nomenclature and Related Documents has been pre851
0003-9861188 $3.00 Copyright All rights
0 1988 by Academic Press, Inc. of reproduction in any form reserved.
852
NOMENCLATURE
pared by the IUB Committee of Editors of Biochemical Journals. It includes all of the recommendations of NC-IUB, JCBN, and their predecessors that are considered to be still current, with any revisions noted, up to about 1986. It is to be published for IUB by the Biochemical Society, 7 Warwick Court, London WClR 5DP, England. NOMENCLATURE
OF PRENOLS
New recommendations on the nomenclature of prenols have now been published (3). The document sets out to systematize existing nomenclature, supplementing it where appropriate. It pays particular attention to stereochemical aspects of prenols and clarifies the different methods that are in use for describing the number and order of isoprene residues of short-chain prenols and those of polyprenols (with more than four isoprene units) and dolichols. Particular attention is paid to naturally occurring prenols and their phosphates, and their biosynthetic relationships are summarized in a chart that includes the EC numbers used in Enzyme Nomenclature for the enzymes involved. Various trivial names, such as geraniol (for transdiprenol), nerol (cis-diprenol), and farnesol (any of four stereoisomers of triprenol) are in common use, and these are listed and defined. Isoprenoids are the precursors of the terpenoids, which are named as hemiterpenoids, monterpenoids, sesquiterpenoids, diterpenoids, sesterterpenoids, triterpenoids, tetraterpenoids (also known as carotenoids) according to the number of pairs of isoprene units they contain. Rubber is an all-cis polymer with many residues, whereas gutta percha is the corresponding all-tram polymer. Other prenol derivatives defined in the document include juvenile hormones and dolichols. The structures of prenols may be represented compactly by a set of four one-letter symbols in which W represents the w-residue (furthest from the hydroxyl group), T a trans-residue, C a &s-residue, and S a saturated (dihydro) residue. For example, geranylgeranyl diphosphate may be symbolized in this system as WTTT-POP. The recommendations are based on the widespread practices of researchers in the field and JCBN hopes that the drawing together of the information into one document will assist the unambiguous description of prenols and their derivatives by both biochemists and chemists. NOMENCLATURE AND SYMBOLS FOR FOLIC ACID AND RELATED COMPOUNDS The folates are a group of heterocyclie compounds based on the 4-[(pteridin-6-ylmethyl)amino]benzoic
ANNOUNCEMENT acid skeleton conjugated with one or more L-glutamate units. They are the subject of recently published recommendations (4) that revise those prepared in 1964. They seek to alter existing practice as little as possible, but to take account of the great increase in knowledge of the stereochemistry that has occurred during the past 20 years. The revised recommendations recognize a simpler use of the prefix dihydro- to mean 7,8-dihydro- than was accepted previously, extending the already recognized use of tetrahydro- in the context of folates to mean 5,6,7,8-tetrahydro-, and taking account of the biological importance of the ?‘&dihydrofolates. All of the known natural stereoisomers have the same configuration at C-6 as (6S)-tetrahydrofolate, with the H on C-6 placed below the plane of the paper when the formula is drawn with the pterin ring system at the left and the benzoic acid group at topright (i.e., arranged so that N-l is at bottom-left and the numbering proceeds clockwise). However, they are variously designated as R or S according to the priority rules in the RS system (5). In cases where a mixture of diastereoisomers is present, the prefix awzbo-may be used to indicate this, as recommended for the nomenclature of tocopherols (6) and of amino acids and peptides (see paragraphs 3AA-13.2 and 3AA-19.2 in (7)); this has the advantage over rotthat it does not imply a mixture of enantiomers (with one enantiomer containing residues of D-ghtamak?) or a mixture in equal proportions of stereoisomers at C-6. Among the names proposed for common substituents, the name formimino for HN=CHis recommended as being more in accord with biochemical practice than the systematic names iminomethyl or formimidoyl, which are little used in biochemistry. The substituents methylene (CH,) and methenyl (CH) form bridges between N-5 and N-IO of reduced folates. In the latter case a positive charge is associated with the N * * * * CHxN structure, and it is suggested that this can be symbolized as -CH+-, as, for example, in (6R)-5,10-CH+-H4 folate to symbolize (GR)-5,10-methenyltetrahydrofolate. NOMENCLATURE
OF TETRAPYRROLES
Provisional recommendations on the nomenclature of tetrapyrroles were prepared by JCBN in 1978, and were published both in full (8) and in a much shorter report (9) that selected items of primary interest in mammalian biochemistry. These recommendations have been widely adopted and the present revision is based on comments received on the provisional document. In the revised recommendations two new trivial names, isobacteriochlorin and sirohydrochlorin, are defined, the names of linear tetrapyrroles are amended; and the system is extended to dipyrrole systems. Tables are provided to show the structures
NOMENCLATURE of the more commonly encountered compounds using the Fischer system for denoting isomers (the 15 isomers of mesoporphin defined by Fischer, as well as some isomers of biliverdin). The revised recommendations have now been published (10). NOMENCLATURE
OF GLYCOPEPTIDES
The recently published recommendations on the nomenclature of glycoproteins, glycopeptides, and peptidoglycans (11) were primarily concerned with the needs of carbohydrate chemists, for whom the naming of the carbohydrate part is the major point. Consequently, neither these recommendations nor those for the naming of peptides generally (7) include advice on the naming of glycopeptides in which both peptide and carbohydrate parts need to be specified. If a compound consists of ammonia both acylated by a peptide (“peptidylated”) and glycosylated, it can be named by taking either the peptide amide or the glycosylamine as the parent compound, according to convenience. An example of such a compound might be called N-[D-Met’, Proa]enkephalinyl-P-D-glucopyranosylamine by taking glucosylamine as the parent compound and adding the peptidyl substituent, or N’.5-(@-D-glucopyranosyl)[D-Met2, Pro’lenkephalinamide by taking the peptide amide as the parent compound and adding the glucosyl substituent. In the latter case, the locant @.5 follows the recommendation in section 3AA-13.4 of the recommendations on amino acids and peptides (7): it means that the group is attached to atom N-1.5, i.e., the nitrogen atom on C-l of the fifth residue of the peptide. CHITOBIOSE There is ambiguity in the literature as to the identity of chitobiose. Although chitin consists of 01-4 linked N-acetylglucosamine residues, chitobiose contains glucosamine residues instead. This convention derives from the fact that chitobiose was originally (12) isolated from acetolysis of chitin as its octaacetate, and the name chitobiose was given to the parent disaccharide by analogy with cellobiose, the repeating disaccharide from cellulose. Subsequent investigation of the linkage between the glucosamine residues of chitin (13) led to the convention that chitobiose is a dimer of glucosamine, so that the repeating unit of chitin is the N-acetylated derivative of chitobiose, i.e., N,N’-diacetylchitobiose. More precisely, chitobiose is the fl(1+4) dimer of glucosamine, symbolized GlcN@-4GlcN in the short form recommended in the document on glycoproteins (ll), and the corresponding N,N’-diacetyl derivative is N-acetyl-D-glucosamine /3(1*4) N-acetyl-D-glucosamine (GlcNAc@4GlcNAc) or N,N’-diacetylchitobiose. By analogy the higher homolog is N,N’,N”-triaeetylchitotriose (GlcNAc@-4GlcNA$-4GlcNAc).
853
ANNOUNCEMENT WHAT
IS rDNA?
The increasingly frequent use of the term recombinant DNA in the scientific literature has led to the appearance of the abbreviation rDNA to denote both the technology itself and the DNA molecules that result from it. However, the same abbreviation was preempted some time ago to refer to ribosomal DNA, the genes coding for ribosimal RNA. Because rRNA is already a widely used biochemical abbreviation, it is a natural extension to designate rDNA for ribosomal DNA. Thus we would discourage the use of rDNA to refer to recombinant DNA. While alternative abbreviations for recombinant DNA have been suggested (14), it hardly seems necessary to have any standard abbreviation for such a broad class of techniques and molecules. THE P-450 GENE
SUPERFAMILY
The confusion generated by the wide variety of names used during the past two decades has led to the constitution by a group of experts of a Committee on Standardized Nomenclature of the P-450 Genes, which has recently published its recommendations (15, 16). We draw the attention of biochemists to these proposals for information, but ask that any comments on them should be directed to the corresponding secretary of the committee: Dr. D. W. Nebert, Building 10, Room 6C-101, National Institutes of Health, Bethesda, Maryland 20892, U.S.A. We also note that NC-IUB referred to the enzymes concerned as heme-thiolate proteins rather than as P-450 proteins or cytochrome P-450 enzymes in the current edition of Enzyme Nomenclature, to avoid the suggestion that they were cytochromes. REFERENCES 1. ROBERTS, R. J. (1987) Nucl. Acids Res. 15, Suppl., r189-r21’7. 2. KESSLER, C., AND H~LTKE, H.-J. (1986) Gene 47, 1-154. 3. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of prenols. Recommendations 1986. Eur. J. Biothem. 167,181-184 (1987); Pure AppL Chem. 59, 683-689 (1987). 4. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbols for folic acid and related compounds. Reccommendations 1986. Eur. J. B&hem. 168, 251-253 (1987); Pure AppL Chem 59, 833-836 (1987). 5. International Union of Biochemistry (1979) Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F, and H (Rigaudy, J., and Klesney, S. P., Eds.), pp. 486-490, Pergamon Press, Oxford.
854
NOMENCLATURE
6. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tocopherols and related compounds. Recommendations 1981. Arch. Biochem. Biophys. 218, 347-348 (1982); Eur. J. B&hem. 123, 473-475 (1982); Mol. Cell Biochem. 49, 183-185 (1982); Pure Appl C&m. 54,1507-1510 (1982). 7. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. Biochem. J. 219,345-373 (1984); Eur. J. Biochem. 138,9-37 (1984); Int. J. Pept. Prot. Res. 24, following p. 84 (1984); J. Biol. Chem. 260, 14-42 (1985); Pure Appl. Chem. 56, 595-624 (1984); Spec. Period Rep. Amino Acids Pept. 16, 387-410 (1985). Corrections: Eur. J. Biochem. 152,l (1985). 8. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1978. Eur. J. Biochem. 108, l-30 (1980); Pure Appl. Chem. 51,2251-2304 (1979). 9. KARLSON, P. (1981) Hoppe-Seylerk
2. Physiol.
ANNOUNCEMENT Chem. 362, VII-XII (1981); J. C&u. Chem C&z. Biochem. 19,43-47 (1981). 10. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986. Pure Appl. Chem. 59,779-832 (1987). 11. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of glycoproteins, glycopeptides, and peptidoglycans. Recommendations 1985. Eur. J. B&hem 159, l-6 (1986); Glycoconjugate J. 3,123-134 (1986); J. Biol Chem. 262,13-18 (1987). 12. BERGMANN,M., ZERVAS,L., AND SILBERKWEIT,E. (1931) Natwwi.ssenscha&n 19,ZO. 13. ZECHMEISTER,L., GRASSMAN,W., TUTH, G., AND BENDER,R. (1932) Chem. Ber. 65,1706. 14. KING, R. C. (1986) Nature (London) 322,780. 15. NEBERT,D. W., ADESNIK, M., COON,M. J., ESTABROOK,R. W., GONZALEZ,F. J., GUENGERICH, F. P., GUNSALUS, I. C., JOHNSON, E. F., KEMPER, B., LEVIN, W., PHILLIPS, I. R., SATO, R., AND WATERMAN,M. R. (1987) DNA 6,1-11. 16. NEBERT,D. W., AND GONZALEZ,F. J. (1987) Annu. Rex Biochem. 56,945-993.
OF BIOCHEMISTRY
Vol. 260, No. 2, February
AND
BIOPHYSICS
1, pp. 851-854,1988
NOMENCLATURE
ANNOUNCEMENT
Newsletter
1988
Nomenclature Committee of IUB (NC-IUB) and IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) NC-IUB and JCBN hope that their Newsletters, designed to inform scientists about the work of the committees, may help the biochemical community. They are intended to call attention to features of recommendations that are recently published or that are in press. Comments on any item in this Newsletter, or any other aspect of biochemical nomenclature, may be sent to any member of the nomenclature committees, or to their secretary, Dr. A. CornishBowden, CNRS-CBM, 31 chemin Joseph-Aiguier, B. P. 71,13402 Marseille, France. There was no Newsletter in 1987. The most recent was therefore the 1986 Newsletter, which was published in Arch. B&hem. Biophys. 244,393-395 (1986); B&hem. Int. 12, following p. 180 (1986); B&hem. .I. 233, I-III (1986); Biol. Chem. Hqwpt-Seyler 367, l-4 (1986); Biosci Rep. 6,121-125 (1986); Eur. J. Biochem 154,485-487 (1986). An abridged version containing JCBN but not NC-IUB material appeared in Chem. Int. 8, No. 4,30-31 (1986). MEMBERSHIP The current membership of NC-IUB and JCBN is as follows: Dr. H. B. F. Dixon (Chairman of NC-IUB and JCBN, UK); Dr. J. R. Bull (JCBN, South Africa); Dr. C. R. Cantor (NC-IUB, U.S.A.); Dr. A. CornishBowden (JCBN: Secretary to both committees; France); Dr C. Liebecq (NC-IUB and JCBN; as representative of the IUB Committee of Editors of Biochemical Journals; Belgium); Dr. J. Reedijk (JCBN; the Netherlands); Dr. N. Sharon (NC-IUB; Israel); Dr. P. Venetianer (NC-IUB and JCBN; Hungary); Dr. J. F. G. Vliegenthart (NC-IUB and JCBN; the Netherlands). In addition the following are associate members: Dr. P. Karlson (NC-IUB; Federal Republic of Germany); Dr. K. Loening (NC-IUB, USA); Dr. G. P. Moss (JCBN; UK); Dr. E. J. Van Lenten (NCIUB, U.S.A.); Dr. E. C. Webb (NC-IUB; Australia). Dr. K. Loening (U.S.A.) retired from JCBN at the end of 1985, and Dr. G. P. Moss retired from JCBN at the end of 1986. Dr. J. R. Bull was appointed by IUPAC to fill one of the vacancies created.
ENZYME
NOMENCLATURE
Supplement 1 to the 1984 edition of Enzyme Ne menclature was published in Eur. J. B&hem. 157, l-26 (1986). It contains 107 entries for new enzymes that came to light after the 1984 edition was finalized at the end of November 1983. It also contains 55 revised entries for enzymes already listed. Work on a second supplement is progressing and NC-IUB hopes that this will be ready for publication toward the end of 1988. NC-IUB plans to issue further supplements as appropriate during the years until the next edition is published so as to keep Enzyme Nomenclature up to date. The 1984 edition was published for IUB by Academic Press Inc., Orlando, Florida, U.S.A. It is still available in both hardback (ISBN O-12-227162-9) at U.S. $45.00 and paperback (ISBN O-12-227163-7) at U.S. $19.50 NC-IUB is heavily dependent on information supplied by biochemists around the world for preparing new entries and modifying old ones. We take this opportunity to repeat our standing invitation to send comments on Enzyme Nomenclature to Emeritus Professor E. C. Webb, l/221 King’s Road, Mundingburra, Townsville, Queensland, Australia 4812, or to any member of NC-IUB or JCBN. A report form for this purpose, which is not copyright and may be freely copied, may be found inside the back cover of Enzyme Nomenclature. (The address shown at the bottom of this form has, however, been superseded by the one given here.) As noted in the 1986 Newsletter, it did not prove practicable to include a complete list of site-specific methyltransferases and deoxyriboncleases (“restriction enzymes”) in the 1984 edition of Enzyme Nomenclature. Such lists have, however, been prepared by Roberts (1) and by Kessler and Holtke (2). These lists are updated annually. BIOCHEMICAL NOMENCLATURE RELATED DOCUMENTS
AND
A new edition of the Compendium Biochemical Nomenclature and Related Documents has been pre851
0003-9861188 $3.00 Copyright All rights
0 1988 by Academic Press, Inc. of reproduction in any form reserved.
852
NOMENCLATURE
pared by the IUB Committee of Editors of Biochemical Journals. It includes all of the recommendations of NC-IUB, JCBN, and their predecessors that are considered to be still current, with any revisions noted, up to about 1986. It is to be published for IUB by the Biochemical Society, 7 Warwick Court, London WClR 5DP, England. NOMENCLATURE
OF PRENOLS
New recommendations on the nomenclature of prenols have now been published (3). The document sets out to systematize existing nomenclature, supplementing it where appropriate. It pays particular attention to stereochemical aspects of prenols and clarifies the different methods that are in use for describing the number and order of isoprene residues of short-chain prenols and those of polyprenols (with more than four isoprene units) and dolichols. Particular attention is paid to naturally occurring prenols and their phosphates, and their biosynthetic relationships are summarized in a chart that includes the EC numbers used in Enzyme Nomenclature for the enzymes involved. Various trivial names, such as geraniol (for transdiprenol), nerol (cis-diprenol), and farnesol (any of four stereoisomers of triprenol) are in common use, and these are listed and defined. Isoprenoids are the precursors of the terpenoids, which are named as hemiterpenoids, monterpenoids, sesquiterpenoids, diterpenoids, sesterterpenoids, triterpenoids, tetraterpenoids (also known as carotenoids) according to the number of pairs of isoprene units they contain. Rubber is an all-cis polymer with many residues, whereas gutta percha is the corresponding all-tram polymer. Other prenol derivatives defined in the document include juvenile hormones and dolichols. The structures of prenols may be represented compactly by a set of four one-letter symbols in which W represents the w-residue (furthest from the hydroxyl group), T a trans-residue, C a &s-residue, and S a saturated (dihydro) residue. For example, geranylgeranyl diphosphate may be symbolized in this system as WTTT-POP. The recommendations are based on the widespread practices of researchers in the field and JCBN hopes that the drawing together of the information into one document will assist the unambiguous description of prenols and their derivatives by both biochemists and chemists. NOMENCLATURE AND SYMBOLS FOR FOLIC ACID AND RELATED COMPOUNDS The folates are a group of heterocyclie compounds based on the 4-[(pteridin-6-ylmethyl)amino]benzoic
ANNOUNCEMENT acid skeleton conjugated with one or more L-glutamate units. They are the subject of recently published recommendations (4) that revise those prepared in 1964. They seek to alter existing practice as little as possible, but to take account of the great increase in knowledge of the stereochemistry that has occurred during the past 20 years. The revised recommendations recognize a simpler use of the prefix dihydro- to mean 7,8-dihydro- than was accepted previously, extending the already recognized use of tetrahydro- in the context of folates to mean 5,6,7,8-tetrahydro-, and taking account of the biological importance of the ?‘&dihydrofolates. All of the known natural stereoisomers have the same configuration at C-6 as (6S)-tetrahydrofolate, with the H on C-6 placed below the plane of the paper when the formula is drawn with the pterin ring system at the left and the benzoic acid group at topright (i.e., arranged so that N-l is at bottom-left and the numbering proceeds clockwise). However, they are variously designated as R or S according to the priority rules in the RS system (5). In cases where a mixture of diastereoisomers is present, the prefix awzbo-may be used to indicate this, as recommended for the nomenclature of tocopherols (6) and of amino acids and peptides (see paragraphs 3AA-13.2 and 3AA-19.2 in (7)); this has the advantage over rotthat it does not imply a mixture of enantiomers (with one enantiomer containing residues of D-ghtamak?) or a mixture in equal proportions of stereoisomers at C-6. Among the names proposed for common substituents, the name formimino for HN=CHis recommended as being more in accord with biochemical practice than the systematic names iminomethyl or formimidoyl, which are little used in biochemistry. The substituents methylene (CH,) and methenyl (CH) form bridges between N-5 and N-IO of reduced folates. In the latter case a positive charge is associated with the N * * * * CHxN structure, and it is suggested that this can be symbolized as -CH+-, as, for example, in (6R)-5,10-CH+-H4 folate to symbolize (GR)-5,10-methenyltetrahydrofolate. NOMENCLATURE
OF TETRAPYRROLES
Provisional recommendations on the nomenclature of tetrapyrroles were prepared by JCBN in 1978, and were published both in full (8) and in a much shorter report (9) that selected items of primary interest in mammalian biochemistry. These recommendations have been widely adopted and the present revision is based on comments received on the provisional document. In the revised recommendations two new trivial names, isobacteriochlorin and sirohydrochlorin, are defined, the names of linear tetrapyrroles are amended; and the system is extended to dipyrrole systems. Tables are provided to show the structures
NOMENCLATURE of the more commonly encountered compounds using the Fischer system for denoting isomers (the 15 isomers of mesoporphin defined by Fischer, as well as some isomers of biliverdin). The revised recommendations have now been published (10). NOMENCLATURE
OF GLYCOPEPTIDES
The recently published recommendations on the nomenclature of glycoproteins, glycopeptides, and peptidoglycans (11) were primarily concerned with the needs of carbohydrate chemists, for whom the naming of the carbohydrate part is the major point. Consequently, neither these recommendations nor those for the naming of peptides generally (7) include advice on the naming of glycopeptides in which both peptide and carbohydrate parts need to be specified. If a compound consists of ammonia both acylated by a peptide (“peptidylated”) and glycosylated, it can be named by taking either the peptide amide or the glycosylamine as the parent compound, according to convenience. An example of such a compound might be called N-[D-Met’, Proa]enkephalinyl-P-D-glucopyranosylamine by taking glucosylamine as the parent compound and adding the peptidyl substituent, or N’.5-(@-D-glucopyranosyl)[D-Met2, Pro’lenkephalinamide by taking the peptide amide as the parent compound and adding the glucosyl substituent. In the latter case, the locant @.5 follows the recommendation in section 3AA-13.4 of the recommendations on amino acids and peptides (7): it means that the group is attached to atom N-1.5, i.e., the nitrogen atom on C-l of the fifth residue of the peptide. CHITOBIOSE There is ambiguity in the literature as to the identity of chitobiose. Although chitin consists of 01-4 linked N-acetylglucosamine residues, chitobiose contains glucosamine residues instead. This convention derives from the fact that chitobiose was originally (12) isolated from acetolysis of chitin as its octaacetate, and the name chitobiose was given to the parent disaccharide by analogy with cellobiose, the repeating disaccharide from cellulose. Subsequent investigation of the linkage between the glucosamine residues of chitin (13) led to the convention that chitobiose is a dimer of glucosamine, so that the repeating unit of chitin is the N-acetylated derivative of chitobiose, i.e., N,N’-diacetylchitobiose. More precisely, chitobiose is the fl(1+4) dimer of glucosamine, symbolized GlcN@-4GlcN in the short form recommended in the document on glycoproteins (ll), and the corresponding N,N’-diacetyl derivative is N-acetyl-D-glucosamine /3(1*4) N-acetyl-D-glucosamine (GlcNAc@4GlcNAc) or N,N’-diacetylchitobiose. By analogy the higher homolog is N,N’,N”-triaeetylchitotriose (GlcNAc@-4GlcNA$-4GlcNAc).
853
ANNOUNCEMENT WHAT
IS rDNA?
The increasingly frequent use of the term recombinant DNA in the scientific literature has led to the appearance of the abbreviation rDNA to denote both the technology itself and the DNA molecules that result from it. However, the same abbreviation was preempted some time ago to refer to ribosomal DNA, the genes coding for ribosimal RNA. Because rRNA is already a widely used biochemical abbreviation, it is a natural extension to designate rDNA for ribosomal DNA. Thus we would discourage the use of rDNA to refer to recombinant DNA. While alternative abbreviations for recombinant DNA have been suggested (14), it hardly seems necessary to have any standard abbreviation for such a broad class of techniques and molecules. THE P-450 GENE
SUPERFAMILY
The confusion generated by the wide variety of names used during the past two decades has led to the constitution by a group of experts of a Committee on Standardized Nomenclature of the P-450 Genes, which has recently published its recommendations (15, 16). We draw the attention of biochemists to these proposals for information, but ask that any comments on them should be directed to the corresponding secretary of the committee: Dr. D. W. Nebert, Building 10, Room 6C-101, National Institutes of Health, Bethesda, Maryland 20892, U.S.A. We also note that NC-IUB referred to the enzymes concerned as heme-thiolate proteins rather than as P-450 proteins or cytochrome P-450 enzymes in the current edition of Enzyme Nomenclature, to avoid the suggestion that they were cytochromes. REFERENCES 1. ROBERTS, R. J. (1987) Nucl. Acids Res. 15, Suppl., r189-r21’7. 2. KESSLER, C., AND H~LTKE, H.-J. (1986) Gene 47, 1-154. 3. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of prenols. Recommendations 1986. Eur. J. Biothem. 167,181-184 (1987); Pure AppL Chem. 59, 683-689 (1987). 4. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbols for folic acid and related compounds. Reccommendations 1986. Eur. J. B&hem. 168, 251-253 (1987); Pure AppL Chem 59, 833-836 (1987). 5. International Union of Biochemistry (1979) Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F, and H (Rigaudy, J., and Klesney, S. P., Eds.), pp. 486-490, Pergamon Press, Oxford.
854
NOMENCLATURE
6. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tocopherols and related compounds. Recommendations 1981. Arch. Biochem. Biophys. 218, 347-348 (1982); Eur. J. B&hem. 123, 473-475 (1982); Mol. Cell Biochem. 49, 183-185 (1982); Pure Appl C&m. 54,1507-1510 (1982). 7. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. Biochem. J. 219,345-373 (1984); Eur. J. Biochem. 138,9-37 (1984); Int. J. Pept. Prot. Res. 24, following p. 84 (1984); J. Biol. Chem. 260, 14-42 (1985); Pure Appl. Chem. 56, 595-624 (1984); Spec. Period Rep. Amino Acids Pept. 16, 387-410 (1985). Corrections: Eur. J. Biochem. 152,l (1985). 8. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1978. Eur. J. Biochem. 108, l-30 (1980); Pure Appl. Chem. 51,2251-2304 (1979). 9. KARLSON, P. (1981) Hoppe-Seylerk
2. Physiol.
ANNOUNCEMENT Chem. 362, VII-XII (1981); J. C&u. Chem C&z. Biochem. 19,43-47 (1981). 10. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986. Pure Appl. Chem. 59,779-832 (1987). 11. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of glycoproteins, glycopeptides, and peptidoglycans. Recommendations 1985. Eur. J. B&hem 159, l-6 (1986); Glycoconjugate J. 3,123-134 (1986); J. Biol Chem. 262,13-18 (1987). 12. BERGMANN,M., ZERVAS,L., AND SILBERKWEIT,E. (1931) Natwwi.ssenscha&n 19,ZO. 13. ZECHMEISTER,L., GRASSMAN,W., TUTH, G., AND BENDER,R. (1932) Chem. Ber. 65,1706. 14. KING, R. C. (1986) Nature (London) 322,780. 15. NEBERT,D. W., ADESNIK, M., COON,M. J., ESTABROOK,R. W., GONZALEZ,F. J., GUENGERICH, F. P., GUNSALUS, I. C., JOHNSON, E. F., KEMPER, B., LEVIN, W., PHILLIPS, I. R., SATO, R., AND WATERMAN,M. R. (1987) DNA 6,1-11. 16. NEBERT,D. W., AND GONZALEZ,F. J. (1987) Annu. Rex Biochem. 56,945-993.