Enzyme Nomenclature. Recommendations 1992
Prepared on behalf of the advisory panel on peptidase nomenclature by Alan J. BARRETT, The Babraham Institute, Cambridge CB2 4AT, England
This document contains further additions and amendments to Enzyme Nomenclature 1992, published by Academic Press, Orlando, Florida. Supplements 1, 2, 3, 4 and 5 were published in Eur. J. Biochem. 223 (1994) 1-5 , Eur. J. Biochem. 232 (1995) 1-6 , Eur. J. Biochem. 237 (1996) 1-5 , Eur. J. Biochem. 250 (1997) 1-6 and Eur. J. Biochem. 264 (1999) 610-650, plus the supplement 6. Families of peptidases are referred to by use of the numbering system of Rawlings & Barrett (Methods Enzymol. 244 (1994) 19-61 and 461-486; Methods Enzymol. 248 (1995) 105-120 and 183-228; MEROPS database at http://meropslinks.iapc.bbsrc.ac.uk/). The full, amended text of subclass EC 3.4 (peptidases) of Enzyme Nomenclature 1992 may be found on the Internet at http://www.qmul.ac.uk/iubmb/enzyme/EC34/. Comments and suggestions on enzyme classification and nomenclature may be sent to Prof. K. F. Tipton, Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland. These changes were approved by NC-IUBMB, November 2000.
An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Recommended name: tripeptidyl-peptidase I
Reaction: Release of an N-terminal tripeptide from a polypeptide, but also endopeptidase activity.
Comments: A lysosomal enzyme active at acidic pH. Deficient in classical late-infantile neuronal ceroid lipofuscinosis brain tissue. In peptidase family A7 (pseudomonapepsin family) containing pepstatin-insensitive endopeptidases. Human gene locus 11p15. Formerly included in EC 3.4.14.8
Links to other databases: BRENDA, EXPASY, MEROPS, CAS registry number: 151662-36-1
Other names: tripeptidyl aminopeptidase; tripeptidyl peptidase
References
1. Ezaki, J., Takeda-Ezaki, M., Oda, K. & Kominami, E. Characterization of endopeptidase activity of tripeptidyl peptidase-I/CLN2 protein which is deficient in classical late infantile neuronal ceroid lipofuscinosis. Biochem. Biophys. Res. Commun. 268 (2000) 904-908. [Medline UI: 20145532]
2. Junaid, M.A., Wu, G.X. & Pullarkat, R.K. Purification and characterization of bovine brain lysosomal pepstatin-insensitive proteinase, the gene product deficient in the human late-infantile neuronal ceroid lipofuscinosis. J. Neurochem. 74 (2000) 287-294. [Medline UI: 20083421]
3. Warburton, M.J. & Bernardini, F. Tripeptidyl-peptidase I deficiency in classical late-infantile neuronal ceroid lipofuscinosis brain tissue. Evidence for defective peptidase rather than proteinase activity. J. Inherited Metab. Dis. 23 (2000) 145-154.
4. Ezaki, J., Tanida, I., Kanehagi, N. & Kominami, E. A lysosomal proteinase, the late infantile neuronal ceroid lipofuscinosis gene (CLN2) product, is essential for degradation of a hydrophobic protein, the subunit c of ATP synthase. J. Neurochem. 72 (1999) 2573-2582. [Medline UI: 99277372]
5. Rawlings, N.D. & Barrett, A.J. Tripeptidyl-peptidase I is apparently the CLN2 protein absent in classical late-infantile neuronal ceroid lipofuscinosis. Biochim. Biophys. Acta 1429 (1999) 496-500. [Medline UI: 99143780]
6. Sleat, D.E., Gin, R.M., Sohar, I., Wisniewski, K., Sklower-Brooks, S., Pullarkat, R.K., Palmer, D.N., Lerner, T.J., Boustany, R.M., Uldall, P., Siakotos, A.N., Donnelly, R.J. & Lobel, P. Mutational analysis of the defective protease in classic late-infantile neuronal ceroid lipofuscinosis, a neurodegenerative lysosomal storage disorder. Am. J. Hum. Genet. 64 (1999) 1511-1523. [Medline UI: 99264233]
Recommended name: carboxypeptidase E
Reaction: Release of C-terminal arginine or lysine residues from polypeptides
Comments: A zinc enzyme, activated by Co2+. Inhibited by 1,10-phenanthroline and other chelating agents. pH Optimum 5.6. Located in storage granules of secretory cells, and active in processing of protein hormones and bioactive peptides. In peptidase family M14 (carboxypeptidase A family). Formerly EC 3.4.17.10, carboxypeptidase H
Links to other databases: BRENDA, EXPASY, MEROPS, CAS registry number: 81876-85-1
Other names: carboxypeptidase H; enkephalin convertase; cobalt-stimulated chromaffin granule carboxypeptidase; insulin granule-associated carboxypeptidase
References
1. Qian, Y.M., Varlamov, O. & Fricker, L.D. Glu300 of rat carboxypeptidase E is essential for enzymatic activity but not substrate binding or routing to the regulated secretory pathway. J. Biol. Chem. 274 (1999) 11582-11586. [Medline UI: 99223470]
2. Fricker, L.D. (1998) Carboxypeptidase E/H. In Handbook of Proteolytic Enzymes (Barrett, A.J., Rawlings, N.D. & Woessner, J.F. eds), p.1341-1344, Academic Press, London.
3. Fricker, L.D. Methods for studying carboxypeptidase E. Methods Neurosci. 23 (1995) 237-250.
4. Manser, E., Fernandez, D., Loo,L., Goh, P.Y., Monfries, C., Hall, C. & Lim,L. Human carboxypeptidase E: isolation and characterisaton of the cDNA, sequence conservation, expression and processing in vitro. Biochem. J. 267 (1990) 517-525. [Medline UI: 90241164]
5. Fricker, L.D. Carboxypeptidase E. Annu. Rev. Physiol. 50 (1988) 309-321. [Medline UI: 88239527]
Recommended Name: cathepsin X
Reaction: Release of C-terminal amino acid residues with broad specificity, but lacks action on C-terminal proline. Shows weak endopeptidase activity
Comments: Cathepsin X is a lysosomal cysteine peptidase of family C1 (papain family). The pH optimum is dependent on the substrate and is 5.0 for the carboxypeptidase activity. Instable above pH 7.0. Compound E-64, leupeptin and antipain are inhibitors, but not cystatin C. Cathepsin X is ubiquitously distributed in mammalian tissues. The propeptide is extremely short (38 amino acid residues) and the proenzyme is catalytically active. Human gene locus: 20q13. Formerly EC 3.4.18.1, cysteine-type carboxypeptidase
Links to other databases: MEROPS CAS registry number: 37217-21-3
Other names: Cathepsin B2; cysteine-type carboxypeptidase; cathepsin IV; cathepsin Z; lysosomal carboxypeptidase B
References:
1. Nägler, D.K., Zhang, R., Tam, W., Sulea, T., Purisima, E.O., & Ménard, R. Human cathepsin X: A cysteine protease with unique carboxypeptidase activity. Biochemistry 38 (1999) 12648-12654. [Medline UI: 98307916]
2. Nägler, D.K. & Ménard, R. Human cathepsin X: A novel cysteine protease of the papain family with a very short proregion and unique insertions. FEBS Lett. 434 (1998) 135-139. [Medline UI: 98408845]
3. Santamaría, I. Velasco, G., Pendás, A.M., Fueyo, A. & López-Otín, C. Cathepsin Z, a novel human cysteine proteinase with a short propeptide domain and a unique chromosomal location. J. Biol. Chem. 273 (1998) 16816-16823. [Medline UI: 98307916]
4. McDonald, J.K. & Ellis, S. On the substrate specificity of cathepsins B1 and B2 including a new fluorogenic substrate for cathepsin B1. Life Sci. 17 (1975) 1269-1276. [Medline UI: 76074711]
5. Otto, K. & Riesenkönig, H. Improved purification of cathepsin B1 and cathepsin B2. Biochim. Biophys. Acta 379 (1975) 462-475. [Medline UI: 75128087]
6. Ninjoor, V., Taylor, S.L. & Tappel, A.L. Purification and characterization of rat liver lysosomal cathepsin B2. Biochim. Biophys. Acta 370 (1974) 308-321. [Medline UI: 75036229]
Recommended Name: cathepsin F
Reaction: The recombinant enzyme cleaves synthetic substrates with Phe and Leu (better than Val) in P2, with high specificity constant (kcat/Km) comparable to that of cathepsin L
Comments: Cathepsin F is a lysosomal cysteine endopeptidase of family C1 (papain family), most activite at pH 5.9. The enzyme is unstable at neutral pH values and is inhibited by compound E-64. Cathepsin F is expressed in most tissues of human, mouse and rat. Human gene locus: 11q13.1-13.3
Links to other databases: MEROPS
References:
1. Santamaría, I., Velasco, G., Pendás, A.M., Paz, A., & López-Otín, C. Molecular cloning and structural and functional chararcterization of cathepsin F, a new cysteine proteinase of the papain family with a long propeptide domain. J. Biol. Chem. 274 (1999) 13800-13809. [Medline UI: 99253926]
2. Nägler, D.K. Sulea, T., & Ménard, R. Full length cDNA of human cathepsin F predicts the presence of a cystatin domain at the N-terminus of the cysteine protease zymogen. Biochem. Biophys. Res. Commun. 257 (1999) 313-318. [Medline UI: 99216276]
3. Wex, T., Levy, B., Wex, H. & Brömme, D. (1999) Human cathepsins F and W: A new subgroup of cathepsins. Biochem. Biophys. Res. Commun. 259 (1999) 401-407. [Medline UI: 99293070]
4. Wang, B., Shi, G.-P., Yao, P.M., Li, Z., Chapman, H.A. & Brömme, D. Human cathepsin F. Molecular cloning, functional expression, tissue localization, and enzymatic characterization. J. Biol. Chem. 273 (1998) 32000-32008. [Medline UI: 99041967]
Recommended Name: cathepsin O
Reaction: The recombinant human enzyme hydrolyses synthetic endopeptidase substrates including Z-Phe-Arg-NHMec and Z-Arg-Arg-NHMec
Comments: Cathepsin O is a lysosomal cysteine peptidase of family C1 (papain family). The recombinant human enzyme is catalytically active at pH 6.0 and is inhibited by compound E-64. Cathepsin O is ubiquitously expressed in human tissues and the human gene locus is 4q31-32
Links to other databases: MEROPS
References:
1. Santamaría, I., Pendás, A.M., & López-Otín, C. Genomic structure and chromosomal localization of a human cathepsin O gene (CTSO). Genomics (1998) 53, 231-234. [Medline UI: 99009338]
2. Velasco, G., Ferrando, A.A., Puente, X.S., Sanchez, L.M. & López-Otín, C. Human cathepsin O. Molecular cloning from a breast carcinoma, production of the active enzyme in Escherichia coli, and expression analysis in human tissues. J. Biol. Chem. 269 (1994) 27136-27142. [Medline UI: 95014586]
Recommended Name: cathepsin V
Reaction: The recombinant enzyme hydrolyses proteins (serum albumin, collagen) and synthetic substrates (Z-Phe-Arg-NHMec > Z-Leu-Arg-NHMec > Z-Val-Arg-NHMec)
Comments: Cathepsin V is a human lysosomal cysteine endopeptidase of family C1 (papain family) that is maximally active at pH 5.7 and unstable at neutral pH. Compound E-64, leupeptin and chicken cystatin are inhibitors. Human cathepsin V shows expression restricted to thymus, testis, corneal epithelium and some colon and breast carcinomas. Human gene locus: 9q22.2
Links to other databases: MEROPS
Other names: Cathepsin L2; cathepsin U
References:
1. Brömme, D., Li, Z., Barnes, M. & Mehler, E. (1999) Human cathepsin V functional expression, tissue distribution, electrostatic surface potential, enzymatic characterization, and chromosomal localization. Biochemistry 38 (1999) 2377-2385. [Medline UI: 99155210]
2. Adachi, W., Kawamoto, S., Ohno, I., Nishida, K., Kinoshita, S., Matsubara, K., & Okubo, K. Isolation and characterization of human cathepsin V: a major proteinase in corneal epithelium. Invest. Ophthalmol. Vis. Sci. 39 (1998) 1789-1796. [Medline UI: 98394384]
3. Santamaría, I., Velasco, G., Cazorla, M., Fueyo, A., Campo, E. & López-Otín, C. Cathepsin L2, a novel human cysteine proteinase produced by breast and colorectal carcinomas. Cancer Res. 58 (1998) 1624-1630. [Medline UI: 98222936]
Recommended Name: nuclear-inclusion-a endopeptidase
Reaction: Hydrolyses glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln+(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Comments: The potyviruses cause diseases in plants, and inclusion bodies appear in the host cell nuclei, protein a of these being the endopeptidase. The enzyme finds practical use when encoded in vectors for the artificial expression of recombinant fusion proteins, since it can confer on them the capacity for autolytic cleavage. It is also reported that transgenic plants expressing the enzyme are resistant to viral infection. Type example of peptidase family C4.
Links to other databases: MEROPS
Other names: potyvirus NIa protease
References:
1. Fellers, J.P., Collins, G.B. & Hunt, A.G. The NIa-proteinase of different plant potyviruses provides specific resistance to viral infection. Crop Sci. 38 (1998) 1309-1319.
2. Kim, D.-H. & Choi, K.Y. (1998) Potyvirus NIa protease. In Handbook of Proteolytic Enzymes (Barrett, A.J., Rawlings, N.D. & Woessner, J.F. eds), p.721-723, Academic Press, London.
3. Takahashi, T., Nakanishi, M., Yao, Y., Uyeda, I. & Serizawa, N. Direct formation of human interleukin-11 by cis-acting system of plant virus protease in Escherichia coli. Biosci. Biotechnol. Biochem. 62 (1998) 953-958. [Medline UI: 98312032]
4. Kim, D.H., Hwang, D.C., Kang, B.H., Lew, J., Han, J.S., Song, B.O.D. & Choi, K.Y. Effects of internal cleavages and mutations in the C-terminal region of NIa protease of turnip mosaic potyvirus on the catalytic activity. Virology 226 (1996) 183-190. [Medline UI: 97124642]