Abstract
The available amino acid sequences of peptidases have been examined, and the enzymes have been allocated to evolutionary families. Some of the families can be grouped together in 'clans' that show signs of distant relationship, but nevertheless, it appears that there may be as many as 60 evolutionary lines of peptidases with separate origins. Some of these contain members with quite diverse peptidase activities, and yet there are some striking examples of convergence. We suggest that the classification by families could be used as an extension of the current classification by catalytic type.
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- Amerik AYu, Antonov V. K., Gorbalenya A. E., Kotova S. A., Rotanova T. V., Shimbarevich E. V. Site-directed mutagenesis of La protease. A catalytically active serine residue. FEBS Lett. 1991 Aug 5;287(1-2):211–214. doi: 10.1016/0014-5793(91)80053-6. [DOI] [PubMed] [Google Scholar]
- Bachovchin W. W., Plaut A. G., Flentke G. R., Lynch M., Kettner C. A. Inhibition of IgA1 proteinases from Neisseria gonorrhoeae and Hemophilus influenzae by peptide prolyl boronic acids. J Biol Chem. 1990 Mar 5;265(7):3738–3743. [PubMed] [Google Scholar]
- Barker W. C., George D. G., Hunt L. T. Protein sequence database. Methods Enzymol. 1990;183:31–49. doi: 10.1016/0076-6879(90)83005-t. [DOI] [PubMed] [Google Scholar]
- Barr P. J. Mammalian subtilisins: the long-sought dibasic processing endoproteases. Cell. 1991 Jul 12;66(1):1–3. doi: 10.1016/0092-8674(91)90129-m. [DOI] [PubMed] [Google Scholar]
- Barrett A. J., Rawlings N. D. Oligopeptidases, and the emergence of the prolyl oligopeptidase family. Biol Chem Hoppe Seyler. 1992 Jul;373(7):353–360. doi: 10.1515/bchm3.1992.373.2.353. [DOI] [PubMed] [Google Scholar]
- Bazan J. F., Fletterick R. J. Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proc Natl Acad Sci U S A. 1988 Nov;85(21):7872–7876. doi: 10.1073/pnas.85.21.7872. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Becker A. B., Roth R. A. An unusual active site identified in a family of zinc metalloendopeptidases. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3835–3839. doi: 10.1073/pnas.89.9.3835. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Behrens M., Michaelis G., Pratje E. Mitochondrial inner membrane protease 1 of Saccharomyces cerevisiae shows sequence similarity to the Escherichia coli leader peptidase. Mol Gen Genet. 1991 Aug;228(1-2):167–176. doi: 10.1007/BF00282462. [DOI] [PubMed] [Google Scholar]
- Bode W., Gomis-Rüth F. X., Huber R., Zwilling R., Stöcker W. Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases. Nature. 1992 Jul 9;358(6382):164–167. doi: 10.1038/358164a0. [DOI] [PubMed] [Google Scholar]
- Chambers T. J., Weir R. C., Grakoui A., McCourt D. W., Bazan J. F., Fletterick R. J., Rice C. M. Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8898–8902. doi: 10.1073/pnas.87.22.8898. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Choi H. K., Tong L., Minor W., Dumas P., Boege U., Rossmann M. G., Wengler G. Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature. 1991 Nov 7;354(6348):37–43. doi: 10.1038/354037a0. [DOI] [PubMed] [Google Scholar]
- Delaney S. J., Hayward D. C., Barleben F., Fischbach K. F., Miklos G. L. Molecular cloning and analysis of small optic lobes, a structural brain gene of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7214–7218. doi: 10.1073/pnas.88.16.7214. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Delbaere L. T., Hutcheon W. L., James M. N., Thiessen W. E. Tertiary structural differences between microbial serine proteases and pancreatic serine enzymes. Nature. 1975 Oct 30;257(5529):758–763. doi: 10.1038/257758a0. [DOI] [PubMed] [Google Scholar]
- DiBenedetto A. J., Harada H. A., Wolfner M. F. Structure, cell-specific expression, and mating-induced regulation of a Drosophila melanogaster male accessory gland gene. Dev Biol. 1990 May;139(1):134–148. doi: 10.1016/0012-1606(90)90284-p. [DOI] [PubMed] [Google Scholar]
- Dietrich R. A., Maslyar D. J., Heupel R. C., Harada J. J. Spatial patterns of gene expression in Brassica napus seedlings: identification of a cortex-specific gene and localization of mRNAs encoding isocitrate lyase and a polypeptide homologous to proteinases. Plant Cell. 1989 Jan;1(1):73–80. doi: 10.1105/tpc.1.1.73. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Drapeau G. R. The primary structure of staphylococcal protease. Can J Biochem. 1978 Jun;56(6):534–544. doi: 10.1139/o78-082. [DOI] [PubMed] [Google Scholar]
- Gorbalenya A. E., Donchenko A. P., Blinov V. M., Koonin E. V. Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Lett. 1989 Jan 30;243(2):103–114. doi: 10.1016/0014-5793(89)80109-7. [DOI] [PubMed] [Google Scholar]
- Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O., Van Beeumen J., Frère J. M., Ghuysen J. M. Primary and predicted secondary structures of the Actinomadura R39 extracellular DD-peptidase, a penicillin-binding protein (PBP) related to the Escherichia coli PBP4. Biochem J. 1992 Mar 15;282(Pt 3):781–788. doi: 10.1042/bj2820781. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guerrero F. D., Jones J. T., Mullet J. E. Turgor-responsive gene transcription and RNA levels increase rapidly when pea shoots are wilted. Sequence and expression of three inducible genes. Plant Mol Biol. 1990 Jul;15(1):11–26. doi: 10.1007/BF00017720. [DOI] [PubMed] [Google Scholar]
- Hartley B. S. Homologies in serine proteinases. Philos Trans R Soc Lond B Biol Sci. 1970 Feb 12;257(813):77–87. doi: 10.1098/rstb.1970.0010. [DOI] [PubMed] [Google Scholar]
- Ikeda M., Yaginuma T., Kobayashi M., Yamashita O. cDNA cloning, sequencing and temporal expression of the protease responsible for vitellin degradation in the silkworm, Bombyx mori. Comp Biochem Physiol B. 1991;99(2):405–411. doi: 10.1016/0305-0491(91)90062-i. [DOI] [PubMed] [Google Scholar]
- Joris B., Ghuysen J. M., Dive G., Renard A., Dideberg O., Charlier P., Frère J. M., Kelly J. A., Boyington J. C., Moews P. C. The active-site-serine penicillin-recognizing enzymes as members of the Streptomyces R61 DD-peptidase family. Biochem J. 1988 Mar 1;250(2):313–324. doi: 10.1042/bj2500313. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kahn P., Cameron G. EMBL Data Library. Methods Enzymol. 1990;183:23–31. doi: 10.1016/0076-6879(90)83004-s. [DOI] [PubMed] [Google Scholar]
- Kelly J. A., Knox J. R., Zhao H., Frère J. M., Ghaysen J. M. Crystallographic mapping of beta-lactams bound to a D-alanyl-D-alanine peptidase target enzyme. J Mol Biol. 1989 Sep 20;209(2):281–295. doi: 10.1016/0022-2836(89)90277-5. [DOI] [PubMed] [Google Scholar]
- Kinoshita T., Fukuzawa H., Shimada T., Saito T., Matsuda Y. Primary structure and expression of a gamete lytic enzyme in Chlamydomonas reinhardtii: similarity of functional domains to matrix metalloproteases. Proc Natl Acad Sci U S A. 1992 May 15;89(10):4693–4697. doi: 10.1073/pnas.89.10.4693. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Koehler S. M., Ho T. H. Hormonal regulation, processing, and secretion of cysteine proteinases in barley aleurone layers. Plant Cell. 1990 Aug;2(8):769–783. doi: 10.1105/tpc.2.8.769. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Le Moual H., Devault A., Roques B. P., Crine P., Boileau G. Identification of glutamic acid 646 as a zinc-coordinating residue in endopeptidase-24.11. J Biol Chem. 1991 Aug 25;266(24):15670–15674. [PubMed] [Google Scholar]
- Li W. B., Bzik D. J., Horii T., Inselburg J. Structure and expression of the Plasmodium falciparum SERA gene. Mol Biochem Parasitol. 1989 Feb;33(1):13–25. doi: 10.1016/0166-6851(89)90037-6. [DOI] [PubMed] [Google Scholar]
- Liao D. I., Remington S. J. Structure of wheat serine carboxypeptidase II at 3.5-A resolution. A new class of serine proteinase. J Biol Chem. 1990 Apr 25;265(12):6528–6531. doi: 10.2210/pdb2sc2/pdb. [DOI] [PubMed] [Google Scholar]
- Light A., Janska H. The amino-terminal sequence of the catalytic subunit of bovine enterokinase. J Protein Chem. 1991 Oct;10(5):475–480. doi: 10.1007/BF01025475. [DOI] [PubMed] [Google Scholar]
- Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
- Matthews B. W., Weaver L. H., Kester W. R. The conformation of thermolysin. J Biol Chem. 1974 Dec 25;249(24):8030–8044. [PubMed] [Google Scholar]
- Mayo M. A., Robinson D. J., Jolly C. A., Hyman L. Nucleotide sequence of potato leafroll luteovirus RNA. J Gen Virol. 1989 May;70(Pt 5):1037–1051. doi: 10.1099/0022-1317-70-5-1037. [DOI] [PubMed] [Google Scholar]
- Medina J. F., Wetterholm A., Rådmark O., Shapiro R., Haeggström J. Z., Vallee B. L., Samuelsson B. Leukotriene A4 hydrolase: determination of the three zinc-binding ligands by site-directed mutagenesis and zinc analysis. Proc Natl Acad Sci U S A. 1991 Sep 1;88(17):7620–7624. doi: 10.1073/pnas.88.17.7620. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Meulenberg J. J., Sellink E., Loenen W. A., Riegman N. H., van Kleef M., Postma P. W. Cloning of Klebsiella pneumoniae pqq genes and PQQ biosynthesis in Escherichia coli. FEMS Microbiol Lett. 1990 Sep 15;59(3):337–343. doi: 10.1016/0378-1097(90)90244-k. [DOI] [PubMed] [Google Scholar]
- Miller M., Jaskólski M., Rao J. K., Leis J., Wlodawer A. Crystal structure of a retroviral protease proves relationship to aspartic protease family. Nature. 1989 Feb 9;337(6207):576–579. doi: 10.1038/337576a0. [DOI] [PubMed] [Google Scholar]
- Ohno S., Emori Y., Imajoh S., Kawasaki H., Kisaragi M., Suzuki K. Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein? Nature. 1984 Dec 6;312(5994):566–570. doi: 10.1038/312566a0. [DOI] [PubMed] [Google Scholar]
- Patthy L. Evolutionary assembly of blood coagulation proteins. Semin Thromb Hemost. 1990 Jul;16(3):245–259. doi: 10.1055/s-2007-1002677. [DOI] [PubMed] [Google Scholar]
- Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pirkle H., Markland F. S., Theodor I., Baumgartner R., Bajwa S. S., Kirakossian H. The primary structure of crotalase, a thrombin-like venom enzyme, exhibits closer homology to kallikrein than to other serine proteases. Biochem Biophys Res Commun. 1981 Mar 31;99(2):715–721. doi: 10.1016/0006-291x(81)91802-7. [DOI] [PubMed] [Google Scholar]
- Polgár L. Prolyl endopeptidase catalysis. A physical rather than a chemical step is rate-limiting. Biochem J. 1992 May 1;283(Pt 3):647–648. doi: 10.1042/bj2830647. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rawlings N. D., Barrett A. J. Bone morphogenetic protein 1 is homologous in part with calcium-dependent serine proteinase. Biochem J. 1990 Mar 1;266(2):622–624. [PMC free article] [PubMed] [Google Scholar]
- Reeck G. R., de Haën C., Teller D. C., Doolittle R. F., Fitch W. M., Dickerson R. E., Chambon P., McLachlan A. D., Margoliash E., Jukes T. H. "Homology" in proteins and nucleic acids: a terminology muddle and a way out of it. Cell. 1987 Aug 28;50(5):667–667. doi: 10.1016/0092-8674(87)90322-9. [DOI] [PubMed] [Google Scholar]
- Roth W. W., Mackin R. B., Spiess J., Goodman R. H., Noe B. D. Primary structure and tissue distribution of anglerfish carboxypeptidase H. Mol Cell Endocrinol. 1991 Jul;78(3):171–178. doi: 10.1016/0303-7207(91)90120-h. [DOI] [PubMed] [Google Scholar]
- Sato S. M., Sargent T. D. Molecular approach to dorsoanterior development in Xenopus laevis. Dev Biol. 1990 Jan;137(1):135–141. doi: 10.1016/0012-1606(90)90014-a. [DOI] [PubMed] [Google Scholar]
- Seelmeier S., Schmidt H., Turk V., von der Helm K. Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6612–6616. doi: 10.1073/pnas.85.18.6612. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sloma A., Rudolph C. F., Rufo G. A., Jr, Sullivan B. J., Theriault K. A., Ally D., Pero J. Gene encoding a novel extracellular metalloprotease in Bacillus subtilis. J Bacteriol. 1990 Feb;172(2):1024–1029. doi: 10.1128/jb.172.2.1024-1029.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stone S. R., Rennex D., Wikstrom P., Shaw E., Hofsteenge J. Inactivation of prolyl endopeptidase by a peptidylchloromethane. Kinetics of inactivation and identification of sites of modification. Biochem J. 1991 Jun 15;276(Pt 3):837–840. doi: 10.1042/bj2760837. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stone S. R., Rennex D., Wikstrom P., Shaw E., Hofsteenge J. Peptidyldiazomethanes. A novel mechanism of interaction with prolyl endopeptidase. Biochem J. 1992 May 1;283(Pt 3):871–876. doi: 10.1042/bj2830871. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Svendsen I., Jensen M. R., Breddam K. The primary structure of the glutamic acid-specific protease of Streptomyces griseus. FEBS Lett. 1991 Nov 4;292(1-2):165–167. doi: 10.1016/0014-5793(91)80859-2. [DOI] [PubMed] [Google Scholar]
- Takahashi K., Inoue H., Sakai K., Kohama T., Kitahara S., Takishima K., Tanji M., Athauda S. B., Takahashi T., Akanuma H. The primary structure of Aspergillus niger acid proteinase A. J Biol Chem. 1991 Oct 15;266(29):19480–19483. [PubMed] [Google Scholar]
- Takeuchi H., Shibano Y., Morihara K., Fukushima J., Inami S., Keil B., Gilles A. M., Kawamoto S., Okuda K. Structural gene and complete amino acid sequence of Vibrio alginolyticus collagenase. Biochem J. 1992 Feb 1;281(Pt 3):703–708. doi: 10.1042/bj2810703. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tang J., James M. N., Hsu I. N., Jenkins J. A., Blundell T. L. Structural evidence for gene duplication in the evolution of the acid proteases. Nature. 1978 Feb 16;271(5646):618–621. doi: 10.1038/271618a0. [DOI] [PubMed] [Google Scholar]
- Thornberry N. A., Bull H. G., Calaycay J. R., Chapman K. T., Howard A. D., Kostura M. J., Miller D. K., Molineaux S. M., Weidner J. R., Aunins J. A novel heterodimeric cysteine protease is required for interleukin-1 beta processing in monocytes. Nature. 1992 Apr 30;356(6372):768–774. doi: 10.1038/356768a0. [DOI] [PubMed] [Google Scholar]
- Tsunasawa S., Masaki T., Hirose M., Soejima M., Sakiyama F. The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease. J Biol Chem. 1989 Mar 5;264(7):3832–3839. [PubMed] [Google Scholar]
- Tsuru D., Shimada S., Maruta S., Yoshimoto T., Oda K., Murao S., Miyata T., Iwanaga S. Isolation and amino acid sequence of a peptide containing an epoxide-reactive residue from the thermolysin-digest of Scytalidium lignicolum acid protease B. J Biochem. 1986 May;99(5):1537–1539. doi: 10.1093/oxfordjournals.jbchem.a135624. [DOI] [PubMed] [Google Scholar]
- Vallee B. L., Auld D. S. Zinc coordination, function, and structure of zinc enzymes and other proteins. Biochemistry. 1990 Jun 19;29(24):5647–5659. doi: 10.1021/bi00476a001. [DOI] [PubMed] [Google Scholar]
- Watanabe H., Abe K., Emori Y., Hosoyama H., Arai S. Molecular cloning and gibberellin-induced expression of multiple cysteine proteinases of rice seeds (oryzains). J Biol Chem. 1991 Sep 5;266(25):16897–16902. [PubMed] [Google Scholar]
- Yu S. F., Lloyd R. E. Identification of essential amino acid residues in the functional activity of poliovirus 2A protease. Virology. 1991 Jun;182(2):615–625. doi: 10.1016/0042-6822(91)90602-8. [DOI] [PubMed] [Google Scholar]
- Zwickl P., Grziwa A., Pühler G., Dahlmann B., Lottspeich F., Baumeister W. Primary structure of the Thermoplasma proteasome and its implications for the structure, function, and evolution of the multicatalytic proteinase. Biochemistry. 1992 Feb 4;31(4):964–972. doi: 10.1021/bi00119a004. [DOI] [PubMed] [Google Scholar]