Introduction: Serine Peptidases and Their Clans

Handbook of Proteolytic Enzymes

Volumn 3, Issue , 2013, Pages 2491-2523

  Rawlings, Neil D ^a   Barrett, Alan J ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84884874366     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-382219-2.00559-7     Document Type: Chapter

References (94)

1. Sichler K., Hopfner K.P., Kopetzki E., Huber R., Bode W., Brandstetter H. The influence of residue 190 in the S1 site of trypsin-like serine proteases on substrate selectivity is universally conserved. FEBS Lett. 2002, 530:220-224.
2. Patthy L. Evolution of blood coagulation and fibrinolysis. Blood Coagul. Fibrinolysis 1990, 1:153-166.
3. Lesk A.M., Fordham W.D. Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J. Mol. Biol. 1996, 258:501-537.
4. Kraut, J. (1971). Chymotrypsinogen: X-ray structure. In The Enzymes. 1st edn, Boyer, P.D. ed. Academic Press, New York, pp. 165-183.
5. Venot N., Sciaky M., Puigserver A., Desnuelle P., Laurent G. Amino acid sequence and disulfide bridges of subunit III, a defective endopeptidase present in the bovine pancreatic 6 S procarboxypeptidase A complex. Eur. J. Biochem. 1986, 157:91-99.
6. Watanabe K., Baba T., Kashiwabara S., Okamoto A., Arai Y. Structure and organization of the mouse acrosin gene. J. Biochem. 1991, 109:828-833.
7. Higaki J.N., Evnin L.B., Craik C.S. Introduction of a cysteine protease active site into trypsin. Biochemistry 1989, 28:9256-9263.
8. Krojer T., Garrido-Franco M., Huber R., Ehrmann M., Clausen T. Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine. Nature 2002, 416:455-459.
9. Speroni S., Rohayem J., Nenci S., Bonivento D., Robel I., Barthel J., Luzhkov V.B., Coutard B., Canard B., Mattevi A. Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0Å resolution. J. Mol. Biol. 2009, 387:1137-1152.
10. Love R.A., Parge H.E., Wickersham J.A., Hostomsky Z., Habuka N., Moomaw E.W., Adachi T., Hostomska Z. The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell 1996, 87:331-342.
11. Verchot J., Herndon K.L., Carrington J.C. Mutational analysis of the tobacco etch potyviral 35-kDa proteinase: Identification of essential residues and requirements for autoproteolysis. Virology 1992, 190:298-306.
12. Tautz N., Kaiser A., Thiel H.J. NS3 serine protease of bovine viral diarrhea virus: Characterization of active site residues, NS4A cofactor domain, and protease-cofactor interactions. Virology 2000, 273:351-363.
13. Xu J., Mendez E., Caron P.R., Lin C., Murcko M.A., Collett M.S., Rice C.M. Bovine viral diarrhea virus NS3 serine proteinase: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication. J. Virol. 1997, 71:5312-5322.
14. Tamura J.K., Warrener P., Collett M.S. RNA-stimulated NTPase activity associated with the p80 protein of the pestivirus bovine viral diarrhea virus. Virology 1993, 193:1-10.
15. Barrette-Ng I.H., Ng K.K., Mark B.L., van Aken D., Cherney M.M., Garen C., Kolodenko Y., Gorbalenya A.E., Snijder E.J., James M.N. Structure of arterivirus nsp4. The smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole. J. Biol. Chem. 2002, 277:39960-39966.
16. Chang J.R., Spilman M.S., Rodenburg C.M., Dokland T. Functional domains of the bacteriophage P2 scaffolding protein: identification of residues involved in assembly and protease activity. Virology 2009, 384:144-150.
17. Chang J.R., Poliakov A., Prevelige P.E., Mobley J.A., Dokland T. Incorporation of scaffolding protein gpO in bacteriophages P2 and P4. Virology 2008, 370:352-361.
18. Schutze H., Ulferts R., Schelle B., Bayer S., Granzow H., Hoffmann B., Mettenleiter T.C., Ziebuhr J. Characterization of White bream virus reveals a novel genetic cluster of nidoviruses. J. Virol. 2006, 80:11598-11609.
19. Otto B.R., Sijbrandi R., Luirink J., Oudega B., Heddle J.G., Mizutani K., Park S.Y., Tame J.R. Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli. J. Biol. Chem. 2005, 280:17339-17345.
20. Dutta P.R., Cappello R., Navarro-Garcia F., Nataro J.P. Functional comparison of serine protease autotransporters of enterobacteriaceae. Infect. Immun. 2002, 70:7105-7113.
21. Rawlings N.D., Barrett A.J., Bateman A. Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes. J. Biol. Chem. 2011, 286:38321-38328.
22. Tajima N., Kawai F., Park S.Y., Tame J.R. A novel intein-like autoproteolytic mechanism in autotransporter proteins. J. Mol. Biol. 2010, 402:645-656.
23. Yoshihara E., Gotoh N., Nishino T., Nakae T. Protein D2 porin of the Pseudomonas aeruginosa outer membrane bears the protease activity. FEBS Lett. 1996, 394:179-182.
24. Abdel-Sater F., El Bakkoury M., Urrestarazu A., Vissers S., Andre B. Amino acid signaling in yeast: casein kinase I and the Ssy5 endoprotease are key determinants of endoproteolytic activation of the membrane-bound Stp1 transcription factor. Mol. Cell Biol. 2004, 24:9771-9785.
25. Lespinet O., Wolf Y.I., Koonin E.V., Aravind L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 2002, 12:1048-1059.
26. Davison A.J. Channel catfish virus: a new type of herpesvirus. Virology 1992, 186:9-14.
27. 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 1999, 1429:496-500.
28. Wlodawer A., Li M., Dauter Z., Gustchina A., Uchida K., Oyama H., Dunn B.M., Oda K. Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes. Nat. Struct. Biol. 2001, 8:442-446.
29. Ollis D.L., Cheah E., Cygler M., Dijkstra B., Frolow F., Franken S.M., Harel M., Remington S.J., Silman I., Schrag J., Sussman J.L., Verscheuren K.H.G., Goldman A. The alpha/beta hydrolase fold. Protein Eng. 1992, 5:197-211.
30. Cygler M., Schrag J.D., Sussman J.L., Harel M., Silman I., Gentry M.K., Doctor B.P. Relationship between sequence conservation and three-dimensional structure in a large family of esterases, lipases, and related proteins. Protein Sci. 1993, 2:366-382.
31. Rawlings N.D., Polgar L., Barrett A.J. A new family of serine-type peptidases related to prolyl oligopeptidase. Biochem. J. 1991, 279:907-908.
32. David F., Bernard A.M., Pierres M., Marguet D. Identification of serine 624, aspartic acid 702, and histidine 734 as the catalytic triad residues of mouse dipeptidyl-peptidase IV (CD26). A member of a novel family of nonclassical serine hydrolases. J. Biol. Chem. 1993, 268:17247-17252.
33. Yamauchi Y., Ejiri Y., Sugimoto T., Sueyoshi K., Oji Y., Tanaka K. A high molecular weight glutamyl endopeptidase and its endogenous inhibitors from cucumber leaves. J. Biochem. 2001, 130:257-261.
34. Rigolet P., Mechin I., Delage M.M., Chich J.F. The structural basis for catalysis and specificity of the X-prolyl dipeptidyl aminopeptidase from Lactococcus lactis. Structure 2002, 10:1383-1394.
35. Soisson S.M., Patel S.B., Abeywickrema P.D., Bryne N.J., Diehl R.E., Hall D.L., Ford R.E., Reid J.C., Rickert K.W., Shipman J.M., Sharma S., Lumb K.J. Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase. BMC Struct. Biol. 2010, 10:16.
36. Oefner C., D'arcy A., Daly J.J., Gubernator K., Charnas R.L., Heinze I., Hubschwerlen C., Winkler F.K. Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis. Nature 1990, 343:284-288.
37. Ghuysen J.M. Serine beta-lactamases and penicillin-binding proteins. Annu. Rev. Microbiol. 1991, 45:37-67.
38. r penicillin-binding proteins of class A. Biochem. J. 1991, 279:223-230.
39. Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O., Van Beeumen J., Frere 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, 282:781-788.
40. Englebert S., Charlier P., Fonze E., To'th Y., Vermeire M., Van Beeumen J., Grandchamps J., Hoffmann K., Leyh-Bouille M., Nguyen-Disteche M., Ghuysen J.M. Crystallization and X-ray diffraction study of the Streptomyces K15 penicillin-binding DD-transpeptidase. J. Mol. Biol. 1994, 241:295-297.
41. Fonze E., Vermeire M., Nguyen-Disteche M., Brasseur R., Charlier P. The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of Streptomyces K15. J. Biol. Chem. 1999, 274:21853-21860.
42. Kelly J.A., Knox J.R., Moews P.C., Hite G.J., Bartolone J.B., Zhao H., Joris B., Frere J.M., Ghuysen J.M. 2.8-A Structure of penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase from Streptomyces R61 and complexes with beta-lactams. J. Biol. Chem. 1985, 260:6449-6458.
43. Lamotte-Brasseur J., Jacob-Dubuisson F., Dive G., Frere J.M., Ghuysen J.M. Streptomyces albus G serine beta-lactamase. Probing of the catalytic mechanism via molecular modelling of mutant enzymes. Biochem. J. 1992, 282:189-195.
44. Strynadka N.C., Adachi H., Jensen S.E., Johns K., Sielecki A., Betzel C., Sutoh K., James M.N. Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution. Nature 1992, 359:700-705.
45. Paetzel M., Strynadka N.C. Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism. Protein Sci. 1999, 8:2533-2536.
46. Eisenbrandt R., Kalkum M., Lurz R., Lanka E. Maturation of IncP pilin precursors resembles the catalytic dyad-like mechanism of leader peptidases. J. Bacteriol. 2000, 182:6751-6761.
47. Botos I., Melnikov E.E., Cherry S., Tropea J.E., Khalatova A.G., Rasulova F., Dauter Z., Maurizi M.R., Rotanova T.V., Wlodawer A., Gustchina A. The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J. Biol. Chem. 2004, 279:8140-8148.
48. Besche H., Zwickl P. The Thermoplasma acidophilum Lon protease has a Ser-Lys dyad active site. Eur. J. Biochem. 2004, 271:4361-4365.
49. Stahlberg H., Kutejova E., Suda K., Wolpensinger B., Lustig A., Schatz G., Engel A., Suzuki C.K. Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits. Proc. Natl Acad. Sci. USA 1999, 96:6787-6790.
50. Lee J., Feldman A.R., Delmas B., Paetzel M. Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction. J. Biol. Chem. 2007, 282:24928-24937.
51. Nobiron I., Galloux M., Henry C., Torhy C., Boudinot P., Lejal N., Da Costa B., Delmas B. Genome and polypeptides characterization of Tellina virus 1 reveals a fifth genetic cluster in the Birnaviridae family. Virology 2008, 371:350-361.
52. Chung I.Y., Paetzel M. Crystal structure of a viral protease intramolecular acyl-enzyme complex. Insights into cis-cleavage at the VP4/VP3 junction of Tellina birnavirus. J. Biol. Chem. 2011, 286:12475-12482.
53. Chen P., Tsuge H., Almassy R.J., Gribskov C.L., Katoh S., Vanderpool D.L., Margosiak S.A., Pinko C., Matthews D.A., Kan C.C. Structure of the human cytomegalovirus protease catalytic domain reveals a novel serine protease fold and catalytic triad. Cell 1996, 86:835-843.
54. Qiu X., Culp J.S., DiLella A.G., Hellmig B., Hoog S.S., Janson C.A., Smith W.W., Abdel-Meguid S.S. Unique fold and active site in cytomegalovirus protease. Nature 1996, 383:275-279.
55. Shieh H.S., Kurumbail R.G., Stevens A.M., Stegeman R.A., Sturman E.J., Pak J.Y., Wittwer A.J., Palmier M.O., Wiegand R.C., Holwerda B.C., Stallings W.C. Three-dimensional structure of human cytomegalovirus protease. Nature 1996, 383:279-282.
56. Tong L., Qian C., Massariol M.J., Bonneau P.R., Cordingley M.G., Lagace L. A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease. Nature 1996, 383:272-275.
57. Qiu X., Janson C.A., Culp J.S., Richardson S.B., Debouck C., Smith W.W., Abdel-Meguid S.S. Crystal structure of varicella-zoster virus protease. Proc. Natl. Acad. Sci. USA 1997, 94:2874-2879.
58. Duda R.L., Martincic K., Hendrix R.W. Genetic basis of bacteriophage HK97 prohead assembly. J. Mol. Biol. 1995, 247:636-647.
59. Grimaud R. Bacteriophage Mu head assembly. Virology 1996, 217:200-210.
60. Liu J., Mushegian A. Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages. J. Bacteriol. 2004, 186:4369-4375.
61. Cheng H., Shen N., Pei J., Grishin N.V. Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease. Protein Sci. 2004, 13:2260-2269.
62. Ponting C.P., Pallen M.J. Beta-Propeller repeats and a PDZ domain in the tricorn protease: predicted self-compartmentalisation and C-terminal polypeptide-binding strategies of substrate selection. FEMS Microbiol. Lett. 1999, 179:447-451.
63. Silber K.R., Keiler K.C., Sauer R.T. Tsp: a tail-specific protease that selectively degrades proteins with nonpolar C termini. Proc. Natl Acad. Sci. USA 1992, 89:295-299.
64. Liao D.I., Qian J., Chisholm D.A., Jordan D.B., Diner B.A. Crystal structures of the photosystem II D1 C-terminal processing protease. Nat. Struct. Biol. 2000, 7:749-753.
65. Brandstetter H., Kim J.S., Groll M., Huber R. Crystal structure of the tricorn protease reveals a protein disassembly line. Nature 2001, 414:466-470.
66. Baird L., Lipinska B., Raina S., Georgopoulos C. Identification of the Escherichia coli sohB gene, a multicopy suppressor of the Htra (DegP) null phenotype. J. Bacteriol. 1991, 173:5763-5770.
67. Kim A.C., Oliver D.C., Paetzel M. Crystal structure of a bacterial signal peptide peptidase. J. Mol. Biol. 2008, 376:352-366.
68. Green J.B., Fricke B., Chetty M.C., von During M., Preston G.F., Stewart G.W. Eukaryotic and prokaryotic stomatins: the proteolytic link. Blood Cells Mol. Dis. 2004, 32:411-422.
69. Kochan J., Murialdo H. Early intermediates in bacteriophage lambda prohead assembly. II. Identification of biologically active intermediates. Virology 1983, 131:100-115.
70. Medina E., Wieczorek D., Medina E.M., Yang Q., Feiss M., Catalano C.E. Assembly and maturation of the bacteriophage lambda procapsid: gpC is the viral protease. J. Mol. Biol. 2010, 401:813-830.
71. Fontoura B.M., Blobel G., Matunis M.J. A conserved biogenesis pathway for nucleoporins: proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96. J. Cell Biol. 1999, 144:1097-1112.
72. Rosenblum J.S., Blobel G. Autoproteolysis in nucleoporin biogenesis. Proc. Natl Acad. Sci. USA 1999, 96:11370-11375.
73. Hodel A.E., Hodel M.R., Griffis E.R., Hennig K.A., Ratner G.A., Xu S., Powers M.A. The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98. Mol. Cell 2002, 10:347-358.
74. Fanuel L., Goffin C., Cheggour A., Devreese B., Van Driessche G., Joris B., Van Beeumen J., Frere J.M. The DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 is the prototype of a new terminal nucleophile hydrolase family. Biochem. J. 1999, 341:147-155.
75. Frere, J.M. & Van Beeumen, J., (2004). DmpA L-aminopeptidase D-Ala esterase/amidase of Ochrobactrum anthropi. In Handbook of proteolytic Enzymes, 2nd edn, Barrett, A.J., Rawlings, N.D., Woessner, J.F. eds. Elsevier, London, pp. 2055-2057.
76. Bompard-Gilles C., Villeret V., Davies G.J., Fanuel L., Joris B., Frere J.M., Van Beeumen J. A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-Ala-esterase/amidase from Ochrobactrum anthropi. Structure 2000, 8:153-162.
77. Cheng H., Grishin N.V. DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain. Protein Sci 2005, 14:1902-1910.
78. Valenti P., Berlutti F., Conte M.P., Longhi C., Seganti L. Lactoferrin functions: current status and perspectives. J. Clin. Gastroenterol. 2004, 38:S127-S129.
79. Hendrixson D.R., Qiu J., Shewry S.C., Fink D.L., Petty S., Baker E.N., Plaut A.G., St Geme J.W. Human milk lactoferrin is a serine protease that cleaves Haemophilus surface proteins at arginine-rich sites. Mol. Microbiol. 2003, 47:607-617.
80. Plaut A.G., Qiu J., St Geme J.W. Human lactoferrin proteolytic activity: analysis of the cleaved region in the IgA protease of Haemophilus influenzae. Vaccine 2000, 19:S148-S152.
81. Anderson B.F., Baker H.M., Norris G.E., Rice D.W., Baker E.N. Structure of human lactoferrin: crystallographic structure analysis and refinement at 2.8 A resolution. J. Mol. Biol. 1989, 209:711-734.
82. Korza H.J., Bochtler M. Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. J. Biol. Chem. 2005, 280:40802-40812.
83. Wang Y., Zhang Y., Ha Y. Crystal structure of a rhomboid family intramembrane protease. Nature 2006, 444:179-180.
84. Conlin C.A., Hakensson K., Liljas A., Miller C.G. Cloning and nucleotide sequence of the cyclic AMP receptor protein-regulated Salmonella typhimurium pepE gene and crystallization of its product, an alpha-aspartyl dipeptidase. J. Bacteriol. 1994, 176:166-172.
85. Brown D.D., Wang Z., Furlow J.D., Kanamori A., Schwartzman R.A., Remo B.F., Pinder A. The thyroid hormone-induced tail resorption program during Xenopus laevis metamorphosis. Proc. Natl Acad. Sci. USA 1996, 93:1924-1929.
86. Dong Y., Huang X., Wu X.Y., Zhao J. Identification of the active site of HetR protease and its requirement for heterocyst differentiation in the cyanobacterium Anabaena sp. strain PCC 7120. J. Bacteriol. 2000, 182:1575-1579.
87. Hara K., Shiota M., Kido H., Ohtsu Y., Kashiwagi T., Iwahashi J., Hamada N., Mizoue K., Tsumura N., Kato H., Toyoda T. Influenza virus RNA polymerase PA subunit is a novel serine protease with Ser624 at the active site. Genes Cells 2001, 6:87-97.
88. Levitin F., Stern O., Weiss M., Gil-Henn C., Ziv R., Prokocimer Z., Smorodinsky N.I., Rubinstein D.B., Wreschner D.H. The MUC1 SEA module is a self-cleaving domain. J. Biol. Chem. 2005, 280:33374-33386.
89. Lin H.H., Chang G.W., Davies J.Q., Stacey M., Harris J., Gordon S. Autocatalytic cleavage of the EMR2 receptor occurs at a conserved G protein-coupled receptor proteolytic site motif. J. Biol. Chem. 2004, 279:31823-31832.
90. Chang G.W., Stacey M., Kwakkenbos M.J., Hamann J., Gordon S., Lin H.H. Proteolytic cleavage of the EMR2 receptor requires both the extracellular stalk and the GPS motif. FEBS Lett. 2003, 547:145-150.
91. Tinel A., Janssens S., Lippens S., Cuenin S., Logette E., Jaccard B., Quadroni M., Tschopp J. Autoproteolysis of PIDD marks the bifurcation between pro-death caspase-2 and pro-survival NF-kappaB pathway. EMBO J. 2007, 26:197-208.
92. Macao B., Johansson D.G., Hansson G.C., Hard T. Autoproteolysis coupled to protein folding in the SEA domain of the membrane-bound MUC1 mucin. Nat. Struct. Mol. Biol. 2006, 13:71-76.
93. Jayasinha V., Nguyen H.H., Xia B., Kammesheidt A., Hoyte K., Martin P.T. Inhibition of dystroglycan cleavage causes muscular dystrophy in transgenic mice. Neuromuscul. Disord. 2003, 13:365-375.
94. Akhavan A., Crivelli S.N., Singh M., Lingappa V.R., Muschler J.L. SEA domain proteolysis determines the functional composition of dystroglycan. FASEB J. 2008, 22:612-621.