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Handbook of Proteolytic Enzymes Second Edition Volume 2 Cysteine, Serine and Threonine Peptidase S

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Handbook of Proteolytic Enzymes Second Edition Volume 2 Cysteine, Serine and Threonine Peptidase s Alan J. Barrett Neil D. Rawlings J. Fred Woessner Editor biographies xxi Contributors xxiii Preface xxxi Introduction i Abbreviations xxxvii CYSTEINE PEPTIDASE S Introduction 331 Clans and families of cysteine peptidases 105 1 332 Catalytic mechanisms of cysteine peptidases 1072 Clan CA Family Cl 333 Cathepsin B 1079 334 Cathepsin F 1087 335 Cathepsin H 1089 336 Cathepsin K 1092 337 Cathepsin L 1097 338 Cathepsin O 1102 339 Cathepsin S 1104 340 Cathepsin V 1107 341 Cathepsin W 1109 342 Cathepsin X 1113 343 Placenta-specific cathepsins 1116 344 Plant cysteine proteinases in germination and senescence 1120 345 Papain 1125 346 Chymopapain 1128 347 Caricain 1130 348 Glycyl endopeptidase 1132 349 Carica candamarcensis endopeptidase 1135 350 Stem bromelain 1136 351 Fruit bromelain 1137 352 Ananain 1139 353 Comosain 1140 354 Ficain 1141 355 Actinidain 1143 356 Asclepain 1146 357 Melains and phytolacains 1148 358 Aleurain 1150 359 Zingiber cysteine proteinases 1151 360 Viral cathepsin 1153 361 Falcipains 1157 362 Cruzipain 1160 363 Histolysain and other Entamoeba cysteine endopeptidases 1164 364 Leishmania CPA, CPB and CPC cysteine proteases 1166 365 Trichomonad and Giardia cysteine endopeptidases 1170 366 Cysteine proteinase-7 of Dictyostelium discoideum 1173 367 Trematode cysteine endopeptidases 1176 368 Helminth cysteine proteases 1183 369 Mite endopeptidase 1 1187 370 Insect homologs of papain 1189 371 Dipeptidyl-peptidase I 1192 372 Bleomycin hydrolase 1197 373 PepC aminopeptidase of lactic acid bacteria 1202 374 Oligopeptidase E 1204 Other families in clan C A 375 p,-Calpain 1206 376 m-Calpain 121 1 377 Muscle calpain p94 1213 378 Other calpains 1217 379 Ubiquitin C-terminal hydrolase 1225 380 Ubiquitin-specific protease Doa4 (Saccharomyces cerevisiae) 1229 381 Ubiquitin-specific proteases 4 and 15 1232 382 Ubiquitin-specific protease 7 1236 383 Ubiquitin isopeptidase T 1239 384 The yeast Apg4/Aut2 protease in autophagy 1243 385 Streptopain 1245 386 Staphopains 1249 387 Translocator-associated bacteriocin leader peptidases 1253 388 YopT protease and its homologs 1257 389 Foot-and-mouth disease virus L-peptidase 1259 390 Potyvirus helper component proteinase 1262 391 Hypovirus cysteine proteases p29 and p48 1264 392 Coronavirus papain-like endopeptidases 1265 393 Sindbis virus nsP2 endopeptidase 1269 394 Rubella nonstructural protease 127 1 395 Tymovirus endopeptidase 1273 396 Blueberry scorch carlavirus endopeptidase 1276 397 Arterivirus papain-like cysteine proteinase a 1277 398 Arterivirus papain-like cysteine proteinase ß 1280 399 Arterivirus Nsp2 cysteine proteinase 1283 400 Closterovirus papain-like cysteine proteinases 1285 Clan CD 401 Caspase-1 1287 402 Caspase-8 1293 403 Caspase-9 1296 404 Caspase-3 and caspase-7 1298 405 Mammalian legumain 1302 406 Schistosome legumain 1305 407 Plant legumain, asparaginyl endopeptidase 1310 408 Glycosylphosphatidylinositol : protein transamidase 1313 409 Clostripain 1317 410 Gingipain R 1319 411 Gingipain K 1328 412 Separase 1333 Clan CE 413 Adenain, the adenovirus endopeptidase 1337 414 Ulpl endopeptidase 1340 415 African swine fever virus processing peptidase 1344 416 Vaccinia virus cysteine proteinase 1348 417 Yersinia YopJ protease 1350 Clan PA subclan C 418 Picornain 3C 1353 419 Picornain 3C (human rhinovirus) 1358 420 Picornain 2A 1361 421 Coxsackie B virus picornain 2A 1365 422 Cowpea mosaic virus 24 kDa proteinase 1368 423 Grapevine fanleaf nepovirus cysteine proteinase 1371 424 Hepatitis A virus picornain 3C 1373 425 Potyvirus Ma protease 1376 426 Calicivirus endopeptidases 1380 427 Coronavirus picornain-like cysteine proteinase 1382 Other clans of cysteine peptidases 428 Prokaryote pyroglutamyl-peptidase 1385 429 Mammalian pyroglutamyl-peptidase I 1389 430 Pyrococcus furiosus protease I 1393 431 y-Glutamyl hydrolase 1396 Cysteine peptidases not assigned to families 432 Dipeptidyl-peptidase VI 1399 433 Pestivirus N1"0 endopeptidase 1401 434 Cathepsin T 1404 435 Cancer procoagulant 1405 436 Prohormone thiol protease 1408 437 Dipeptidyl-dipeptidase 1413 SERINE AND THREONINE PEPTIDASE S Introduction 438 Serine peptidases and their clans 1417 439 Catalytic mechanisms of serine and threonine peptidases 1440 Clan PA subclan S Family Si 440 - Glutamyl endopeptidase I 1448 441 Exfoliative toxins 1451 442 Lysyl endopeptidase 1454 443 Streptogrisin A 1456 444 Streptogrisin B 1458 445 Glutamyl endopeptidase II 1462 446 a-Lytic protease 1465 447 Yeast-lytic endopeptidase (Rarobacter) 1471 448 DegP or protease Do 1472 449 Human HtrA proteases 1476 450 Trypsin (Streptomyces exfoliatus and S. albidoflavus) 1480 451 Trypsin (Streptomyces erythraeus) 1481 452 Trypsin 1483 453 Human trypsins 1489 454 Metridin 1493 455 Chymotrypsin 1495 456 Chymotrypsin C 150 1 457 Pancreatic elastase 1504 458 Pancreatic elastase II 1508 459 Pancreatic endopeptidase E 1510 460 Cercarial elastase (Schistosoma) 151 1 461 Enteropeptidase 1513 462 Leukocyte elastase 1517 463 Cathepsin G 1524 464 Myeloblastin 1526 465 Chymases 1531 466 Tryptases 1535 467 Mastin 1544 468 Cattle duodenase and sheep mast cell proteinase 1 1545 469 Granzyme A 1547 470 Granzyme B : 1549 471 Granzyme K 1552 472 Granzyme M 1554 473 Stratum corneum chymotryptic enzyme 1556 474 Matriptase 1559 475 Acrosin 1562 476 Xenopus oviductin 1565 477 Spermosin 1567 478 The tissue kallikrein gene cluster 1569 479 Human kallikrein 1, tissue kallikrein 1577 480 Human kallikrein 2 158 1 481 Human kallikrein 3, prostate-specific antigen 1583 482 Neurosin or human kallikrein 6 1585 483 Myelencephalon-specific protease 1587 484 Neuropsin, human tissue kallikrein 8 159 1 485 Human tissue kallikrein 10 1593 486 Human kallikrein 11 or hippostasin 1595 487 Mouse proteinase A 1598 488 Mouse kallikreins mK13 and mK26 1599 489 Mouse y-renin, kallikrein 16 1601 490 Mouse kallikrein 9, epidermal growth factor-binding protein 1602 491 Mouse y-nerve growth factor 1603 492 Mouse proteinase F 1604 493 Rat tissue kallikrein 1606 494 Rat kallikrein 2, tonin 1608 495 Rat kallikrein 10, salivary gland proteinase K 161 1 496 Prostase 1612 497 Complement factor D 1615 498 Complement component C1r 1617 499 Complement component C 1 s 1620 500 Mannan-binding lectin-associated serine proteases 1623 501 Complement component C2 : the classical and lectin pathway C3/C5 convertases 1627 502 Factor B and the alternative pathway C3/C5 convertase 1632 503 Complement factor I 1637 504 Coagulation factor XIIa 1642 505 Plasma prekallikrein and kallikrein 1644 506 Coagulation factor XIa 165 1 507 Coagulation factor IXa 1655 508 Coagulation factor VIIa 1659 509 Coagulation factor X 1662 510 Thrombin 1667 511 Protein C 1673 512 u-Plasminogen activator 1677 513 t-Plasminogen activator 1684 514 Earthworm fibrinolytic enzymes 1689 515 Plasmin 1692 516 Hepsin 1699 517 Testisin 1702 518 Epitheliasin 1704 519 Corin 1706 520 Prostasin 1708 521 Guanidinobenzoatase 171 0 522 Hepatocyte growth factor activator 171 2 523 Hyaluronan-binding protease 171 3 524 Venombin A 171 5 525 Venombin AB 1723 526 Russell's viper venom factor V activator 1724 527 Scutelarin 1727 528 Platelet-aggregating endopeptidase of Bothrops jararaca venom 1729 529 Brachyurins 1730 530 Hypodermins A and B 1734 531 Serine endopeptidase allergens from Dermatophagoides species 1736 532 Limulus coagulation factor C 1740 533 Limulus coagulation factor B 1742 534 Limulus clotting enzyme 1743 535 Limulus coagulation factor G 1745 536 Prophenoloxidase-activating enzyme 1746 537 Snake protease of Drosophila 1750 538 Easter protease of Drosophila 1752 539 Gastrulation defective protease of Drosophila 1754 540 Nudel protease of Drosophila 1756 Other families in clan PA(S ) 541 IgA1-specific serine endopeptidase 1758 542 Serine protease autotransporters of Enterobacteriaceae 1761 543 Hap gene product of Haemophilus influenzae 1765 544 Togavirin 1767 545 Flavivirin 1769 546 Hepacivirin 1773 547 Potyvirus P1 proteinase 1779 548 Pestivirus NS2-3/NS3 serine peptidase 1781 549 Arterivirus serine proteinase 1784 Clan SB Family S8 550 Subtilisins 1786 551 Thermitase 1792 552 Bacillopeptidase F 1795 553 Thermus strain Rt41A-type protease 1796 554 Aqualysin I : 1799 555 Bacillus strain AK.1 protease 1801 556 Lactocepin: the cell envelope-associated endopeptidase of lactococci 1803 557 C5a peptidase 1808 558 Dichelobacter (sheep foot-rot) basic serine proteinase 181 1 559 Trepolisin 181 3 560 Lantibiotic leader peptidases 1815 561 Tripeptidyl-peptidase S 1817 562 Archaean serine protease's 1818 563 Cerevisin 1824 564 Oryzin 1827 565 Proteinase K 1829 566 Cuticle-degrading endopeptidase 1832 567 Thermomycolin 1834 568 P69 endopeptidases of the tomato plant 1835 569 Cucumisin 1838 570 Plasmodium subtilisins 1841 571 Proprotein convertase SKI-1/SIP 1845 572 Leucyl endopeptidase 1847 573 Kexin 1849 574 Limulus kexin 1854 575 Proprotein convertases of Caenorhabditis elegans 1855 576 Furin 1858 577 Proprotein convertase 1 1861 578 Proprotein convertase 2 1865 579 Proprotein convertase 4 1868 580 Proprotein convertase PACE4 1871 581 Proprotein convertase 5 1874 582 Proprotein convertase 7 1877 583 Bacterial members of subfamily S8B 1880 584 Tripeptidyl-peptidase II 1882 Family S53 585 Sedolisin 1886 586 Sedolisin-B 1888 587 Kumamolisin 1889 588 Physarolisin 1891 589 Tripeptidyl-peptidase I 1893 Clan S C Family S9 590 Prolyl oligopeptidase 1897 591 Oligopeptidase B 1900 592 Dipeptidyl-peptidase IV 1905 593 Dipeptidyl-peptidases A and B 1910 594 Dipeptidyl-peptidases
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    (19) TZZ _¥_T (11) EP 2 164 943 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C11D 3/386 (2006.01) D06M 16/00 (2006.01) 12.03.2014 Bulletin 2014/11 C12N 9/08 (2006.01) C11D 3/00 (2006.01) C12N 9/42 (2006.01) (21) Application number: 08760676.0 (86) International application number: (22) Date of filing: 06.06.2008 PCT/EP2008/057106 (87) International publication number: WO 2008/151999 (18.12.2008 Gazette 2008/51) (54) A PROCESS FOR COMBINED BIOPOLISHING AND BLEACH CLEAN-UP VERFAHREN FÜR KOMBINIERTE BIOPOLIERUNG UND BLEICHREINIGUNG PROCEDE POUR BIOPOLISSAGE ET NETTOYAGE PAR UN AGENT DE BLANCHIMENT COMBINES (84) Designated Contracting States: (56) References cited: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR WO-A-00/71808 WO-A-99/32708 HR HU IE IS IT LI LT LU LV MC MT NL NO PL PT WO-A-03/002810 WO-A1-02/38717 RO SE SI SK TR WO-A1-91/17243 WO-A1-96/29397 WO-A1-2004/059075 WO-A2-2006/101584 (30) Priority: 11.06.2007 EP 07109969 WO-A2-2007/019442 CN-A- 1 584 192 GB-A- 2 216 149 PT-A- 101 152 (43) Date of publication of application: US-A- 5 700 769 US-A- 6 140 109 24.03.2010 Bulletin 2010/12 • ROY S K, DEY S K, RAHA S K, CHAKRABARTY S (60) Divisional application: L: "Purification and properties of an extracellular 13196997.4 endoglucanase from Myceliophthora thermophila", JOURNAL OF GENERAL (73) Proprietor: Novozymes A/S MICROBIOLOGY, vol.
  • SARS-Cov-2) Papain-Like Proteinase(Plpro

    SARS-Cov-2) Papain-Like Proteinase(Plpro

    JOURNAL OF VIROLOGY, Oct. 2010, p. 10063–10073 Vol. 84, No. 19 0022-538X/10/$12.00 doi:10.1128/JVI.00898-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Papain-Like Protease 1 from Transmissible Gastroenteritis Virus: Crystal Structure and Enzymatic Activity toward Viral and Cellular Substratesᰔ Justyna A. Wojdyla,1† Ioannis Manolaridis,1‡ Puck B. van Kasteren,2 Marjolein Kikkert,2 Eric J. Snijder,2 Alexander E. Gorbalenya,2 and Paul A. Tucker1* EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany,1 and Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, Netherlands2 Received 27 April 2010/Accepted 15 July 2010 Coronaviruses encode two classes of cysteine proteases, which have narrow substrate specificities and either a chymotrypsin- or papain-like fold. These enzymes mediate the processing of the two precursor polyproteins of the viral replicase and are also thought to modulate host cell functions to facilitate infection. The papain-like protease 1 (PL1pro) domain is present in nonstructural protein 3 (nsp3) of alphacoronaviruses and subgroup 2a betacoronaviruses. It participates in the proteolytic processing of the N-terminal region of the replicase polyproteins in a manner that varies among different coronaviruses and remains poorly understood. Here we report the first structural and biochemical characterization of a purified coronavirus PL1pro domain, that of transmissible gastroenteritis virus (TGEV). Its tertiary structure is compared with that of severe acute respiratory syndrome (SARS) coronavirus PL2pro, a downstream paralog that is conserved in the nsp3’s of all coronaviruses.