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Home , Acrosin, Actinidain, Adenain, Aminopeptidase, Ananain, Asclepain

Handbook of Proteolytic Second Edition Volume 2 , 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 B 1079 334 1087 335 1089 336 1092 337 1097 338 1102 339 1104 340 1107 341 1109 342 1113 343 Placenta-specific 1116 344 Plant cysteine proteinases in germination and senescence 1120 345 1125 346 1128 347 1130 348 Glycyl 1132 349 Carica candamarcensis endopeptidase 1135 350 Stem 1136 351 1137 352 1139 353 Comosain 1140 354 1141 355 1143 356 1146 357 Melains and phytolacains 1148 358 Aleurain 1150 359 Zingiber cysteine proteinases 1151 360 Viral cathepsin 1153 361 Falcipains 1157 362 1160 363 Histolysain and other Entamoeba cysteine 1164 364 CPA, CPB and CPC cysteine 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 1197 373 PepC of lactic acid 1202 374 E 1204 Other families in clan C A 375 p,- 1206 376 m-Calpain 121 1 377 Muscle calpain p94 1213 378 Other 1217 379 Ubiquitin C-terminal hydrolase 1225 380 Ubiquitin-specific Doa4 () 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 1245 386 Staphopains 1249 387 Translocator-associated bacteriocin leader peptidases 1253 388 YopT protease and its homologs 1257 389 Foot-and-mouth disease L-peptidase 1259 390 Potyvirus helper component proteinase 1262 391 Hypovirus cysteine proteases p29 and p48 1264 392 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 -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 : transamidase 1313 409 1317 410 R 1319 411 1328 412 1333 Clan CE 413 , 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 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 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 procoagulant 1405 436 Prohormone protease 1408 437 Dipeptidyl- 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 1454 443 Streptogrisin A 1456 444 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 (Streptomyces exfoliatus and S. albidoflavus) 1480 451 Trypsin (Streptomyces erythraeus) 1481 452 Trypsin 1483 453 Human trypsins 1489 454 1493 455 1495 456 150 1 457 Pancreatic 1504 458 II 1508 459 Pancreatic endopeptidase E 1510 460 Cercarial elastase (Schistosoma) 151 1 461 1513 462 Leukocyte elastase 1517 463 1524 464 1526 465 1531 466 1535 467 Mastin 1544 468 Cattle duodenase and sheep proteinase 1 1545 469 A 1547 470 : 1549 471 Granzyme K 1552 472 Granzyme M 1554 473 Stratum corneum chymotryptic 1556 474 1559 475 1562 476 Xenopus 1565 477 1567 478 The tissue cluster 1569 479 Human kallikrein 1, tissue kallikrein 1577 480 Human kallikrein 2 158 1 481 Human kallikrein 3, prostate-specific 1583 482 Neurosin or human kallikrein 6 1585 483 Myelencephalon-specific protease 1587 484 Neuropsin, human tissue 159 1 485 Human tissue kallikrein 10 1593 486 Human kallikrein 11 or hippostasin 1595 487 Mouse proteinase A 1598 488 Mouse mK13 and mK26 1599 489 Mouse y-, 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 161 1 496 Prostase 1612 497 Complement 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 1637 504 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 1662 510 1667 511 1673 512 u- 1677 513 t-Plasminogen activator 1684 514 Earthworm fibrinolytic enzymes 1689 515 1692 516 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 3 524 171 5 525 Venombin AB 1723 526 Russell's viper factor V activator 1724 527 Scutelarin 1727 528 -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 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 autotransporters of Enterobacteriaceae 1761 543 Hap gene product of Haemophilus influenzae 1765 544 Togavirin 1767 545 1769 546 1773 547 Potyvirus P1 proteinase 1779 548 Pestivirus NS2-3/NS3 serine peptidase 1781 549 Arterivirus serine proteinase 1784 Clan SB Family S8 550 1786 551 1792 552 Bacillopeptidase F 1795 553 Thermus strain Rt41A-type protease 1796 554 Aqualysin I : 1799 555 Bacillus strain AK.1 protease 1801 556 : the cell envelope-associated endopeptidase of lactococci 1803 557 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 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 SKI-1/SIP 1845 572 Leucyl endopeptidase 1847 573 1849 574 Limulus kexin 1854 575 Proprotein convertases of 1855 576 1858 577 1861 578 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 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 1900 592 Dipeptidyl-peptidase IV 1905 593 Dipeptidyl-peptidases A and B 1910 594 Dipeptidyl-peptidases IV and V of Aspergillus 191 1 595 Fibroblast activation protein a 1913 596 Acylaminoacyl-peptidase 1917 Other families in clan SC 597 Serine C including carboxypeptidase Y 1919 598 Lysosomal 1923 599 Serine 1929 600 Peptidyl-glycinamidase 1932 601 X-Pro dipeptidyl-peptidase 1934 602 Lysosomal Pro-X carboxypeptidase 1936 603 Dipeptidyl-peptidase II 1938 604 1943 605 Tripeptidyl-peptidases A, B and C 1947 Clan SE 606 Penicillin-binding protein 5, a serine-type D-Ala-D-Ala carboxypeptidase 1950 607 Murein DD-endopeptidase PBP-7 1953 608 Streptomyces K15 D-Ala-D-Ala transpeptidase 1956 609 Streptomyces R61 D-Ala-D-Ala carboxypeptidase 1959 610 D-Stereospecific aminopeptidase DmpB 1963 611 Alkaline D-peptidase 1966 612 Penicillin-binding protein 4 1967 613 Muramoyl pentapeptide carboxypeptidase 1970 614 Actinomadura R39 D-Ala-D-Ala carboxypeptidase 1971 Clan SF 615 Repressor LexA 1974 616 UmuD and UmuD' 1976 617 I 198 1 618 Signal peptidases of Bacillus subtilis 1985 619 Organellar signal peptidases 1988 620 Signal peptidase (eukaryote) 199 1 621 Birnavirus VP4 processing endopeptidase 1995 622 Endopeptidase La 1998 623 PIM1 mitochondrial endopeptidase 2003 Clan SH 624 Cytomegalovirus 2006 625 Herpesvirus assemblin 2009 626 Human herpesvirus type 6 assemblin 201 1 627 Epstein-Barr virus assemblin 2014 628 Varicella-zoster virus assemblin 2015 Other clans of serine peptidases 629 2017 630 Clp endopeptidase homologs in plants and animals 2023

631 Tsp protease 2027 632 C-Terminal processing peptidase of chloroplasts 2028 633 Tricorn protease 203 1 634 Dipeptidase E 2033 Serine peptidases not assigned to family 635 Cell-associated endopeptidase of Trichophyton and Coccidioides 2035 636 Dipeptidyl-peptidase 7 of Porphyromonas gingivalis 2037 637 Protease IV 2039 638 Drosophila Rhomboid-1 2041 639 Sporulation factor SpoIVB 2043 Clan PB 640 Introduction : clan PB containing N-terminal nucleophile peptidases 2047 641 Self-processing cysteine-dependent N-terminal nucleophile 2049 642 Dipeptidase DA 2052 643 Glutaryl-7-aminocephalosporanic acid acylase precursor 2053 644 DmpA L-aminopeptidase D-Ala esterase/amidase of Ochrobactrum anthropi 2055 645 Archaean 2058 646 Bacterial proteasome 206 1 647 Hs1VU protease 2064 648 Eukaryotic 20S proteasome 2068 649 26S Proteasome 2077 650 Glycosylasparaginase precursor and other self-processing N-terminal nucleophile amidohydrolases 2086 651 y-Glutamyl, transpeptidase and its precursor 2090 Unsequenced serine peptidases 652 Unsequenced serine peptidases 2095 653 Endopeptidase So 2095 654 VlPase : chain hydrolyzing vasoactive intestinal 2097 Peptidases of Uncertain Catalytic Type 655 Peptidases of unknown catalytic type 2103 656 Glu-Glu dipeptidase 2105 657 Non-stereospecific dipeptidase 2106 658 LD-Dipeptidase 2108 659 X-Methyl-His dipeptidase 2109 660 Tubulinyl-Tyr carboxypeptidase 211 1 661 N-Formylmethionyl peptidase 2114 662 ß-Aspartyl-peptidase 211 5 663 Destabilase 211 6 664 Murein tetrapeptide LD- 211 8 665 Murein endopeptidase MepA 2120 666 Murein endopeptidase P5 2122 667 Isoprenylated protein peptidase Reel 2123 668 Bacteriophage T4 prohead endopeptidase 2127 669 Lit protease 2129 670 Hepatitis C virus endopeptidase 2 2132 671 Self-splicing proteins 2136 Appendix 1 Organisms mentioned in the Handbook A1.1-A1.17 Appendix 2 Suppliers cited in the Handbook A2.1-A2.3 Index I.1-I.73