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PAS domain

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Although the PAS domain exhibits a degree of sequence variability, the three-dimensional structure of the PAS domain core is broadly conserved. This core consists of a five-stranded antiparallel β-sheet and several α-helices. Structural changes, as a result of signaling, predominantly originate
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Liu, Yu C.; Machuca, Mayra A.; Beckham, Simone A.; Gunzburg, Menachem J.; Roujeinikova, Anna (1 October 2015). "Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains".
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found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key
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Within Mammals, both PAS domains play important roles. PAS A is responsible for the protein-protein interactions with other PAS domain proteins, while PAS B has a more versatile role. It mediates interactions with
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identity, meaning they are surprisingly dissimilar. PAS domains are frequently found on proteins with other environmental sensing mechanisms. Also, many PAS domains are attached to photoreceptive cells.
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of the BHLH protein. PAS domains containing BHLH proteins form a BHLH-Pas protein, typically found and encoded in HIF, which require both the PAS domain and BHLH domain and the Clock gene.
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binding. Furthermore, PAS domains containing the NPAS2 protein have been shown to be a substitute for the Clock gene in mutant mice who lack the Clock gene completely.
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PAS domains are found in a large number of organisms from bacteria to mammals. The PAS domain was named after the three proteins in which it was first discovered:
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to bind via their PAS domains. That activator complex regulates Per1, Per2, and Per3 which all have PAS domains that are used to bind to cryptochromes 1 and 2 (
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Since the initial discovery of the PAS domain, a large quantity of PAS domain binding sites have been discovered in bacteria and eukaryotes. A subset called
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Crystallographic structure of the PAS domain of the bacterial oxygen sensor protein fixL. The protein is depicted as a rainbow colored cartoon (
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of the core to the covalently-attached effector domain. In 1998, the PAS domain core architecture was first characterized in the structure of
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Hennig, Sven; Strauss, Holger M.; Vanselow, Katja; Yildiz, Özkan; Schulze, Sabrina; Arens, Julia; Kramer, Achim; Wolf, Eva (28 April 2009).
707:. In many proteins, a dimer of PAS domains is required, whereby one binds a ligand and the other mediates interactions with other proteins. 2024: 737: 677: 1969: 846: 1434:
McIntosh, Brian; Hogenesch, John; Bradfield, Christopher (2010). "Mammalian Per-Arnt-Sim Proteins in Environmental Adaptation".
1984: 2107: 1892: 209: 1847: 1770: 1337: 952: 1095:"Structural and Functional Analyses of PAS Domain Interactions of the Clock Proteins Drosophila PERIOD and Mouse PERIOD2" 901:"A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure" 1436: 728:
Often in the bacterial kingdom, PAS domains are positioned at the amino terminus of signaling proteins such as sensor
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family). The following mammalian genes contain PAS binding domains: Per1, Per2, Per3, Cry1, Cry2, Bmal, Clk, Pasd1.
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Harmer, Stacey L.; Panda, Satchidananda; Kay, Steve A. (28 November 2003). "Molecular Bases of Circadian Rhythms".
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A PAS domain is found in the ZTL and NPH1 genes. These domains are very similar to the PAS domain found in the
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via the PER PAS domain. The following genes contain PAS binding domains: PER, Tim, CLK, CYC.
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Dunham CM, Dioum EM, Tuckerman JR, Gonzalez G, Scott WG, Gilles-Gonzalez MA (July 2003).
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The circadian clock that is currently understood for mammals begins when light activates
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ligand is shown as sticks (carbon = white, nitrogen = blue, oxygen = red, iron = orange).
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attach via a PAS domain, activating the translation of PER, which then associates to
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Ke, Qingdong; Costa, Max (1 November 2006). "Hypoxia-Inducible Factor-1 (HIF-1)".
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Debruyne JP, Noton E, Lambert CM, Maywood ES, Weaver DR, Reppert SM (May 2006).
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Proceedings of the National Academy of Sciences of the United States of America
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Rosato, Ezio; Tauber, Eran; Kyriacou, Charalambos P. (1 January 2006).
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Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J (March 2004).
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Somers, David; Schultz, Thomas; Kay, Steve; Milnamow, Maureen (2000).
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Möglich, Andreas; Ayers, Rebecca A.; Moffat, Keith (14 October 2009).
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Möglich, Andreas; Ayers, Rebecca A.; Moffat, Keith (14 October 2009).
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Wang, G. L.; Jiang, B. H.; Rue, E. A.; Semenza, G. L. (6 June 1995).
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The PAS domains that are known share less than 20% average
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proteins are responsive to oxygen, light and voltage.
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aryl hydrocarbon receptor nuclear translocator protein
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Henry, Jonathan T.; Crosson, Sean (1 January 2011).
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Henry, Jonathan T.; Crosson, Sean (1 January 2011).
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These signals propagate via the 14: 1487:10.1146/annurev.cellbio.17.1.215 1212:10.1111/j.1432-1033.2004.04023.x 1000:Acta Crystallographica Section D 1606:Jones, Susan (1 January 2004). 845:and other small molecules like 1: 1527:10.1016/S0092-8674(00)80841-7 1338:Annual Review of Microbiology 1163:10.1016/S0960-9822(06)00352-6 953:Annual Review of Microbiology 161:Available protein structures: 1576:10.1016/j.neuron.2006.03.041 1112:10.1371/journal.pbio.1000094 711:Examples of PAS in organisms 1437:Annual Review of Physiology 857:(HIF) also help to mediate 2124: 801: 780:In the presence of light, 773: 756:In the presence of light, 749: 699:photoactive yellow protein 1793: 1400:10.1016/j.str.2009.08.011 1252:10.1016/j.str.2009.08.011 1059:10.1016/j.str.2009.08.011 1020:10.1107/S139900471501384X 836:Other mammalian PAS roles 156: 26: 855:hypoxia inducible factor 704:Halorhodospira halophila 659:period circadian protein 1727:10.1073/pnas.92.12.5510 1625:10.1186/gb-2004-5-6-226 1302:10.1038/sj.ejhg.5201547 849:, but PAS B domains in 734:cyclic-di-GMP syntheses 1671:10.1124/mol.106.027029 1659:Molecular Pharmacology 2108:Protein superfamilies 671:single-minded protein 736:and hydrolases, and 1718:1995PNAS...92.5510W 1012:2015AcCrD..71.2127L 2090: 2089: 1712:(12): 5510–5514. 1246:(10): 1282–1294. 1053:(10): 1282–1294. 1006:(10): 2127–2136. 917:10.1021/bi0343370 730:histidine kinases 717:pairwise sequence 618: 617: 614: 613: 210:structure summary 41:= red) while the 2115: 1780: 1773: 1766: 1757: 1750: 1749: 1739: 1729: 1697: 1691: 1690: 1665:(5): 1469–1480. 1654: 1648: 1647: 1637: 1627: 1603: 1597: 1596: 1578: 1554: 1548: 1547: 1529: 1505: 1499: 1498: 1468: 1462: 1461: 1431: 1422: 1421: 1411: 1379: 1373: 1372: 1362: 1328: 1315: 1314: 1304: 1280: 1274: 1273: 1263: 1231: 1225: 1224: 1214: 1190: 1184: 1183: 1165: 1141: 1135: 1134: 1124: 1114: 1090: 1081: 1080: 1070: 1038: 1032: 1031: 994: 988: 987: 977: 943: 937: 936: 896: 886: 639:structural motif 609: 603: 597: 591: 585: 579: 573: 567: 561: 555: 549: 543: 537: 531: 525: 519: 513: 507: 501: 495: 489: 483: 477: 471: 465: 459: 453: 447: 441: 435: 429: 423: 417: 411: 405: 399: 393: 387: 381: 375: 369: 363: 357: 351: 345: 339: 333: 327: 321: 315: 309: 303: 297: 291: 285: 279: 273: 267: 261: 255: 249: 243: 237: 231: 225: 158: 31: 19: 2123: 2122: 2118: 2117: 2116: 2114: 2113: 2112: 2093: 2092: 2091: 2086: 1789: 1787:Protein domains 1784: 1754: 1753: 1699: 1698: 1694: 1656: 1655: 1651: 1605: 1604: 1600: 1556: 1555: 1551: 1507: 1506: 1502: 1470: 1469: 1465: 1433: 1432: 1425: 1394:(10): 1282–94. 1381: 1380: 1376: 1330: 1329: 1318: 1282: 1281: 1277: 1233: 1232: 1228: 1205:(6): 1198–208. 1199:Eur. J. Biochem 1192: 1191: 1187: 1143: 1142: 1138: 1105:(4): e1000094. 1092: 1091: 1084: 1040: 1039: 1035: 996: 995: 991: 945: 944: 940: 898: 888: 887: 883: 878: 838: 818: 806: 800: 778: 772: 754: 748: 726: 713: 686: 651: 643:circadian clock 605: 599: 593: 587: 581: 575: 569: 563: 557: 551: 545: 539: 533: 527: 521: 515: 509: 503: 497: 491: 485: 479: 473: 467: 461: 455: 449: 443: 437: 431: 425: 419: 413: 407: 401: 395: 389: 383: 377: 371: 365: 359: 353: 347: 341: 335: 329: 323: 317: 311: 305: 299: 293: 287: 281: 275: 269: 263: 257: 251: 245: 239: 233: 227: 221: 46: 17: 12: 11: 5: 2121: 2119: 2111: 2110: 2105: 2095: 2094: 2088: 2087: 2085: 2084: 2079: 2074: 2069: 2064: 2059: 2054: 2049: 2044: 2039: 2034: 2029: 2028: 2027: 2017: 2012: 2007: 2002: 1997: 1992: 1987: 1982: 1977: 1972: 1967: 1962: 1957: 1952: 1947: 1942: 1941: 1940: 1935: 1930: 1925: 1915: 1910: 1905: 1900: 1895: 1890: 1885: 1880: 1875: 1870: 1865: 1860: 1855: 1850: 1845: 1840: 1835: 1830: 1825: 1820: 1815: 1810: 1805: 1800: 1794: 1791: 1790: 1785: 1783: 1782: 1775: 1768: 1760: 1752: 1751: 1692: 1649: 1612:Genome Biology 1598: 1549: 1520:(3): 319–329. 1500: 1463: 1423: 1374: 1316: 1295:(6): 729–738. 1275: 1226: 1185: 1156:(11): R674–7. 1136: 1082: 1033: 989: 938: 911:(25): 7701–8. 880: 879: 877: 874: 837: 834: 817: 814: 802:Main article: 799: 794: 774:Main article: 771: 766: 758:White Collar-1 750:Main article: 747: 742: 725: 722: 712: 709: 685: 682: 674: 673: 667: 661: 650: 647: 634:protein domain 616: 615: 612: 611: 219: 213: 212: 207: 201: 200: 187: 181: 180: 170: 163: 162: 154: 153: 148: 142: 141: 128: 122: 121: 116: 110: 109: 104: 98: 97: 92: 86: 85: 80: 73: 72: 67: 61: 60: 57: 53: 52: 48: 47: 32: 24: 23: 16:Protein domain 15: 13: 10: 9: 6: 4: 3: 2: 2120: 2109: 2106: 2104: 2101: 2100: 2098: 2083: 2080: 2078: 2075: 2073: 2070: 2068: 2065: 2063: 2060: 2058: 2055: 2053: 2050: 2048: 2045: 2043: 2040: 2038: 2035: 2033: 2030: 2026: 2023: 2022: 2021: 2018: 2016: 2013: 2011: 2008: 2006: 2003: 2001: 1998: 1996: 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904: 884: 863: 839: 819: 809: 807: 796: 779: 768: 755: 744: 727: 714: 702: 687: 675: 652: 629: 625: 622:Per-Arnt-Sim 621: 619: 2082:zinc finger 1481:: 215–253. 1444:: 625–645. 1345:: 261–286. 960:: 261–286. 843:chaperonins 804:Arabidopsis 797:Arabidopsis 701:(PYP) from 689:within the 51:Identifiers 2103:PAS domain 2097:Categories 1618:(6): 226. 1150:Curr. Biol 876:References 870:C-Terminus 810:Neurospora 776:Drosophila 769:Drosophila 752:Neurospora 745:Neurospora 173:structures 39:C-terminus 35:N-terminus 1970:EcoEI_R_C 1388:Structure 1240:Structure 1047:Structure 897:​; 695:α-helices 684:Structure 649:Discovery 604:​, 598:​, 592:​, 586:​, 580:​, 574:​, 568:​, 562:​, 556:​, 550:​, 544:​, 538:​, 532:​, 526:​, 520:​, 514:​, 508:​, 502:​, 496:​, 490:​, 484:​, 478:​, 472:​, 466:​, 460:​, 454:​, 448:​, 442:​, 436:​, 430:​, 424:​, 418:​, 412:​, 406:​, 400:​, 394:​, 388:​, 382:​, 376:​, 370:​, 364:​, 358:​, 352:​, 346:​, 340:​, 334:​, 328:​, 322:​, 316:​, 310:​, 304:​, 298:​, 292:​, 286:​, 280:​, 274:​, 268:​, 262:​, 256:​, 250:​, 244:​, 238:​, 232:​, 226:​, 119:PDOC50112 95:IPR013767 1679:16887934 1644:15186484 1593:19028601 1585:16675400 1536:10847686 1495:11687489 1458:20148691 1418:19836329 1369:21663441 1311:16721409 1270:19836329 1221:15009198 1180:14105830 1131:19402751 1077:19836329 1028:26457436 984:21663441 933:14090693 925:12820879 724:Bacteria 190:RCSB PDB 90:InterPro 37:= blue, 22:PAS fold 2000:Kringle 1893:CGI-121 1863:BTB/POZ 1746:7539918 1714:Bibcode 1687:2522614 1544:3013788 1409:3092527 1360:3298442 1261:3092527 1172:9382818 1122:2671562 1068:3092527 1008:Bibcode 975:3298442 830:CRY 1,2 816:Mammals 691:β-sheet 678:PAS LOV 663:Arnt – 610:​ 151:cd00130 114:PROSITE 70:PF00989 1744:  1734:  1685:  1677:  1642:  1635:463060 1632:  1591:  1583:  1563:Neuron 1542:  1534:  1493:  1456:  1416:  1406:  1367:  1357:  1309:  1268:  1258:  1219:  1178:  1170:  1129:  1119:  1075:  1065:  1026:  982:  972:  931:  923:  859:ligand 847:dioxin 669:Sim – 657:Per – 630:domain 205:PDBsum 179:  169:  139:SUPFAM 83:CL0183 56:Symbol 2015:NACHT 1938:Pyrin 1918:Death 1883:Cache 1818:ADF-H 1737:41725 1683:S2CID 1589:S2CID 1540:S2CID 1176:S2CID 929:S2CID 851:NPAS2 822:BMAL1 632:is a 135:SCOPe 126:SCOP2 102:SMART 2067:WD40 2062:TRIO 1995:HEAT 1990:FYVE 1985:FGGY 1980:ENTH 1960:DHR2 1955:DHR1 1950:DHHC 1933:CARD 1913:CVHN 1868:BZIP 1843:BESS 1828:ARID 1823:ANTH 1808:ACDC 1742:PMID 1675:PMID 1640:PMID 1581:PMID 1532:PMID 1514:Cell 1491:PMID 1454:PMID 1414:PMID 1365:PMID 1307:PMID 1266:PMID 1217:PMID 1168:PMID 1127:PMID 1073:PMID 1024:PMID 980:PMID 921:PMID 894:1y28 866:BHLH 824:and 784:and 607:3pyp 601:3phy 595:2pyr 589:2pyp 583:2phy 577:2d02 571:2d01 565:1y28 559:1xj6 553:1xj4 547:1xj3 541:1xj2 535:1xfq 529:1xfn 523:1wa9 517:1vb6 511:1v9z 505:1v9y 499:1uwp 493:1uwn 487:1ugu 481:1ts8 475:1ts7 469:1ts6 463:1ts0 457:1t1c 451:1t1b 445:1t1a 439:1t19 433:1t18 427:1s67 421:1s66 415:1s4s 409:1s4r 403:1s1z 397:1s1y 391:1oti 385:1ote 379:1otd 373:1otb 367:1ota 361:1ot9 355:1ot6 349:1odv 343:1nwz 337:1mzu 331:1lt0 325:1lsx 319:1lsw 313:1lsv 307:1ll8 301:1kou 295:1gsx 289:1gsw 283:1gsv 277:1f9i 271:1f98 265:1ew0 259:1drm 253:1dp9 247:1dp8 241:1dp6 235:1d7e 229:1d06 223:1byw 198:PDBj 194:PDBe 177:ECOD 167:Pfam 131:2phy 79:clan 77:Pfam 65:Pfam 43:heme 2077:YTH 2057:SUN 2052:SH3 2047:SH2 2032:PDZ 2025:LOV 2020:PAS 2010:LRR 2005:LIM 1975:EF1 1945:DEP 1928:DED 1908:CUT 1903:CUB 1898:CRM 1888:CBS 1858:BPS 1853:BMC 1848:BIR 1838:BEN 1833:BAR 1813:ACT 1803:ABM 1732:PMC 1722:doi 1667:doi 1630:PMC 1620:doi 1571:doi 1522:doi 1518:101 1483:doi 1446:doi 1404:PMC 1396:doi 1355:PMC 1347:doi 1297:doi 1256:PMC 1248:doi 1207:doi 1203:271 1158:doi 1117:PMC 1107:doi 1063:PMC 1055:doi 1016:doi 970:PMC 962:doi 913:doi 890:PDB 826:CLK 790:Tim 786:CYC 782:CLK 762:FRQ 626:PAS 217:PDB 185:PDB 146:CDD 107:PAS 59:PAS 2099:: 2072:X8 2042:PX 2037:PH 1965:DM 1923:DD 1878:C2 1873:C1 1798:3H 1740:. 1730:. 1720:. 1710:92 1708:. 1704:. 1681:. 1673:. 1663:70 1661:. 1638:. 1628:. 1614:. 1610:. 1587:. 1579:. 1567:50 1565:. 1561:. 1538:. 1530:. 1516:. 1512:. 1489:. 1479:17 1477:. 1452:. 1442:72 1440:. 1426:^ 1412:. 1402:. 1392:17 1390:. 1386:. 1363:. 1353:. 1343:65 1341:. 1335:. 1319:^ 1305:. 1293:14 1291:. 1287:. 1264:. 1254:. 1244:17 1242:. 1238:. 1215:. 1201:. 1197:. 1174:. 1166:. 1152:. 1148:. 1125:. 1115:. 1101:. 1097:. 1085:^ 1071:. 1061:. 1051:17 1049:. 1045:. 1022:. 1014:. 1004:71 1002:. 978:. 968:. 958:65 956:. 950:. 927:. 919:. 909:42 907:. 903:. 892:: 764:. 740:. 732:, 628:) 620:A 196:; 192:; 175:/ 137:/ 133:/ 1779:e 1772:t 1765:v 1748:. 1724:: 1716:: 1689:. 1669:: 1646:. 1622:: 1616:5 1595:. 1573:: 1546:. 1524:: 1497:. 1485:: 1460:. 1448:: 1420:. 1398:: 1371:. 1349:: 1313:. 1299:: 1272:. 1250:: 1223:. 1209:: 1182:. 1160:: 1154:7 1133:. 1109:: 1103:7 1079:. 1057:: 1030:. 1018:: 1010:: 986:. 964:: 935:. 915:: 624:(

Index


N-terminus
C-terminus
heme
Pfam
PF00989
Pfam
CL0183
InterPro
IPR013767
SMART
PAS
PROSITE
PDOC50112
SCOP2
2phy
SCOPe
SUPFAM
CDD
cd00130
Pfam
structures
ECOD
PDB
RCSB PDB
PDBe
PDBj
PDBsum
structure summary
PDB

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