Ubiquitin‐specific protease 4 is inhibited by its ubiquitin‐like domain

Name: Work Video:
Duration: 3 min 30 s
Mark P.A. Luna‐Vargas; Alex C. Faesen; Willem J. van Dijk; Michael Rapé; Alexander Fish; Titia K. Sixma
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3072, 3088, 3096, 3108, 3198, 3202, 3231, 3268, 3292, 3301, 3306, 3310, 3346, 3374, 3395, 3404, 3425, 3466, 3474, 3485, 3523, 3572, 3624, 3654, 3695, 3699, 3747, 3760, 3770, 3871, 4034, 4045, 4057, 4067, 4086, 4094, 4121, 4132, 4153, 4161, 4199, 4217, 4230, 4256, 4265, 4271, 4289, 4313, 4329, 4352, 4364, 4381, 4389, 4409, 4420, 4436, 4446, 4477, 4499, 4526, 4534, 4567, 4575, 4598, 4604, 4619, 4639, 4651, 4675, 4686, 4699, 4712, 4737, 4745, 4787, 4809, 4822, 4863, 4882, 4908, 4915, 4950, 4962, 4974], 'Biochemistry': [24, 56, 90, 146, 180, 214, 246, 280, 336, 370, 418], 'and': [25, 57, 91, 121, 147, 181, 215, 247, 281, 311, 337, 371, 411, 419, 438, 502, 578, 696, 757, 901, 978, 1006, 1093, 1122, 1128, 1160, 1170, 1185, 1190, 1197, 1220, 1253, 1272, 1281, 1313, 1337, 1356, 1368, 1428, 1443, 1456, 1483, 1491, 1551, 1570, 1585, 1596, 1600, 1647, 1707, 1754, 1774, 1836, 1872, 1953, 1984, 2113, 2120, 2274, 2291, 2306, 2351, 2366, 2373, 2408, 2563, 2595, 2658, 2739, 2802, 2871, 2951, 2953, 2970, 2998, 3006, 3204, 3242, 3270, 3362, 3369, 3416, 3434, 3500, 3586, 3632, 3645, 3785, 3788, 3796, 3803, 3830, 3844, 3882, 3888, 3910, 3913, 3925, 3937, 3957, 4011, 4027, 4032, 4049, 4084, 4116, 4150, 4174, 4263, 4320, 4350, 4379, 4407, 4434, 4490, 4595, 4636, 4735, 4772, 4820, 4835, 4860, 4905], 'Center': [26, 58, 92, 148, 182, 216, 248, 282, 338, 372, 420], 'for': [27, 42, 59, 74, 93, 108, 134, 149, 164, 183, 198, 217, 232, 249, 264, 283, 298, 324, 339, 354, 373, 388, 421, 468, 803, 1146, 1963, 2062, 2073, 2086, 2089, 2249, 2266, 2362, 2369, 2404, 2480, 2490, 2736, 2751, 2780, 2816, 2959, 3123, 3163, 3195, 3280, 3519, 3529, 3578, 3686, 3832, 3838, 3848, 3994, 4003, 4014, 4021, 4030, 4405, 4460, 4523, 4900], 'Biomedical': [28, 60, 94, 150, 184, 218, 250, 284, 340, 374, 422], 'Genetics,': [29, 61, 95, 151, 185, 219, 251, 285, 341, 375, 423], 'The': [30, 39, 62, 71, 96, 105, 152, 161, 186, 195, 220, 229, 252, 261, 286, 295, 342, 351, 376, 385, 424, 433, 653, 722, 867, 1436, 1564, 1578, 1738, 1892, 1925, 1936, 2344, 2455, 2746, 2753, 3354, 3464, 3665, 4059, 4372, 4485, 4558, 4769, 4927], 'Netherlands': [31, 40, 63, 72, 97, 106, 153, 162, 187, 196, 221, 230, 253, 262, 287, 296, 343, 352, 377, 386, 425, 434], 'Cancer': [32, 64, 98, 154, 188, 222, 254, 288, 344, 378, 426, 4051, 4496], 'Institute,': [33, 65, 99, 155, 189, 223, 255, 289, 345, 379, 427], 'Plesmanlaan': [34, 66, 100, 156, 190, 224, 256, 290, 346, 380, 428], '121,': [35, 67, 101, 157, 191, 225, 257, 291, 347, 381, 429], '1066': [36, 68, 102, 158, 192, 226, 258, 292, 348, 382, 430], 'CX,': [37, 69, 103, 159, 193, 227, 259, 293, 349, 383, 431], 'Amsterdam,': [38, 70, 104, 160, 194, 228, 260, 294, 350, 384, 432], 'Search': [41, 73, 107, 133, 163, 197, 231, 263, 297, 323, 353, 387], 'more': [43, 75, 109, 135, 165, 199, 233, 265, 299, 325, 355, 389, 731, 1791, 1823], 'papers': [44, 76, 110, 136, 166, 200, 234, 266, 300, 326, 356, 390], 'this': [46, 78, 112, 138, 168, 202, 236, 268, 302, 328, 358, 392, 469, 599, 630, 1096, 2148, 2526, 2683, 3111, 3554, 3591, 3733, 3758, 4985], 'author': [47, 79, 113, 139, 169, 203, 237, 269, 303, 329, 359, 393], 'Alex': [48, 51, 238, 241, 400], 'C': [49, 52, 239, 242, 401, 3437, 4556, 4633, 4728], 'Faesen': [50, 53, 240, 243], 'Willem': [80, 84, 270, 274, 403], 'J': [81, 85, 271, 275, 404, 4127, 4359, 4384, 4529, 4877, 4942], 'van': [82, 86, 272, 276, 405, 487, 4885], 'Dijk': [83, 87, 273, 277], 'Michael': [114, 116, 304, 306, 407], 'Rape': [115, 117, 305, 307, 4766], 'Department': [118, 308], 'Molecular': [120, 310, 437], 'Cell': [122, 312, 439, 4326, 4417, 4442, 4601, 4616, 4806, 4911, 4943], 'Biology,': [123, 313, 440], 'University': [124, 314, 441], 'California': [126, 316, 443], 'at': [127, 317, 444, 1825, 1977, 2313, 2530, 3540, 3835, 3984, 4221, 4780], 'Berkeley,': [128, 129, 318, 319, 445, 446], 'California,': [130, 320, 447], '94720': [131, 321, 448], 'USA': [132, 322, 449], 'Alexander': [140, 142, 330, 332, 409], 'Fish': [141, 143, 331, 333], 'Titia': [170, 175, 360, 365, 412], 'K': [171, 176, 361, 366, 413, 4452, 4925], 'Sixma': [172, 177, 362, 367, 414, 4588, 4890], 'Corresponding': [173, 363], 'Author': [174, 364, 394], 'Information': [395, 4070], 'Luna-Vargas1,': [399], 'Faesen1,': [402], 'Dijk1,': [406], 'Rape2,': [408], 'Fish1': [410], '1': [415, 1158], '1Division': [416], '2Department': [435], '*Corresponding': [450], 'author.': [451], 'Tel:+31': [452], '20': [453, 458], '512': [454, 459], '1959;': [455], 'Fax:': [456], '+31': [457], '1954;': [460], 'E-mail:': [461], '[email': [462], 'protected]': [463], 'EMBO': [464, 3985, 4358, 4706, 4876], 'Reports': [465], '(2011)12:365-372https://doi.org/10.1038/embor.2011.33': [466], 'Retraction(s)': [467], 'article': [470, 500], 'Retraction:': [471], "'Ubiquitin-specific": [472], "domain'": [480], 'MP': [482], 'Luna-Vargas,': [483], 'AC': [484], 'Faesen,': [485], 'WJ': [486], 'Dijk,': [488], 'M': [489, 4081, 4260, 4669, 4767], 'Rape,': [490], 'Fish,': [492], 'TK': [493], 'Sixma07': [494], 'January': [495], '2014': [496], 'PDFDownload': [497], 'PDF': [498], 'text': [501], 'main': [503], 'figures.': [504], 'ToolsAdd': [505], 'to': [506, 574, 649, 694, 717, 880, 919, 961, 1008, 1019, 1359, 1407, 1612, 1627, 1640, 1687, 1856, 2078, 2095, 2126, 2155, 2192, 2229, 2268, 2301, 2406, 2412, 2447, 2482, 2497, 2551, 2561, 2782, 2814, 2878, 2890, 2913, 2931, 2945, 2966, 3010, 3018, 3125, 3329, 3377, 3495, 3650, 3720, 3776, 3858, 3906, 3945, 4171, 4249, 4611, 4872], 'favoritesDownload': [507], 'CitationsTrack': [508], 'CitationsPermissions': [509], 'Figures': [510], '&': [511, 670, 680, 700, 704, 860, 1403, 3893], 'Info': [512], 'USP4': [513, 546, 586, 921, 943, 966, 1016, 1087, 1131, 1252, 1575, 1750, 1802, 1894, 1907, 2018, 2203, 2475, 2784, 3119, 3147, 3184, 3269, 3493, 3594, 3716, 3752], 'a': [515, 528, 753, 761, 923, 958, 968, 986, 1201, 1228, 1387, 1537, 1673, 1841, 1945, 1957, 1992, 2216, 2233, 2302, 2426, 2461, 2467, 2554, 2574, 2651, 2728, 2756, 2804, 2989, 3085, 3143, 3160, 3178, 3225, 3249, 3420, 3483, 3489, 3504, 3515, 3601, 3636, 3764, 3931, 3946, 3964, 4219, 4245, 4314, 4457, 4826, 4867, 4934], 'member': [516], 'the': [518, 537, 541, 548, 563, 575, 581, 605, 617, 632, 642, 656, 689, 728, 736, 821, 846, 871, 881, 887, 894, 909, 940, 1009, 1020, 1038, 1045, 1049, 1063, 1079, 1083, 1089, 1120, 1130, 1144, 1181, 1211, 1282, 1303, 1310, 1331, 1339, 1346, 1353, 1399, 1413, 1440, 1446, 1450, 1463, 1467, 1471, 1475, 1485, 1489, 1492, 1532, 1583, 1608, 1615, 1641, 1657, 1682, 1688, 1694, 1704, 1708, 1745, 1749, 1756, 1770, 1799, 1830, 1862, 1865, 1868, 1874, 1886, 1928, 1940, 1964, 2016, 2028, 2037, 2043, 2054, 2060, 2063, 2092, 2097, 2115, 2129, 2139, 2160, 2168, 2187, 2194, 2202, 2213, 2230, 2245, 2262, 2275, 2311, 2398, 2413, 2432, 2448, 2451, 2474, 2485, 2509, 2516, 2544, 2566, 2578, 2587, 2590, 2600, 2606, 2617, 2627, 2634, 2637, 2643, 2660, 2671, 2690, 2693, 2700, 2707, 2711, 2725, 2737, 2760, 2775, 2783, 2789, 2793, 2817, 2825, 2829, 2833, 2838, 2843, 2850, 2858, 2864, 2879, 2885, 2892, 2909, 2916, 2932, 2946, 2967, 2972, 2981, 3053, 3061, 3064, 3073, 3094, 3097, 3105, 3126, 3135, 3173, 3183, 3199, 3219, 3229, 3239, 3243, 3253, 3266, 3293, 3299, 3307, 3311, 3325, 3330, 3378, 3392, 3423, 3475, 3497, 3508, 3520, 3560, 3573, 3597, 3621, 3693, 3696, 3700, 3721, 3727, 3743, 3748, 3768, 4041, 4122, 4147, 4154, 4250, 4280, 4353, 4410, 4431, 4437, 4527, 4563, 4568, 4612, 4679, 4696, 4733, 4738, 4773, 4781, 4800, 4823, 4864, 4873, 4938], 'ubiquitin-specific': [519, 1323, 2006, 2388, 3035, 3338, 4123, 4559, 4643, 4967], '(USP)': [521, 725], 'family': [522, 726, 873, 1206], 'deubiquitinating': [524, 666, 1741, 1763, 1910, 3022, 4087, 4316, 4355, 4599, 4680, 4740, 4775, 4802], 'enzymes': [525, 658, 667, 2907, 2927, 3116], 'that': [526, 536, 765, 844, 907, 982, 1104, 1210, 1622, 1655, 1678, 1702, 1787, 1818, 1857, 1861, 2072, 2138, 2186, 2473, 2547, 2558, 2571, 2670, 2715, 2724, 2732, 2815, 2824, 2873, 2884, 3090, 3172, 3218, 3456, 3553, 3681, 3708, 3750, 3757, 4062], 'has': [527, 547, 566, 612, 922, 933, 2553, 2573, 2733], 'role': [529, 615, 989, 1637, 1727, 1800, 3166, 3309, 3421], 'in': [530, 616, 623, 735, 796, 827, 870, 904, 939, 974, 990, 999, 1139, 1263, 1277, 1291, 1302, 1308, 1536, 1568, 1574, 1598, 1602, 1607, 1614, 1620, 1649, 1723, 1728, 1761, 1796, 1803, 1846, 1909, 1920, 1944, 1972, 1974, 2109, 2123, 2128, 2150, 2161, 2167, 2431, 2499, 2515, 2602, 2639, 2706, 2851, 2857, 2915, 2986, 2988, 3013, 3054, 3060, 3110, 3148, 3167, 3182, 3210, 3238, 3251, 3289, 3314, 3357, 3367, 3372, 3422, 3428, 3479, 3564, 3635, 3640, 3667, 3742, 3804, 3822, 3827, 3877, 3917, 4223, 4283, 4318, 4321, 4465, 4492, 4517, 4831, 4937, 4965], 'spliceosome': [531, 1021, 1046, 3744], 'regulation.': [532], 'Here,': [533, 1031, 1075], 'we': [534, 1076, 1126, 1148, 1768, 1955, 2102, 2158, 2224, 2395, 2422, 2624, 2787, 2848, 2922, 3042, 3083, 3247, 3705], 'show': [535, 760, 1094, 1712, 2546, 3171], 'crystal': [538, 758, 1080, 1408, 3200, 3545], 'structure': [539, 1081, 1121, 1258, 1268, 1341, 3201, 3546, 3789, 4312, 4433, 4463], 'minimal': [542, 1229], 'catalytic': [543, 564, 576, 755, 763, 882, 929, 941, 1084, 1107, 1132, 1230, 1244, 1261, 1333, 1348, 1414, 1533, 1746, 1751, 1832, 1895, 2019, 2065, 2082, 2195, 2785, 2947, 3075, 3185, 3476, 3606, 3622, 4118], 'conserved': [549, 608, 762, 4830], 'USP-like': [550], 'fold': [551, 848, 3603, 3619], 'with': [552, 580, 639, 730, 798, 1025, 1154, 1266, 1363, 1386, 1449, 1474, 1557, 1725, 1753, 1798, 2165, 2212, 2232, 2261, 2278, 2323, 2329, 2348, 2352, 2402, 2460, 2466, 2478, 2525, 2565, 2646, 2679, 2792, 2855, 3058, 3146, 3193, 3212, 3296, 3503, 3559, 3580, 3600, 3818, 3841, 3845, 3901, 3919, 3934, 4016, 4023, 4323, 4614], 'typical': [554], 'ubiquitin-binding': [555], 'site.': [556, 2416], '(Ubl)': [559, 825], 'inserted': [561], 'into': [562, 1119, 1777, 3228, 3265, 3973, 4732], 'autoregulatory': [567, 1102], 'function.': [568, 3592], 'This': [569, 1208, 1604, 2241, 2822, 3129, 3344, 3570, 3652, 4036], 'Ubl': [570, 836, 868, 889, 924, 936, 1091, 1097, 2747, 2757, 2776, 2795, 2826, 2839, 2865, 2886, 2910, 2933, 2939, 2968, 3011, 3127, 3175, 3206, 3220, 3254, 3281, 3294, 3312, 3331, 3349, 3355, 3389, 3509, 3512, 3534, 3555, 3602, 3618, 3663, 3722, 3765, 3842], 'can': [572, 692, 1987, 2841, 3117, 3714], 'bind': [573, 2411, 2914, 2930, 2944, 3009], 'compete': [579, 2401], 'ubiquitin': [582, 609, 4192, 4281, 4324, 4373, 4676, 4928], 'substrate,': [583, 2619], 'partially': [584, 1105, 3187, 3256], 'inhibiting': [585], 'activity': [587, 654, 911, 1108, 1174, 1742, 1747, 1853, 1888, 2099, 2152, 2196, 2629, 2645, 2845, 2894, 2974, 2983, 3107, 3120, 3190, 3259, 3465, 3522, 3660, 3698, 3801, 4525], 'against': [588, 1200, 1933, 2650, 2662, 3853], 'different': [589, 829, 1978, 2314, 2663], 'substrates.': [590], 'Interestingly,': [591, 1809, 2484], 'other': [592, 1411, 1503, 2905, 2925, 3114, 3846], 'USPs,': [593, 1412], 'such': [594, 3320, 3399, 3430, 3711], 'as': [595, 947, 957, 1100, 1276, 1352, 1672, 1844, 1991, 2450, 2584, 2586, 2611, 2613, 2743, 2958, 3100, 3321, 3364, 3366, 3400, 3413, 3431, 3478, 3712, 3740, 3890], 'USP39,': [596, 3322, 3713], 'could': [597, 2106, 2400, 2457, 2928, 2943, 3047, 3131, 3679, 3734], 'relieve': [598, 3324], 'inhibition.': [600, 1111], 'Introduction': [601, 4170], 'Post-translational': [602], 'modification': [603, 3684], 'small,': [606], 'highly': [607], '(Ub)': [610], 'protein': [611, 950, 2044, 3435, 3574, 3783, 4462, 4827, 4869], 'an': [613, 637, 934, 1101, 1215, 1234, 1364, 1419, 2418, 2500, 3014, 3069, 3164, 3347, 3471, 3526, 3616, 3675, 3771], 'essential': [614, 4899], 'regulation': [618, 3424, 3506, 3517, 3762], 'many': [620], 'cellular': [621], 'processes': [622], 'eukaryotes': [624], '(Pickart,': [625], '2004;': [626, 672, 674, 742, 1497], 'Hochstrasser,': [627, 671], '2009).': [628, 686, 750, 817], 'In': [629, 1665, 1765, 2012, 2215, 2417, 3642, 3703], 'process,': [631], 'carboxy-terminus': [633], 'Ub': [635, 647, 770, 1626, 1663, 1686, 2250, 2273, 2347, 2403, 2438, 2452, 2479, 2491, 2550, 2560, 2618, 2901, 3194, 3226, 3273, 3972], 'forms': [636, 3142], 'isopeptide': [638], 'lysines': [640], 'on': [641, 646, 1037, 1078, 1166, 1592, 2042, 2297, 2327, 2582, 2689, 3093, 3208, 3284, 3930, 3941, 3963], 'target': [643], 'proteins,': [644], 'or': [645, 807, 878, 1905, 2027, 2173, 2264, 3068, 3412, 3481, 3488, 3689, 3809, 3975], 'itself,': [648], 'form': [650], 'poly-Ub': [651], 'chains.': [652], 'conjugating': [657], 'E1–E2–E3': [659], 'actively': [661], 'balanced': [662], 'through': [663, 1840, 2897, 3260, 3470, 3482, 3507, 3661, 4702], 'hydrolysis': [664, 1771], '(DUBs;': [668], 'Amerik': [669, 4078], 'Pickart,': [673, 3894], 'Nijman': [675, 743, 4578], 'et': [676, 684, 740, 744, 748, 773, 778, 782, 786, 790, 811, 815, 832, 864, 915, 953, 993, 1003, 1013, 1028, 1054, 1058, 1072, 1495, 1507, 1511, 1515, 1519, 1523, 1529, 1632, 1652, 1731, 1735, 1806, 2769, 3151, 3155, 3381, 3385, 3409, 3439, 3443, 3583, 3612, 4670, 4691], 'al,': [677, 685, 741, 745, 749, 774, 779, 783, 787, 791, 812, 816, 833, 865, 916, 954, 994, 1004, 1014, 1029, 1055, 1059, 1073, 1496, 1508, 1512, 1516, 1520, 1524, 1530, 1633, 1653, 1732, 1736, 1807, 2770, 3152, 3156, 3382, 3386, 3410, 3440, 3444, 3584], '2005;': [678, 746, 776, 813, 1509], 'Deshaies': [679, 4184], 'Joazeiro,': [681], '2009;': [682, 702, 1056, 3153], 'Komander': [683, 747, 814, 4423], 'Deregulation': [687], 'ubiquitination': [690, 4779], 'pathway': [691], 'lead': [693], 'cancer': [695, 4284], 'neurodegenerative': [697], 'diseases': [698], '(Hoeller': [699], 'Dikic,': [701], 'Lopez-Otin': [703, 4480, 4632], 'Hunter,': [705], '2010).': [706, 792, 1030, 1808], 'More': [707], 'than': [708, 732, 1794, 1829, 1902, 2025, 2071, 2088, 2557, 2687], '100': [709], 'putative': [710], 'DUBs': [711, 3046, 3847], 'are': [712, 794, 838, 874, 1274, 1289, 1378, 1838, 2512, 3459, 3647], 'known': [713, 946], 'so': [714, 2108], 'far,': [715], 'belonging': [716], 'five': [718], 'subfamilies': [719, 858], 'isopeptidases.': [721], 'Ub-specific': [723], 'largest,': [729], '60': [733], 'members': [734, 4029], 'human': [737, 4224, 4642, 4801, 4966], 'genome': [738], '(Quesada': [739, 1494], 'USPs': [751, 793, 830, 2979, 3082, 3136, 3467, 3524, 3625, 3655], 'share': [752, 845], 'papain-like': [754], 'structures': [759, 1409, 1505], 'core': [764], 'undergoes': [766], 'conformational': [767, 2717], 'changes': [768, 2718], 'after': [769, 1662, 2238, 2730], 'binding': [771, 906, 1629, 1689, 2226, 2267, 2318, 2337, 2405, 2415, 2444, 2464, 2481, 2529, 2548, 2588, 2610, 2694, 2781, 3124, 3264, 3275, 3300, 3328, 3709, 3719, 4382, 4871], '(Hu': [772, 914, 1506, 1528, 1651, 1730], '2002,': [775], 'Avvakumov': [777, 1510, 1734, 4097], '2006;': [780, 784, 862, 1513, 1517], 'Renatus': [781, 1514, 4668], 'Köhler': [785, 1518, 4392], '2010;': [788, 1521], 'Samara': [789, 1522, 4715], 'variable': [795], 'size': [797, 1167], 'modular': [799], 'architecture': [801, 1250], 'including,': [802], 'example,': [804, 3687], 'TRAF-like,': [805], 'DUSP': [806, 3562], 'Znf': [808], 'domains': [809, 826, 837, 869, 3356, 3390, 3513, 4964], '(Nijman': [810], 'Sequence': [818, 3608], 'analysis': [819, 2051, 2520, 3609, 4638], 'predicted': [820, 2763, 3174], 'presence': [822, 2169, 2433, 2709, 2754, 2859, 3062, 3095], 'Ub-like': [824], '17': [828, 964], '(Zhu': [831], '2007).': [834, 866, 2771, 3445], 'Integrated': [835], 'stretches': [839], '45–80': [841], 'amino': [842, 3549], 'acids': [843, 1135, 1454, 1460, 1479, 2118, 2798, 3550, 3568], 'β-grasp': [847, 4155], 'Ub,': [850, 1318, 1999, 2288, 2383, 3028, 3333], 'but': [851, 931, 1660, 2059, 2543, 4145], 'often': [852], 'have': [853, 985, 3137, 3419, 3451, 3590, 3706, 4064], 'poor': [854], 'sequence': [855, 3453, 4377], 'conservation': [856], 'among': [857], '(Kiel': [859], 'Serrano,': [861], 'Burroughs': [863, 4135], 'USP': [872, 1205, 1504, 2906, 2926, 3115, 3318, 3810], 'located': [875], 'amino-terminally,': [876], 'within': [877, 2759, 3177, 3538, 3604, 3620], 'C-terminally': [879], 'domain.': [883, 942, 1833, 2934, 3128, 3332, 3510, 3607, 3664, 4705], 'Structural': [884, 3287, 4403, 4673, 4730], 'studies': [885], 'N-terminal': [888, 926, 1191], 'USP14': [892, 913, 1650], 'confirmed': [893], 'Ubl-fold': [895], '(Protein': [896], 'Data': [897, 3949, 4072, 4175], 'Bank': [898], '(PDB):': [899], '1WGG)': [900], 'showed': [902, 1209], 'involvement': [903], 'proteasome': [905, 3379], 'promotes': [908], 'DUB': [910, 1173, 1887, 2098, 2151, 2183, 2844, 2893, 2982, 3106, 3189, 3258, 3521, 3599, 3659, 3701], '2005).': [917, 3387, 3895], 'Similar': [918, 1406], 'USP14,': [920, 3370], 'domain,': [930, 1092, 2786, 3076, 4825], 'it': [932, 983, 1032, 1358, 2105, 2122, 2572, 2697, 2874, 3101, 3158, 3754], 'additional': [935, 2716], 'embedded': [938, 3181, 3634], 'was': [944, 1638, 2069, 2280, 2308, 2339, 2762, 3091, 3875, 3899, 3915, 3928, 3961, 4038], 'previously': [945], 'ubiquitous': [948], 'nuclear': [949], '(UNP)': [951], '(Gupta': [952], '1993).': [955], 'Identified': [956], 'proto-oncogene': [959, 4220], 'related': [960, 3649, 4248], 'Tre': [962], '2/Tre': [963], '(USP6),': [965], 'shows': [967, 1701, 1817, 3217, 3552], 'consistently': [969], 'elevated': [970], 'gene': [971, 4247], 'expression': [972, 4216], 'level': [973, 4566], 'small': [975], 'cell': [976, 4564], 'tumours': [977], 'lung': [979, 4225], 'adenocarcinomas,': [980], 'suggesting': [981], 'may': [984, 3323], 'possible': [987, 997], 'causative': [988], 'neoplasia': [991], '(Gray': [992], '1995).': [995], 'Besides': [996], 'roles': [998], 'Wnt': [1000, 4939], 'signalling': [1001], '(Zhao': [1002], '2009)': [1005], 'recruitment': [1007, 3373], 'A2A': [1010, 4569], 'receptor': [1011], '(Milojevic': [1012], '2006),': [1015], 'recruited': [1018], 'complex': [1023, 1047, 1237, 3145, 3211, 4322, 4771], 'formation': [1024], 'Sart3': [1026, 3581], '(Song': [1027, 1805, 3582], 'preferentially': [1033], 'deubiquitinates': [1034], 'K63-linked': [1035], 'chains': [1036, 4660], 'U4': [1039], 'component': [1040, 1043], 'Prp3.': [1041], 'Another': [1042], 'catalytically': [1050, 1538], 'inactive': [1051, 3066, 3070, 3472], 'USP39': [1052, 2950, 3005, 3141], '(Sowa': [1053, 3150], 'Song': [1057, 3154, 4336, 4748], '2010),': [1060, 1525, 3157], 'which': [1061, 1164, 1721, 2811, 3252, 3290, 3668], 'controls': [1062, 4906], 'messenger': [1064], 'RNA': [1065], 'levels': [1066], 'Aurora': [1068], 'B': [1069], '(van': [1070], 'Leuken': [1071, 4886], '2008).': [1074], 'report': [1077], 'without': [1088, 1755, 1820], 'internal': [1090, 3761], 'how': [1095], 'acts': [1099], 'inhibits': [1106, 1740, 1885, 3188, 3257, 3298], 'competitive': [1110, 1993, 2621, 2677, 2898, 3261], 'Results': [1112], 'Identification': [1113], 'USP4–D1D2': [1115, 1260, 1332, 1340, 1382, 1417, 1700, 1819, 1904, 1971, 2026, 2074, 2127, 2166, 2208, 2228, 2248, 2279, 2307, 2328, 2349, 2363, 2424, 2446, 2498, 2856, 3109, 3203, 3232, 3974], 'To': [1116, 1142, 2145, 2772, 2835], 'gain': [1117], 'insight': [1118], 'function': [1123, 3345, 3371, 3717, 4085, 4264, 4435, 4736, 4821], 'USP4,': [1125, 1666, 2101, 2847, 2896, 2921, 3539], 'expressed': [1127, 2112], 'purified': [1129, 2114, 2794, 3889], '(amino': [1134, 1453, 1459, 1478, 2117, 2797, 3567], '296–954,': [1136], 'Fig': [1137, 1176, 1194, 1224, 1433, 1499, 1562, 1719, 1782, 1814, 1849, 1880, 2133, 2176, 2221, 2256, 2540, 2765, 2800, 2868, 3019], '1A)': [1138, 2801], 'Escherichia': [1140], 'coli.': [1141], 'improve': [1143], 'chances': [1145], 'crystallization,': [1147], 'used': [1149], 'limited': [1150], 'proteolysis.': [1151], 'After': [1152], 'treatment': [1153, 1213], 'thermolysin,': [1155], 'two': [1156, 1239, 1642], 'fragments—domain': [1157], '(D1)': [1159], '2': [1161], '(D2)—were': [1162], 'obtained,': [1163], 'copurified': [1165], 'exclusion': [1168], 'chromatography': [1169], 'together': [1171, 1582, 2564], 'retained': [1172], '(supplementary': [1175, 1193, 1223, 1848, 2132, 2175, 2539, 2764, 2867], 'S1A,B': [1177], 'online).': [1178, 1376, 1435, 1501, 1784, 1882, 2135, 2178], 'We': [1179, 1335, 1743, 1785, 2111, 2136, 2205, 2441, 2641, 2668, 2881, 2935, 3051, 3170, 3990], 'identified': [1180, 3615], 'composition': [1182], 'D1': [1184, 1271, 1437, 1584, 1835], 'D2': [1186, 1273, 1468, 1586, 1837], 'using': [1187, 1345, 1398, 1760, 3816, 3863, 3953], 'mass': [1188, 3995], 'spectrometry': [1189], 'sequencing': [1192], 'S1C': [1195], 'online)': [1196, 1816, 2870], 'compared': [1198, 1744, 2496, 3876], 'them': [1199], 'multi-sequence': [1202], 'alignment': [1203, 4464], 'members.': [1207], 'removed': [1214], 'insertion': [1216], 'between': [1217, 1951, 3462, 4488], 'Leu': [1218, 1221], '481': [1219], '766': [1222], 'S2': [1225, 1500, 1850, 2766], 'online),': [1226, 1851, 2542], 'yielding': [1227], 'consisting': [1232], 'enzymatically': [1235], 'active': [1236, 1464, 1472, 1658, 1901, 2024], 'fragments:': [1240], 'USP4–D1D2.': [1241, 1247, 2090, 2144, 2269, 2483], 'Figure': [1242, 1883, 2258, 2963, 3278], '1.The': [1243], '(A)': [1248, 1897, 2286, 2977, 3286], 'Domain': [1249], 'fragments': [1254, 2277], 'expressed.': [1255], '(B)': [1256, 1903, 2289, 3004, 3303], 'Crystal': [1257, 4311], 'cartoon': [1264], 'representation,': [1265], 'secondary': [1267], 'elements': [1269], 'labelled.': [1270], 'coloured': [1275], '(A).': [1278], 'Catalytic': [1279], 'triad': [1280, 1534], 'cysteines': [1283, 1591], '(yellow)': [1284], 'coordinating': [1285], 'zinc': [1286], '(grey': [1287], 'sphere)': [1288], 'shown': [1290, 3707], 'stick': [1292], 'representation.': [1293], '(C,': [1294], 'D)': [1295], 'Superposition': [1296, 1692, 3197], 'six': [1298, 1379, 1695], 'non-crystallographic': [1299, 1696], 'symmetry-related': [1300, 1697], 'copies': [1301], 'asymmetric': [1304], 'unit': [1305], 'showing': [1306, 1860, 2472], 'flexibility': [1307, 1713], '(C)': [1309, 1906, 2292, 3007, 3316], 'zinc-finger': [1311, 1565, 1605, 1705, 3244, 3491, 3501], 'ribbon': [1312, 1566, 1606, 1706, 3502], '(D)': [1314, 1916, 2320], 'blocking': [1315, 1675, 1710, 3240, 3486, 3490, 3498], 'loops,': [1316], 'BL1–3.': [1317], 'ubiquitin;': [1319, 2000, 2384, 3029, 3334], 'Ubl,': [1320, 2003, 2385, 3032, 3335], 'ubiquitin-like;': [1321, 2004, 2386, 3033, 3336], 'USP,': [1322, 2005, 2387, 3034, 3337], 'protease.': [1324, 2007, 2389, 3036, 3339], 'Download': [1325, 1327, 2008, 2010, 2390, 2392, 3037, 3039, 3340, 3342], 'figure': [1326, 2009, 2391, 3038, 3341], 'PowerPoint': [1328, 2011, 2393, 3040, 3343], 'Structure': [1329, 4349, 4683, 4819, 4859], 'crystallized': [1336], 'determined': [1338], 'molecular': [1343, 2156], 'replacement': [1344], 'USP8': [1347, 1571, 1621, 3074], '(PDB:': [1350, 3214, 3547], '2GFO)': [1351], 'search': [1354], 'molecule,': [1355], 'refined': [1357], '2.4': [1360], 'Å': [1361, 1394, 1546], 'resolution': [1362], 'R/Rfree': [1365], '0.178/0.21': [1367], 'good': [1369], 'geometry': [1370], '(Fig': [1371, 1430, 1576, 1669, 1779, 1811, 1877, 2052, 2439, 2506, 2656, 2820, 2961, 3078, 3233, 3276, 3724, 3731], '1B;': [1372, 1431], 'supplementary': [1373, 1432, 1498, 1781, 1813, 1879, 3793], 'Table': [1374], 'S1': [1375], 'There': [1377], 'molecules': [1380, 1698], 'per': [1383], 'asymmetrical': [1384], 'unit,': [1385], 'pairwise': [1388], 'root-mean-square': [1389], 'deviation': [1390], 'approximately': [1392, 2079], '0.7': [1393], 'over': [1395, 2310, 2425], '344': [1396], 'residues': [1397], 'PISA': [1400], 'program': [1401], '(Krissinel': [1402], 'Henrick,': [1404], '2004).': [1405], 'resembles': [1418], 'extended': [1420], 'right': [1421], 'hand': [1422, 3230, 3267], 'comprising': [1423], 'three': [1424, 1709, 4466], 'domains:': [1425], 'Fingers,': [1426], 'Thumb': [1427, 1441], 'Palm': [1429, 1493], 'S3': [1434], 'fragment': [1438, 1469], 'contains': [1439], 'part': [1444, 1487, 2831], 'Fingers': [1447, 1490, 1609], 'Cys': [1451, 1549], 'box': [1452, 1458, 1477], '303–320)': [1455], 'QQD': [1457], '390–403)': [1461], 'site,': [1465, 1659], 'whereas': [1466], 'completes': [1470], 'site': [1473, 1630, 2919], 'His': [1476, 1542, 1552], '864–885,': [1480], '894–903,': [1481], '915–922)': [1482], 'makes': [1484], 'remaining': [1486], 'Like': [1502], 'except': [1526], 'USP7': [1527, 1847, 3209], '2002),': [1531], 'competent': [1539], 'configuration,': [1540], 'wherein': [1541], '711-ND1': [1543], '3.2': [1545], 'away': [1547], 'from': [1548], '311-SG': [1550], '711-ND2': [1553], 'hydrogen': [1555], 'bonding': [1556], 'Asp': [1558], '898-OD1': [1559], '(2.7': [1560], 'Å;': [1561, 1718], '1B).': [1563], 'observed': [1567, 1786, 1943, 1956, 2137, 2225, 2442, 3741], 'USP2': [1569], 'present': [1573], '1B,C).': [1577], 'Zn2+': [1579], 'ion': [1580], 'brings': [1581], 'domains,': [1587, 3418], 'tetrahedrally': [1588], 'coordinated': [1589], 'anti-parallel': [1593], 'β-strands': [1594], 'β1': [1595], 'β2': [1597], 'D1,': [1599], 'β4': [1601], 'D2.': [1603], 'seems': [1611, 2094, 2714, 2912, 3494], 'be': [1613, 1988, 2458, 3132, 3735], 'contracted': [1616], "'closed-hand'": [1617], 'configuration': [1618], 'seen': [1619], 'blocks': [1623], 'access': [1624, 1680], '(Avvakumov': [1631], '2006).': [1634, 1737], 'similar': [1636, 1855, 2813], 'assigned': [1639], 'Ub-binding': [1643, 2918], 'surface': [1644, 2217, 4565], 'loops': [1645, 1668, 1711, 3241, 3487, 3499], '(BL1': [1646], 'BL2)': [1648], '2002)': [1654], 'block': [1656], 'relocate': [1661], 'binding.': [1664, 2622, 2902, 3196], 'both': [1667, 1703, 1827, 3081], '1D)—as': [1670], 'well': [1671, 2585, 2612, 3365], 'third': [1674], 'loop': [1676], '(BL3)': [1677], 'hinders': [1679], 'C-terminal': [1683], 'tail': [1684], 'pocket—are': [1690], 'observed.': [1691], '(maximal': [1714], 'Cα': [1715], 'displacement': [1716], '1C,D),': [1720], 'agreement': [1724, 1797], 'their': [1726, 1852, 3457], 'activation': [1729, 1866, 3087, 3728, 4408], '2002;': [1733], 'insert': [1739, 1821, 1871, 1941, 1965, 2093, 2116, 2140, 2188, 2204, 2263, 2276, 2326, 2399, 2430, 2476, 2607, 2638, 2761, 2819, 2942, 3180, 3843], 'large': [1757, 3179], 'insert,': [1758, 2231, 2738, 3012, 3099, 3638], 'vitro': [1762], 'assays.': [1764, 1924, 3799, 3850, 3880], 'these': [1766, 2181, 2537, 3045, 3448], 'assays': [1767, 1976, 2015, 3808, 3812, 3840], 'followed': [1769], 'K63-': [1773], 'K48-linked': [1775], 'di-Ub': [1776, 1789, 1912, 1922, 3884], 'mono-Ub': [1778, 1919, 1929], '2A,B;': [1780], 'S4A,B': [1783], 'K63': [1788, 1911, 1921, 3883], 'efficiently': [1792], 'degraded': [1793], 'K48,': [1795], 'splicing': [1804], 'quantification': [1810], '2D;': [1812], 'S4D': [1815], 'efficient': [1824], 'degrading': [1826], 'di-Ubs': [1828], 'complete': [1831, 2818], 'When': [1834, 2046], 'fused': [1839], 'short': [1842], 'linker,': [1843], 'found': [1845, 2669, 2803, 2872, 2954, 3537], 'USP4–D1D2,': [1859, 2407, 2562, 2810], 'cause': [1863], 'lack': [1869], 'not': [1873, 2040, 2703, 2742, 3103, 3589, 3596], 'chain': [1875], 'break': [1876], '2C;': [1878], 'S4C': [1881], '2.Insert': [1884], 'USP4CD.': [1890, 1967, 2976, 3976], '(A–C)': [1891, 2270], 'full-length': [1893, 2353], 'much': [1899], 'less': [1900, 2023], 'fusion': [1908, 2029], '(Coomassie-stained': [1913], 'SDS–PAGE': [1914], 'gels).': [1915], 'Quantification': [1917], 'cleavage': [1923], 'intensity': [1926], 'band': [1930], 'plotted': [1932], 'time.': [1934], '(E)': [1935, 2343], 'inhibitory': [1937], 'effect': [1938, 3130], 'Ub-AMC': [1946, 1975, 2130, 2990, 3056, 3798, 3817, 3854], 'assay.': [1947], 'On': [1948], 'comparing': [1949], 'Kcat/Km': [1950], 'USP4CD': [1952, 2087, 2354, 2370, 2489, 2552, 2701, 2960, 2985, 3049, 3059, 3089, 3297], 'D1D2,': [1954], '90': [1958, 1985], 'times': [1959], 'lower': [1960, 2081, 2597, 2686, 2734], 'enzyme': [1961, 2726, 3821, 3898, 4317, 4356, 4776, 4803], 'efficiency': [1962, 2083], 'containing': [1966, 2941], '(F)': [1968], 'Inhibition': [1969], 'trans': [1973, 2162, 2852, 2987, 3055, 3805], 'Ubl-insert': [1979], 'concentrations': [1980, 2331, 2532, 2649, 2655], '(5,': [1981], '15,': [1982, 3628], '45': [1983], 'μM)': [1986, 2068], 'jointly': [1989], 'fit': [1990, 3223], 'inhibitor.': [1994], 'SDS–PAGE,': [1995], 'SDS–polyacrylamide': [1996, 3907], 'gel': [1997, 3908], 'electrophoresis;': [1998], 'Ub-AMC,': [2001, 3030], 'ubiquitin-7-amido-4-methylcoumarin;': [2002, 3031], 'Ub-7-amido-4-methylcoumarin': [2013], '(Ub-AMC)': [2014], 'intact': [2017, 2064, 2488], 'also': [2022, 2569, 2929, 3657], 'protein.': [2030], 'As': [2031, 2091, 2577, 2908, 3140], 'only': [2032, 2493, 3235, 3598], 'AMC': [2033], 'cleaved': [2035], 'off,': [2036], 'inhibition': [2038, 2163, 2200, 2664, 2678, 2752, 2853, 2876, 2899, 3262, 3283, 3326, 3670, 3806, 3839, 3873], 'dependent': [2041, 2581, 3092], 'target.': [2045], 'analysed': [2047, 2625, 3043], 'Michaelis–Menten': [2049], 'kinetic': [2050, 3861], '2E)': [2053], 'Vmax': [2055], 'values': [2056, 2361], 'were': [2057, 2295, 2356, 2673, 3814, 3856, 3886, 3951], 'similar,': [2058], 'Km': [2061, 2579, 2603], '(13.5': [2067], 'weaker': [2070], '(0.20': [2075], 'μM),': [2076], 'leading': [2077], '90-fold': [2080], 'overall': [2084], '(kcat/Km)': [2085], 'inhibit': [2096, 2193, 2842, 2891], 'tested': [2103, 2206, 2396, 2642, 2936], 'whether': [2104, 2147, 2207, 2397, 2626, 2774, 2837, 2924, 2937, 3044], 'do': [2107], 'trans.': [2110, 2640], '483–765)': [2119], 'added': [2121], 'increasing': [2124, 2435, 2861], 'amounts': [2125, 2436, 2862], 'assay': [2131, 2164, 2854, 2991, 3016, 3057], 'S5A': [2134], 'slows': [2141], 'deubiquitination': [2142], 'investigate': [2146], 'reduction': [2149], 'due': [2154], 'crowding,': [2157], 'repeated': [2159, 2849, 3052], 'either': [2171], 'SUMO': [2172], 'BSA': [2174], 'S6': [2177, 2869], 'Neither': [2179], 'reduced': [2182], 'activity,': [2184], 'confirming': [2185], 'intrinsically': [2190, 3065], 'able': [2191], 'USP4.': [2198, 3285, 3315, 3641, 3651], 'Competitive': [2199], 'would': [2209, 2409, 3222, 3691], 'directly': [2210], 'interact': [2211], 'insert.': [2214, 2712, 2834, 2880], 'plasmon': [2218], 'resonance': [2219], '(SPR;': [2220], '3B)': [2222], 'experiment,': [2223, 2518], 'Kd': [2234, 2486, 2567, 2583, 2805], '1.32': [2236], 'μM': [2237, 2808, 3903], 'equilibrium': [2239], 'fitting.': [2240], 'affinity': [2242, 2246, 2598, 2735], 'closely': [2243, 3648], 'resembled': [2244], 'itself': [2251, 3671], '(Kd': [2252], '1.39': [2254], 'μM;': [2255], '3A).': [2257], '3.Ubiquitin': [2259], 'competes': [2260, 2477], 'Ubl-domain': [2265, 3449, 3669], 'Interaction': [2271], 'studied': [2281, 2357], 'SPR': [2283, 2419, 2522, 2790, 3015, 3924, 3927, 4024], 'experiments.': [2284], 'Top:': [2285], 'GST-tagged': [2287], 'GST-insert': [2290, 2449, 3936], 'GST-Ubl': [2293, 3938], 'immobilized': [2296, 2324, 3940], 'anti-GST': [2298, 3942], 'antibodies': [2299, 3943], 'coupled': [2300, 3944], 'CM5': [2303, 3947], 'Biacore': [2304, 3932], 'chip': [2305, 2312], 'flowed': [2309, 2423], 'concentrations.': [2315], 'Bottom:': [2316], 'Langmuir': [2317], 'curves.': [2319], 'Competition': [2321], 'experiment': [2322, 2421, 2505, 2791], 'GST': [2325], 'varying': [2330, 2647], 'Ub.': [2333, 3302], 'one-site': [2335, 2462], 'competition': [2336, 2420, 2463], 'model': [2338, 2465, 3250, 3288, 3305], 'fitted': [2340, 2459, 2659], '(Ki=1.4': [2341], 'μM).': [2342], 'interaction': [2345, 3291, 3579, 4804, 4828], '(left)': [2350], '(right)': [2355], 'ITC.': [2359, 3926], 'Thermodynamic': [2360], '(ΔH=−14.3': [2364], 'kcal/mol': [2365, 2372], 'ΔS=−16.9': [2367], 'cal/mol/deg),': [2368], '(ΔH=−11.4': [2371], 'ΔS=−10.0': [2374], 'cal/mol/deg).': [2375], 'GST,': [2376, 3024], 'glutathione': [2377, 2427], 'S-transferase;': [2378], 'ITC,': [2379], 'isothermal': [2380, 2501], 'titration': [2381, 2502], 'calorimetry;': [2382], 'Therefore,': [2394], 'therefore': [2410, 2741, 2882], 'same': [2414], 'S-transferase': [2428], '(GST)-tagged': [2429], '3D).': [2440], 'decreasing': [2443], 'concentration': [2453, 3855], 'increased.': [2454], 'data': [2456, 2538, 2661, 2672, 2695, 4007, 4025], 'Ki': [2468], '1.4': [2470], 'μM,': [2471], 'fourfold': [2494], 'less,': [2495], 'calorimetry': [2503], '(ITC)': [2504], '3E).': [2507], 'Although': [2508, 2682, 3726], 'exact': [2510], 'Kds': [2511], 'slightly': [2513, 2596], 'tighter': [2514], 'ITC': [2517, 3960], 'qualitative': [2519], 'experiments': [2523], 'agrees': [2524], 'assessment.': [2527], 'Non-specific': [2528], 'high': [2531, 2956], 'precluded': [2533], 'detailed': [2534], 'fitting': [2535, 3870], 'S7': [2541], 'curves': [2545], 'slower': [2555, 2575], 'off-rate': [2556], 'value': [2568, 2684], 'suggest': [2570], 'on-rate.': [2576], 'rate,': [2589], 'combination': [2591], 'slow': [2593], 'kinetics': [2594], 'explains': [2599, 2698], 'differences': [2601], 'values.': [2604], 'Apparently,': [2605, 3113], 'prevents': [2608], 'rapid': [2609, 2614], 'release': [2615, 3694], 'allowing': [2620], 'Finally': [2623], 'enzymatic': [2628, 2644, 3393, 4637], 'competitively': [2631], 'addition': [2635], 'inhibitor': [2648], 'range': [2652], 'substrate': [2654, 2917, 3274], '2F),': [2657], 'models': [2665, 3874], '(Copeland,': [2666], '2000).': [2667], 'best': [2674], 'explained': [2675], 'Ki=47': [2680], 'μM.': [2681], 'expected': [2688], 'basis': [2691, 4404, 4674], 'alone,': [2696], 'why': [2699], 'completely': [2704], 'continuous': [2708], 'It': [2713], 'take': [2719], 'place.': [2720], 'One': [2721, 3678], 'possibility': [2722], 'reaches': [2727], 'state': [2729], 'turnover': [2731], 'effectively': [2744], 'inhibited.': [2745], 'sufficient': [2750, 2779, 2889], 'online;': [2767], 'Zhu': [2768, 3611, 4953], 'test': [2773, 2836], 'performed': [2788, 3815, 3916, 3929, 3962], '483–571,': [2799], '1.36': [2807], 'towards': [2809], '3C).': [2821], 'suggests': [2823], 'functional': [2830, 4149, 4524, 4596], 'provides': [2875], 'equal': [2877], 'conclude': [2883], 'Regulation': [2903], 'wondered': [2923], 'our': [2938], 'USP8,': [2952], 'similarly': [2955], 'affinities': [2957], '4B,C).': [2962], '4.USP39CD': [2964], 'binds': [2965, 4695], 'increases': [2971], 'deubiquitinating-enzyme': [2973], 'Other': [2978, 3317, 3388], 'activate': [2980, 3715], '(USP39CD:': [2992], '10,': [2993], '20,': [2994], '50,': [2995], '100,': [2996], '500': [2997], '1,000': [2999, 3002], 'nM;': [3000], 'USP8CD-mut:': [3001], 'nM).': [3003], 'USP8-mut': [3008], 'analogous': [3017], '2B.': [3020], 'DUB,': [3021], 'enzyme;': [3023], 'glutathione-S-transferase;': [3025], 'mut,': [3026], 'mutant;': [3027], 'Then,': [3041], 'modulate': [3048], 'activity.': [3050], 'USP39CD': [3067], 'variant': [3071], 'USP8CD-mut': [3077], '4A).': [3079], 'For': [3080, 3780], 'observe': [3084], 'modest': [3086, 3730], 'Ubl-containing': [3098], 'does': [3102], 'increase': [3104], 'manner.': [3112], 'regulate': [3118, 3391, 3751], 'competing': [3122, 3192], 'larger': [3133, 3637], 'when': [3134], 'further': [3138, 3505, 3682, 3738], 'interactions.': [3139], 'stable': [3144], 'cells': [3149], 'prime': [3161], 'candidate': [3162], 'activating': [3165], 'vivo.': [3168], 'Discussion': [3169], 'any': [3205], 'Ub-aldehyde': [3213], '1NBF),': [3215], 'respectively,': [3216], 'like': [3224, 3639], 'molecule': [3227], '5A),': [3234], 'requiring': [3236], 'movements': [3237], 'ribbon.': [3245, 3492], 'Hence,': [3246], 'propose': [3248], 'thus': [3271], 'preventing': [3272], '5B).': [3277], '5.Model': [3279], 'Schematic': [3304], 'auto-inhibitory': [3308], 'enzymes,': [3319], 'integrated': [3348, 3617], 'relatively': [3352], 'new.': [3353], 'proteasomal': [3358], 'shuttle': [3359], 'factors': [3360], 'Rad23': [3361], 'Dsk2,': [3363], 'Parkin': [3368, 4694], 'ubiquitinated': [3375], 'proteins': [3376, 3429], '(Sakata': [3380], '2003;': [3383], 'Hu': [3384, 4292, 4332], 'activities': [3394], 'immune-response': [3396], 'inducible': [3397], 'kinases': [3398, 4489], 'IKKβ': [3401], '(a': [3402], 'subunit': [3403, 4698], 'IκB': [3405, 4518], 'kinase': [3406, 3436, 4519], 'complex;': [3407], 'May': [3408, 4502], '2004),': [3411], 'PB1': [3414, 4824, 4865], '(Phox': [3415], 'Bem1)': [3417], 'signal': [3426], 'transduction': [3427], 'P62,': [3432], 'MEK5': [3433], '(Terasawa': [3438], '2001;': [3441], 'Sumimoto': [3442, 4812, 4854], 'However,': [3446, 3593], 'all': [3447], 'families': [3450], 'low': [3452], 'similarities,': [3454], 'indicating': [3455], 'functions': [3458], 'probably': [3460, 3656], 'distinct': [3461], 'subfamilies.': [3463], 'regulated': [3469, 3673], 'conformation': [3473, 4120], 'triad,': [3477], 'USP7,': [3480], 'series': [3484], 'combine': [3496], 'Whether': [3511], 'provide': [3514], 'common': [3516], 'mechanism': [3518], 'interesting': [3527], 'question': [3528], 'future': [3530, 4613], 'research.': [3531], 'second': [3533], 'N-terminus.': [3542], 'recent': [3544], '3JYU,': [3548], '139–226)': [3551], 'interacts': [3557], 'extensively': [3558], 'adjacent': [3561], '(domain': [3563], 'USP)': [3565], '27–125).': [3569], 'region': [3571], 'primarily': [3576], 'important': [3577], '2010)': [3585], 'hence': [3587], 'might': [3588], 'al': [3613, 4671, 4692], '(2007)': [3614, 4143, 4818, 4959], '6,': [3626], '11,': [3627], '19,': [3629], '31,': [3630], '32': [3631], '43,': [3633], 'particular,': [3643], 'USP11': [3644], 'USP15': [3646], 'subgroup': [3653], 'regulates': [3658, 4562], 'way': [3666], 'exciting': [3676], 'question.': [3677], 'imagine': [3680], 'post-translational': [3683], 'by,': [3685], 'phosphorylation': [3688], 'acetylation': [3690], 'enable': [3692], 'full': [3697], 'enzyme.': [3702], 'addition,': [3704], 'partners': [3710], '5C).': [3725], '4A),': [3732], 'increased': [3736], 'interactions,': [3739], 'complex.': [3745], 'Regardless': [3746], 'mechanisms': [3749, 4351], 'activation,': [3753], 'clear': [3756], 'type': [3759], 'allows': [3767], 'creation': [3769], 'extremely': [3772], 'fast': [3773, 4461], 'response': [3774], 'element': [3775], 'external': [3777], 'signals.': [3778], 'Methods': [3779, 4662], 'plasmids,': [3781], 'cloning,': [3782], 'preparation': [3784], 'identification,': [3786], 'crystallization': [3787], 'determination': [3790], 'procedures,': [3791], 'see': [3792], 'information': [3794, 3981], 'online': [3795, 3987], 'references.': [3797], 'Quantitative': [3800], '(triplicate)': [3802, 3813], '(duplicate)': [3807, 3950], 'modulation': [3811, 3849], '10': [3819], 'nM': [3820, 3897], '30': [3823], 'μl': [3824], 'reaction': [3825], 'volume': [3826], '384-well': [3828], 'plates': [3829], 'preincubated': [3831], '15': [3833], 'min': [3834], '21°': [3836], 'C,': [3837, 4368, 4481, 4629, 4921], 'Initial': [3851], 'velocities': [3852], 'computed': [3857], 'derive': [3859], 'steady-state': [3860], 'parameters': [3862], 'GraphPad': [3864, 3958], 'Prism5': [3865], '(GraphPad': [3866], 'Software': [3867], 'Inc.).': [3868], 'Non-linear': [3869], 'four': [3872], 'GraphPad.': [3878], 'Di-Ub': [3879], 'K48': [3881], 'substrates': [3885], 'produced': [3887], 'described': [3891], '(Raasi': [3892], '75': [3896], 'incubated': [3900], '3': [3902], 'di-Ub,': [3904], 'subjected': [3905], 'electrophoresis': [3909], 'image': [3911], 'analysis,': [3912, 4018, 4026], 'quantitation': [3914], 'duplicate': [3918], 'TINA': [3920], '2.09': [3921], '(Raytest': [3922], 'Co.).': [3923], 'T-100,': [3933], 'GST-Ub,': [3935], 'chip.': [3948], 'processed': [3952], 'BiaEvaluation': [3954], '(GE': [3955], 'Healthcare)': [3956], 'Prism5.': [3959], 'VP-ITC': [3965], 'Micro': [3966], 'Calorimeter': [3967], '(MicroCal,': [3968], 'Inc.)': [3969], 'titrating': [3971], 'Accession': [3977], 'number.': [3978], '2Y6E.': [3979], 'Supplementary': [3980], 'available': [3983], 'reports': [3986], '(http://www.emboreports.org).': [3988], 'Acknowledgements': [3989], 'thank': [3991], 'J.': [3992], 'Lebbink': [3993], 'spectrometry,': [3996], 'European': [3997, 4042], 'Synchrotron': [3998], 'Radiation': [3999], 'Facility': [4000], 'beamline': [4001], 'scientists': [4002], 'assistance': [4004], 'during': [4005], 'X-ray': [4006], 'collection,': [4008], 'A.': [4009], 'Perrakis': [4010], 'P.': [4012], 'Rucktooa': [4013], 'help': [4015, 4022], 'crystallographic': [4017], 'R.G.': [4019], 'Hibbert': [4020], 'lab': [4028], 'discussion': [4031], 'sharing': [4033], 'reagents.': [4035], 'study': [4037], 'supported': [4039], 'Union': [4043], 'Network': [4044], 'Excellence': [4046], 'project': [4047], 'RUBICON': [4048], 'Dutch': [4050], 'Society': [4052], 'Project': [4053], 'KWF': [4054], '2008-4014.': [4055], 'Conflict': [4056], 'Interest': [4058], 'authors': [4060], 'declare': [4061], 'they': [4063], 'no': [4065], 'conflict': [4066], 'interest.': [4068], 'Supporting': [4069], 'Supplemental': [4071], '(PDF': [4073], 'document,': [4074], '8.8': [4075], 'MB)': [4076], 'References': [4077], 'AY,': [4079], 'Hochstrasser': [4080, 4259], '(2004)': [4082, 4453, 4512, 4609, 4634], 'Mechanism': [4083, 4173], 'enzymes.': [4088, 4600], 'Biochim': [4089], 'Biophys': [4090, 4646], 'Acta': [4091, 4468], '1695:': [4092], '189–207CrossrefCASPubMedWeb': [4093], 'Science®Google': [4095, 4133, 4162, 4200, 4231, 4257, 4272, 4290, 4330, 4365, 4390, 4421, 4447, 4478, 4500, 4535, 4576, 4605, 4620, 4652, 4687, 4713, 4746, 4788, 4810, 4883, 4916, 4951, 4975], 'Scholar': [4096, 4134, 4163, 4183, 4201, 4232, 4258, 4273, 4291, 4331, 4366, 4391, 4422, 4448, 4479, 4501, 4536, 4577, 4606, 4621, 4653, 4667, 4688, 4714, 4747, 4789, 4811, 4841, 4884, 4917, 4952, 4976], 'GV,': [4098], 'Walker': [4099], 'JR,': [4100], 'Xue': [4101], 'S,': [4102, 4138, 4552, 4631, 4655, 4815, 4851], 'Finerty': [4103], 'PJ,': [4104], 'Mackenzie': [4105], 'F,': [4106, 4755], 'Newman': [4107], 'EM,': [4108], 'Dhe-Paganon': [4109], 'S': [4110, 4428, 4511], '(2006)': [4111, 4371, 4557, 4672], 'Amino-terminal': [4112], 'dimerization,': [4113], 'NRDP1–rhodanese': [4114], 'interaction,': [4115], '8': [4125], '(USP8).': [4126], 'Biol': [4128, 4157, 4386, 4443, 4471, 4530, 4664], 'Chem': [4129, 4531], '281:': [4130], '38061–38070CrossrefCASPubMedWeb': [4131], 'AM,': [4136, 4587], 'Balaji': [4137], 'Iyer': [4139], 'LM,': [4140], 'Aravind': [4141], 'L': [4142, 4370], 'Small': [4144], 'versatile:': [4146], 'extraordinary': [4148], 'structural': [4151], 'diversity': [4152], 'fold.': [4156], 'Direct': [4158], '2:': [4159], '18CrossrefCASPubMedWeb': [4160], 'Copeland': [4164, 4235], 'RA': [4165], '(2000)': [4166], 'Enzymes:': [4167], 'Practical': [4169], 'Structure,': [4172], 'Analysis,': [4176], 'pp': [4177], '270–290,': [4178], 'UK:': [4179], 'WileyWiley': [4180], 'Online': [4181, 4362, 4475, 4710, 4880, 4948, 4972], 'LibraryGoogle': [4182], 'RJ,': [4185, 4887], 'Joazeiro': [4186], 'CA': [4187], '(2009)': [4188, 4261, 4278, 4429, 4798, 4926], 'RING': [4189], 'E3': [4191], 'ligases.': [4193], 'Annu': [4194], 'Rev': [4195, 4440, 4495], 'Biochem': [4196, 4645], '78:': [4197], '399–434CrossrefCASPubMedWeb': [4198], 'Gray': [4202, 4241], 'DA,': [4203], 'Inazawa': [4204], 'J,': [4205, 4753, 4757], 'Gupta': [4206, 4233], 'K,': [4207, 4234, 4853], 'Wong': [4208], 'A,': [4209, 4393, 4583, 4625, 4627], 'Ueda': [4210], 'R,': [4211, 4956], 'Takahashi': [4212], 'T': [4213, 4483, 4817, 4958], '(1995)': [4214], 'Elevated': [4215], 'Unph,': [4218], '3p21.3,': [4222], 'tumors.': [4226], 'Oncogene': [4227, 4253], '10:': [4228, 4444, 4497], '2179–2183CASPubMedWeb': [4229], 'NG,': [4236], 'Gilbert': [4237], 'DJ,': [4238], 'Jenkins': [4239], 'NA,': [4240], 'DA': [4242], '(1993)': [4243], 'Unp,': [4244], 'mouse': [4246], 'tre': [4251], 'oncogene.': [4252], '8:': [4254], '2307–2310CASPubMedWeb': [4255], 'Origin': [4262], 'proteins.': [4267], 'Nature': [4268, 4286], '458:': [4269], '422–429CrossrefCASPubMedWeb': [4270], 'Hoeller': [4274], 'D,': [4275, 4424, 4759], 'Dikic': [4276], 'I': [4277], 'Targeting': [4279], 'system': [4282], 'therapy.': [4285], '456:': [4287], '438–444CrossrefCASWeb': [4288], 'M,': [4293, 4297, 4333, 4397, 4554], 'Li': [4294, 4296, 4298, 4334], 'P,': [4295, 4335], 'W,': [4299, 4305], 'Yao': [4300, 4723], 'T,': [4301, 4538, 4724, 4847], 'Wu': [4302], 'JW,': [4303, 4761], 'Gu': [4304], 'Cohen': [4306, 4344, 4725], 'RE,': [4307, 4345, 4726], 'Shi': [4308, 4346], 'Y': [4309, 4347], '(2002)': [4310], 'UBP-family': [4315], 'isolation': [4319], 'aldehyde.': [4325], '111:': [4327], '1041–1054CrossrefCASPubMedWeb': [4328], 'L,': [4337], 'Jeffrey': [4338], 'PD,': [4339], 'Chenova': [4340], 'TA,': [4341], 'Wilkinson': [4342], 'KD,': [4343], '(2005)': [4348, 4592, 4658], 'proteasome-associated': [4354], 'USP14.': [4357], '24:': [4360, 4785], '3747–3756Wiley': [4361], 'LibraryCASPubMedWeb': [4363, 4476, 4711, 4881, 4949, 4973], 'Kiel': [4367], 'Serrano': [4369], 'superfold:': [4375], 'structure-based': [4376], 'alignments': [4378], 'characterization': [4380], 'epitopes.': [4383], 'Mol': [4385, 4441, 4571, 4663, 4944], '355:': [4387], '821–844CrossrefCASPubMedWeb': [4388], 'Zimmerman': [4394], 'E,': [4395, 4399, 4450, 4542, 4548, 4550], 'Schneider': [4396], 'Hurt': [4398], 'Zheng': [4400], 'N': [4401], '(2010)': [4402, 4484, 4729, 4768], 'assembly': [4406, 4734], 'heterotetrameric': [4411], 'SAGA': [4412, 4739], 'histone': [4413], 'H2B': [4414], 'deubiquitinase': [4415], 'module.': [4416, 4741], '141:': [4418], '606–617CrossrefCASPubMedWeb': [4419], 'Clague': [4425], 'MJ,': [4426, 4503], 'Urbe': [4427], 'Breaking': [4430], 'chains:': [4432], 'deubiquitinases.': [4438], 'Nat': [4439, 4494], '550–563CrossrefCASPubMedWeb': [4445], 'Krissinel': [4449], 'Henrick': [4451], 'Secondary-structure': [4454], 'matching': [4455], '(ssm),': [4456], 'new': [4458, 4935], 'tool': [4459], 'dimensions.': [4467], 'Crystallogr': [4469, 4472], 'D': [4470], '60:': [4473], '2256–2268Wiley': [4474], 'Hunter': [4482], 'regulatory': [4486], 'crosstalk': [4487], 'proteases': [4491], 'cancer.': [4493], '278–292CrossrefCASPubMedWeb': [4498], 'Larsen': [4504], 'SE,': [4505], 'Shim': [4506], 'JH,': [4507], 'Madge': [4508], 'LA,': [4509], 'Ghosh': [4510], 'novel': [4514, 4641, 4868], 'β': [4520], 'required': [4522], 'kinase.': [4528], '279:': [4532], '45528–45539CrossrefCASPubMedWeb': [4533], 'Milojevic': [4537], 'Reiterer': [4539], 'V,': [4540, 4623], 'Stefan': [4541], 'Korkhov': [4543], 'VM,': [4544], 'Dorostkar': [4545], 'MM,': [4546], 'Ducza': [4547], 'Ogris': [4549], 'Boehm': [4551], 'Freissmuth': [4553], 'Nanoff': [4555], 'Usp4': [4561], 'receptor.': [4570], 'Pharmacol': [4572], '69:': [4573, 4970], '1083–1094CrossrefCASPubMedWeb': [4574], 'SM,': [4579], 'MP,': [4581, 4889], 'Velds': [4582], 'Brummelkamp': [4584], 'TR,': [4585], 'Dirac': [4586], 'TK,': [4589, 4891], 'Bernards': [4590], 'R': [4591], 'genomic': [4594], 'inventory': [4597], '123:': [4602], '773–786CrossrefCASPubMedWeb': [4603], 'Pickart': [4607, 4656], 'CM': [4608, 4657], 'Back': [4610], 'ubiquitin.': [4615], '116:': [4617], '181–190CrossrefCASPubMedWeb': [4618], 'Quesada': [4622], 'Diaz-Perales': [4624], 'Gutierrez-Fernandez': [4626], 'Garabaya': [4628], 'Cal': [4630], 'Cloning': [4635], '22': [4640], 'proteases.': [4644, 4968], 'Res': [4647], 'Commun': [4648], '314:': [4649], '54–62CrossrefCASPubMedWeb': [4650], 'Raasi': [4654], 'Ubiquitin': [4659], 'synthesis.': [4661], '301:': [4665], '47–55CASPubMedGoogle': [4666], 'recognition': [4677, 4862], 'USP2.': [4682], '14:': [4684], '1293–1302CrossrefCASPubMedWeb': [4685], 'Sakata': [4689], 'E': [4690], '(2003)': [4693], 'Rpn10': [4697], '26S': [4700], 'proteasomes': [4701], 'Rep': [4707], '4:': [4708], '301–306Wiley': [4709], 'NL,': [4716], 'Datta': [4717], 'AB,': [4718], 'Berndsen': [4719], 'CE,': [4720], 'Zhang': [4721], 'X,': [4722, 4954], 'Wolberger': [4727], 'insights': [4731], 'Science': [4742], '328:': [4743], '1025–1029CrossrefCASPubMedWeb': [4744], 'EJ,': [4749, 4793], 'Werner': [4750], 'SL,': [4751], 'Neubauer': [4752], 'Stegmeier': [4754], 'Aspden': [4756], 'Rio': [4758], 'Harper': [4760, 4796], 'Elledge': [4762], 'SJ,': [4763], 'Kirschner': [4764], 'MW,': [4765], 'Prp19': [4770], 'Usp4Sart3': [4774], 'control': [4777], 'reversible': [4778], 'spliceosome.': [4782], 'Genes': [4783], 'Dev': [4784], '1434–1447CrossrefCASPubMedWeb': [4786], 'Sowa': [4790], 'ME,': [4791], 'Bennett': [4792], 'Gygi': [4794], 'SP,': [4795], 'JW': [4797], 'Defining': [4799], 'landscape.': [4805], '138:': [4807], '389–403CrossrefCASPubMedWeb': [4808], 'H,': [4813, 4843, 4849, 4855], 'Kamakura': [4814], 'Ito': [4816, 4846], 'module': [4829, 4870], 'animals,': [4832], 'fungi,': [4833], 'amoebas,': [4834], 'plants.': [4836], 'Sci': [4837], 'STKE': [4838], '2007:': [4839], 're6CrossrefPubMedGoogle': [4840], 'Terasawa': [4842], 'Noda': [4844], 'Y,': [4845], 'Hatanaka': [4848], 'Ichikawa': [4850], 'Ogura': [4852], 'Inagaki': [4856], 'F': [4857], '(2001)': [4858], 'ligand': [4861], 'domain:': [4866], 'PC': [4874], 'motif.': [4875], '20:': [4878], '3947–3956Wiley': [4879], 'Wolthuis': 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