Active site alanine mutations convert deubiquitinases into high‐affinity ubiquitin‐binding proteins

Name: Work Video:
Duration: 3 min 30 s
Marie E. Morrow; Michael T. Morgan; Marcello Clerici; Kateřina Growková; Ming Yan; David Komander; Titia K. Sixma; Michal Šimíček; Cynthia Wolberger
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'favoritesDownload': [601], 'CitationsTrack': [602], 'CitationsPermissions': [603], 'ShareFacebookTwitterLinked': [604], 'InMendeleyWechatReddit': [605], 'Figures': [606], '&': [607], 'Info': [608], 'Abstract': [609], 'A': [610, 1059, 1381, 2039], 'common': [611, 1060], 'strategy': [612], 'exploring': [614], 'biological': [616, 1020], 'roles': [617, 907], 'deubiquitinating': [619, 761, 1166, 1597, 3067, 3084], 'enzymes': [620, 903, 926, 1052, 1177, 1195, 1487], '(DUBs)': [621, 904], 'in': [622, 640, 651, 787, 841, 895, 908, 941, 1019, 1038, 1070, 1114, 1143, 1150, 1254, 1450, 1479, 1508, 1567, 1602, 1684, 1790, 1949, 2059, 2113, 2146, 2431, 2443, 2452, 2562, 2612, 2631, 2656, 2710, 2862, 2889, 2981, 3159, 3165, 3186, 3253, 3320, 3362, 3393, 3411, 3503, 3574, 3642, 3707, 3720, 3740, 3786, 3822, 3825, 3846, 3871, 3966, 3991, 3994, 4086, 4173, 4189, 4209, 4247, 4320], 'different': [623], 'pathways': [624, 1047, 1072, 1149], 'is': [625, 656, 1073, 1119, 1199, 1267, 1560, 1565, 1734, 2069, 2141, 2262, 2441, 2450, 2473, 2573, 2625, 2662, 2713, 2721, 3033, 3212, 3237, 3318, 3323, 3333, 3344, 3582, 3670, 3833, 4083, 4194, 4227, 4300], 'study': [627], 'effects': [629, 701, 798, 894, 1301, 1331, 3398, 3467, 3879], 'replacing': [631, 4108], 'wild-type': [633, 1865, 1875, 1982, 2118, 2148, 2220, 2285, 2571, 3008, 3404, 3435, 3470, 3491, 3558], 'DUB': [634, 649, 709, 716, 816, 1069, 1081, 1155, 1266, 1335, 1374, 1405, 1552, 1609, 1637, 1656, 1674, 1696, 1744, 1761, 1818, 1832, 1861, 1872, 1972, 2081, 2276, 2387, 2917, 2972, 2992, 3039, 3265, 3290, 3621, 3754, 3849, 3860, 4088, 4191], 'with': [635, 658, 746, 1109, 1138, 1168, 1311, 1327, 1477, 1640, 1645, 1662, 1765, 1772, 1826, 1840, 1881, 1900, 2046, 2071, 2105, 2127, 2151, 2164, 2180, 2192, 2215, 2231, 2264, 2401, 2556, 2592, 2667, 2684, 2884, 2931, 3017, 3110, 3123, 3229, 3355, 3422, 3507, 3530, 3568, 3578, 3647, 3927, 3936, 3951, 4061, 4113, 4233, 4281, 4289], 'catalytically': [637, 1085, 1756, 3619, 3709], 'inactive': [638, 899, 1086, 1757, 2916, 2980, 3620, 3710], 'mutant': [639, 785, 854, 1154, 1265, 1306, 1425, 1464, 1803, 1867, 1893, 2140, 2389, 2624, 2660, 2976, 3338, 3472, 3589, 3768, 3805, 3828, 3859], 'cells.': [641, 3823], 'We': [642, 735, 880, 1229, 1352, 1469, 1797, 1850, 2895, 2923, 3087, 3347, 3463, 3714, 4074, 4133, 4314], 'report': [643, 1230], 'here': [644, 1231, 1354, 1907, 2459, 2785, 3884, 4002], 'that': [645, 702, 737, 1218, 1232, 1355, 1471, 1505, 1529, 1564, 2145, 2617, 2706, 2903, 2925, 2970, 3005, 3262, 3332, 3339, 3349, 3479, 3550, 3571, 3622, 3717, 3802, 3836, 3985, 4082, 4107, 4135, 4180, 4229, 4236, 4263, 4273, 4278, 4316], 'commonly': [647], 'studied': [648], 'mutation,': [650], 'which': [652, 825, 869, 964, 1100, 1115, 1174, 1188, 1589, 1611, 3032, 3187, 3708], 'catalytic': [654, 1117, 1183, 1616, 1782, 2882, 2906, 2961, 3092, 3844, 4149], 'cysteine': [655, 745, 766, 1107, 1118, 1137, 1360, 1437, 1476, 1544, 2068, 2501, 2883, 2930, 2962, 3016, 3036, 3118, 3354, 3367, 3681, 3700, 3897, 3906, 3933, 3954, 3998, 4018, 4112, 4241, 4324], 'replaced': [657, 2263], 'alanine,': [659, 2072], 'can': [660, 748, 965, 1238, 1256, 1676, 2254, 3247, 4296], 'dramatically': [661, 769, 1239, 3727], 'increase': [662, 840, 1240, 1253, 2058, 2655, 2709, 3264, 3573, 3728, 3753], 'affinity': [664, 730, 755, 772, 843, 859, 1242, 1255, 1371, 1420, 1461, 1548, 1693, 1730, 1741, 1800, 1854, 2060, 2274, 2493, 2510, 2542, 2620, 2657, 2686, 2712, 2913, 2989, 3022, 3090, 3266, 3687, 3730, 3755, 3975], 'some': [666, 774, 942, 1226, 1233], 'DUBs': [667, 750, 775, 786, 805, 845, 855, 961, 1018, 1037, 1105, 1128, 1244, 1307, 1323, 1484, 1512, 2700, 2894, 3310, 3369, 3478, 3683, 3692, 3711, 3769, 3806, 3829, 3890, 3908, 3918, 3947, 3956, 4020, 4326], 'ubiquitin.': [669, 734, 757, 813, 1468, 2520], 'Overexpression': [670], 'these': [672, 693, 783, 804, 1051, 1305, 1500, 3273, 3289, 3564, 3767, 4174, 4207, 4213], 'tight-binding': [673, 1334], 'mutants': [674, 694, 1219, 1336, 1786, 1940, 3093, 3274, 3283, 3291, 3386, 3500, 3581], 'thus': [675, 1337, 1456, 2270, 3923, 3970], 'has': [676, 1049, 1277, 1293, 1701, 1717, 2504, 2638, 3046, 3701], 'potential': [678, 802, 1340, 3294], 'sequester': [680, 812, 1282, 3627], 'cellular': [681, 896, 1071, 2527, 3774, 3837], 'pools': [682], 'monoubiquitin': [684, 847, 1422, 1585, 1899, 1979, 2393, 2997, 3732], 'ubiquitin': [686, 721, 860, 909, 916, 935, 948, 977, 1248, 1273, 1284, 1292, 1317, 1328, 1412, 1444, 1535, 1555, 1641, 1682, 1880, 2048, 2063, 2088, 2106, 2122, 2173, 2209, 2251, 2280, 2402, 2417, 2496, 2547, 2554, 2568, 2591, 2606, 2636, 2666, 2672, 2751, 2800, 2887, 2940, 3190, 3341, 3510, 3526, 3640, 3650, 3689, 3785, 3815, 3873, 3928, 3977, 4048, 4096, 4116, 4127, 4143, 4171, 4186, 4245], 'chains.': [687, 780, 1251, 1287, 3428], 'As': [688, 2560, 3255, 3429], 'result,': [690], 'cells': [691, 788, 1151, 3166, 3219, 3254, 3394, 3413, 3432, 3437, 3450, 3505, 3657], 'expressing': [692, 1152, 3220, 3433, 3438, 3451, 3469, 3658], 'may': [695, 1224, 1308, 3271, 3850, 4151, 4205], 'display': [696], 'unpredictable': [697], 'dominant': [698, 796, 892], 'negative': [699, 797, 893], 'physiological': [700, 3278], 'are': [703, 1101, 1106, 1129, 1156, 1211, 1581, 2107, 2701, 2758, 2772, 2867, 3199, 3284, 3551, 3566, 3712, 3770, 3807, 3830, 3891, 4237, 4274], 'not': [704, 1268, 2212, 2663, 3133, 3334, 3454, 4059, 4220], 'related': [705], 'loss': [707], 'activity.': [710, 1228], 'structure': [712, 1400, 2077, 2115, 2384, 2395, 2440], 'SAGA': [715, 1404, 1551, 1558, 1579, 1600, 1971, 2080, 2386, 2971], 'module': [717, 1406, 1553, 1638, 1657, 1675, 1697, 1745, 1762, 1819, 1833, 1862, 1873, 1973, 2082, 2388, 2973, 2993], 'bound': [718, 1409, 1822, 1836, 1879, 1894, 2085, 2120, 2391, 2404, 2470], 'free': [720, 1247, 1283, 1291, 1411, 1467, 2062, 2087, 2165, 2279, 2519, 2546, 2669, 3784, 3814, 3872], 'reveals': [722, 1413], 'structural': [724, 2053, 4068], 'basis': [725, 1416, 2054], '30-fold': [728], 'higher': [729, 2273, 3546], 'Ubp8C146A': [732, 1408, 1835, 1892, 2084, 2162, 4062], 'show': [736, 1353, 1470, 3455, 4106], 'an': [738, 1122, 1495, 2128, 2557, 2581, 2676, 2851, 3111, 3129, 3423, 3649, 3958, 4077], 'alternative': [739, 2899, 4078], 'option,': [740], 'substituting': [741, 1133, 1472, 2926, 3350], 'active': [743, 764, 817, 886, 1112, 1135, 1206, 1234, 1358, 1435, 1453, 1474, 1517, 1542, 1767, 2066, 2135, 2193, 2221, 2260, 2499, 2586, 2695, 2900, 2928, 3015, 3116, 3258, 3352, 3492, 3698, 3742, 3912, 3931, 3968, 4012, 4026, 4045, 4110, 4223, 4332], 'arginine,': [747], 'inactivate': [749, 2935], 'while': [751, 1488, 3370, 4090, 4119], 'also': [752, 1489, 1677, 1851, 2682, 3034, 3139, 3371, 3464, 3541, 3605, 3752, 4120, 4301, 4311], 'decreasing': [753], 'Synopsis': [758], 'Mutation': [759, 814, 1540], 'enzyme': [762, 1090, 1452, 1465, 2119, 2572, 2661, 2937, 3137, 4123], '(DUB)': [763], 'increases': [770, 1369, 1547, 2491], 'mono-': [777, 1376, 3268], 'polyubiquitin': [779, 808, 876, 922, 1250, 1286, 2918, 3024, 3043, 3163, 3270, 3330, 3445, 3535, 3575, 3593, 3628, 3757, 3797, 3818, 3863], 'Expression': [781], 'could': [789, 2933, 3357, 3922, 4264, 4279], 'therefore': [790, 2255, 3808], 'give': [791, 1297], 'rise': [792, 1298], 'spurious': [794], 'or': [795, 848, 1146, 1249, 1324, 1377, 1776, 1866, 1877, 1927, 1978, 2679, 2920, 3269, 3311, 3407, 3663, 3867, 4035, 4270, 4276], 'due': [799, 1161, 2626, 2714, 3583, 3853, 4063, 4285], 'protect': [807, 1316, 3596, 3625, 3862], 'from': [809, 867, 917, 1274, 1319, 1586, 2022, 2183, 2475, 2855, 3306, 3598, 3656, 3865], 'cleavage': [810, 1320, 1793, 1922, 1947, 2984, 3599, 3866, 4198], 'cysteines': [819], 'relieves': [822], 'steric': [823, 1431, 2432, 2718, 3964, 4287], 'hindrance,': [824], 'allows': [826], 'tighter': [827, 1848], 'binding': [828, 842, 861, 1491, 1729, 1750, 1974, 2033, 2711, 2729, 2752, 2809, 2824, 2833, 2843, 2888, 2941, 3143, 3152, 3168, 3374, 4099, 4126, 4144, 4166], "ubiquitin's": [830, 2435], 'C-terminus.': [831], 'In': [832, 850, 1303, 1664, 1736, 2160, 2420, 4098], 'vitro,': [833], 'C-to-A': [834, 853], 'lead': [836], '10–150-fold': [839], 'polyubiquitin.': [849, 3376, 3402], 'cells,': [851, 3321], 'overexpressed': [852], 'act': [856], 'as': [857, 993, 995, 1007, 1009, 1190, 1527, 1607, 1619, 1621, 1931, 2189, 2191, 2281, 2534, 2536, 2671, 2720, 2908, 2910, 2998, 4056], 'high': [858, 1460, 3686], 'domains,': [862], 'thereby': [863, 1315], 'sequestering': [864], 'ubiquitinated': [865, 878, 1646, 1699, 2921, 3517, 3631, 4298], 'deubiquitination,': [868], 'leads': [870], 'dramatic': [873, 2506, 2629, 3325], 'accumulation': [874, 3326], 'substrates.': [879, 2922, 3632], 'recommend': [881, 1504, 4315], 'use': [883, 1515], 'arginine': [885, 1478, 1528, 2885, 2932, 2966, 3018, 3130, 3245, 3356, 4114, 4139, 4159, 4202], 'avoid': [890, 1215, 1513, 4259, 4327], 'undesired': [891], 'studies': [897, 1510, 1634, 3364, 3679, 3996, 4322], 'DUBs.': [900, 3602, 3899, 4000, 4175], 'Introduction': [901], 'Deubiquitinating': [902], 'play': [905], 'fundamental': [906], 'signaling': [910, 1148, 2533, 3071, 3079], 'through': [911], 'their': [912, 972, 3397, 3729, 3777], 'ability': [913, 1280, 1668, 3586, 3856, 4137, 4156], 'remove': [915], 'target': [918], 'disassemble': [921], 'chains': [923, 1318, 2919, 3025, 3044, 3164, 3331, 3460, 3536, 3549, 3576, 3594, 3629, 3641, 3644, 3819, 3864, 4235, 4262, 4272], '1.': [924, 1965, 2288], 'These': [925, 3980], 'cleave': [927, 1678], 'isopeptide': [929], 'linkage': [930], 'between': [931, 947, 2246, 2412], 'C-terminus': [933, 2049, 2210], 'substrate': [938, 951, 1144, 4215], 'lysine': [939, 4295], 'or,': [940], 'cases,': [943], 'peptide': [945, 2678, 2853], 'bond': [946], 'protein': [952, 1025, 2978, 3009, 4267, 4283, 4292], 'N-terminus.': [953], 'human': [955, 1362, 2513], 'genome': [956], 'encodes': [957], 'than': [959, 3537, 3773, 4240], '90': [960], '2,': [962], '3,': [963, 2564], 'be': [966, 1160, 2213, 2642, 3358, 3554, 3852, 3989, 4152, 4256, 4297, 4312], 'grouped': [967], 'families': [969, 1002], 'based': [970, 3200], 'on': [971, 1499, 2508, 2775, 2870, 3201, 3399], 'fold:': [973], 'ubiquitin-specific': [974], 'protease': [975, 1127, 3368, 3682, 3898, 3907, 3955, 3999, 4019, 4325], '(USP),': [976], 'carboxyl-terminal': [978], 'hydrolase': [979, 1227, 4117], '(UCH),': [980], 'ovarian': [981], 'tumor': [982], 'family': [983, 1615, 2515, 2699, 3029], '(OTU),': [984], 'Machado–Joseph': [985], 'domain': [986, 991, 1098, 2647], '(MJD)': [987], 'family,': [988, 1099], 'JAMM/MPN': [990], '(JAMM),': [992], 'well': [994, 1008, 1620, 2190, 2535, 2909], 'recently': [997, 3047], 'discovered': [998], 'MINDY': [999, 3944, 4050], 'ZUFSP': [1001, 3946], '4-6.': [1003], 'Studies': [1004], 'deletions': [1006], 'disease-causing': [1010], 'have': [1012, 1338, 1649, 1941, 3292, 3715, 3909, 4075, 4178], 'revealed': [1013, 1650], 'specific': [1014, 3425], 'functions': [1015], 'individual': [1017], 'processes': [1021], 'proteasomal': [1023], 'degradation,': [1024], 'trafficking,': [1026], 'transcription,': [1027], 'DNA': [1028], 'repair,': [1029], 'infection,': [1030], 'inflammation': [1032], '7.': [1033], 'involvement': [1035], 'variety': [1040, 1680, 2525], 'oncogenic': [1042], '8,': [1043], 'inflammation,': [1044], 'neurodegenerative': [1046], '9': [1048], 'made': [1050], 'attractive': [1053], 'targets': [1054], 'drug': [1056], 'discovery': [1057], '10.': [1058], 'approach': [1061, 3361], 'determining': [1063], 'role': [1065], 'particular': [1068, 3848], 'knock': [1075], 'down': [1076], 'expression': [1077], 'endogenous': [1080], 'express': [1083], 'version': [1087], '11-13.': [1091], 'With': [1092], 'exception': [1094], 'JAMM': [1097], 'metalloproteases,': [1102], 'all': [1103, 1570, 2125, 4317], 'other': [1104, 1322, 1732, 1747, 1957, 3309, 3601, 3896, 3953, 4017, 4222, 4230, 4305], 'proteases': [1108], 'papain-like': [1111], 'activated': [1120], 'adjacent': [1123], 'histidine': [1124], '14.': [1125], 'Cysteine': [1126], 'typically': [1130], 'inactivated': [1131, 3135], 'another': [1139], 'residue.': [1140], 'Resulting': [1141], 'changes': [1142], 'ubiquitination': [1145], 'downstream': [1147], 'generally': [1157], 'assumed': [1158], 'absence': [1164, 1780], 'activity,': [1167], 'notable': [1170], 'exceptions': [1171], 'OTUB1,': [1173], 'inhibits': [1175], 'E2': [1176], 'mechanism': [1180], 'independent': [1181], 'activity': [1184, 1533, 1598, 1783, 1915, 1948, 2652, 2907, 3058, 3845, 4089, 4118], '15-17': [1185], 'OTUD4,': [1187], 'serves': [1189], 'scaffold': [1192], 'USP': [1194, 1481, 1614, 2407, 2514, 2698, 2890, 3722, 3886, 3917, 4148], '18.': [1196], 'Whereas': [1197, 1817, 1871], 'serine': [1198, 1222, 1774], 'most': [1201], 'conservative': [1202], 'substitution': [1203, 1223, 1386, 1429, 2042, 2490, 3252, 3615, 3960, 4309], 'cysteine,': [1208, 1769, 2588, 3494], 'substitutions': [1210, 1237, 1520, 1525, 3246, 3261, 3719, 3739, 3882, 3987, 4081, 4140, 4329], 'often': [1212], 'used': [1213], 'possibility': [1217], 'containing': [1220, 1407, 1763, 1820, 1834, 1863, 1874, 2083, 2580, 2974, 2994, 3489, 3693], 'retain': [1225, 3542], 'cysteine-to-alanine': [1236, 2489, 3260, 3282, 3383, 3580, 3718, 3738, 3881], 'either': [1246, 1773, 1864, 2675, 3659], 'This': [1252, 3038], 'confound': [1257], 'interpretation': [1259, 1343], 'cell-based': [1261, 1506, 3363, 3678, 3705, 3992, 4318], 'experiments,': [1262], 'since': [1263, 2225], 'only': [1269, 2256, 3134], 'incapable': [1270, 4124], 'cleaving': [1272], 'substrates': [1275, 1313, 1683, 1733, 1748, 2801, 3298], 'but': [1276, 3138], 'gained': [1278], 'Altering': [1288], 'levels': [1289, 3400, 3442, 3457, 3544], 'been': [1294, 1702, 1718, 1942, 2639, 3048], 'shown': [1295, 1932, 1943, 2442, 2451, 2561, 2640, 3049, 3883, 4054], 'off-target': [1300], '19.': [1302], 'addition,': [1304], 'stably': [1309], 'associate': [1310], '(poly)ubiquitinated': [1312], 'prevent': [1325, 2939, 4212], 'interaction': [1326], 'receptors.': [1329], 'such': [1333, 1526, 3281], 'confuse': [1342], 'because': [1344, 2942], 'gain': [1347], 'tight': [1349], 'function.': [1351], 'mutating': [1356], 'USP4': [1363, 2494, 2521, 2544, 2579, 2651, 2731, 2754, 2795, 2805, 2820, 2835, 2845], 'yeast': [1365, 1557], 'Ubp8': [1366, 1764, 1868, 1876, 2040, 2184, 2253, 2399, 2964, 3724, 3745, 4102], 'diubiquitin': [1378, 1690, 1807, 1825, 1839, 1977, 3100, 3122, 3146, 3158, 3176, 3185], '10–150-fold.': [1380], 'similar': [1382, 2685, 3915, 3925], 'effect': [1383, 2507], 'was': [1387, 1787, 1933, 2548, 2738, 2979, 3002, 3177, 3191, 3409, 3934], 'previously': [1388], 'found': [1389, 2112, 3716], 'OTU': [1392, 1483, 2892, 3028, 3748, 3888, 4146], 'enzymes,': [1393], 'Cezanne': [1394], '20': [1395], 'OTULIN': [1397, 3316], '21.': [1398, 3346], 'heterotetrameric': [1403], 'molecular': [1415, 3547], 'increased': [1419, 3441, 3543], 'enzyme.': [1426, 2286, 4252], 'alleviates': [1430], 'hindrance': [1432], 'sulfhydryl,': [1438], 'allowing': [1439], 'C-terminal': [1441, 2174, 2233, 2248, 2414, 2436, 2680, 4170, 4187], 'carboxylate': [1442, 2170, 2249, 2415, 2437], 'form': [1446, 3924], 'additional': [1447], 'hydrogen': [1448, 2044, 2178, 2242], 'bonds': [1449, 2179, 2363], 'accounting': [1457], 'representative': [1480, 3208, 3233, 3666], 'inactivates': [1485, 4115], 'disrupting': [1490], 'ubiquitin,': [1493, 2166, 2236], 'generating': [1494], 'inert': [1496], 'DUB.': [1497], 'Based': [1498], 'findings,': [1501], 'we': [1502, 1752, 2073, 2704, 2958, 3381, 4105, 4218], 'strongly': [1503], 'vivo': [1509, 3995, 4321], 'instead': [1523, 3851], 'utilize': [1524], 'ablate': [1530], 'both': [1531, 1785, 1802, 2934], 'enzymatic': [1532], 'binding.': [1536, 1849, 4097], 'Results': [1537], 'Discussion': [1539], 'complex': [1559, 1605, 2163, 2397], 'transcriptional': [1562, 3056], 'coactivator': [1563, 3057], 'involved': [1566], 'transcription': [1568, 1591], 'RNA': [1571], 'polymerase': [1572], 'II': [1573], 'genes': [1574], '22,': [1575], '23.': [1576], 'Among': [1577], 'activities': [1580], 'removal': [1583], 'histone': [1587, 1671], 'H2B,': [1588, 1672], 'promotes': [1590], 'initiation': [1592], 'elongation': [1594], '24.': [1595], 'resides': [1601], 'four-protein': [1604], 'known': [1606], 'module,': [1610], 'comprises': [1612], 'subunit,': [1617], 'Ubp8,': [1618], 'Sgf11,': [1622], 'Sus1,': [1623], 'N-terminal': [1626, 2558], '~100': [1627], 'residues': [1628, 2156, 2185], 'Sgf73': [1630], '25,': [1631], '26.': [1632], 'Structural': [1633], 'complexed': [1639], 'aldehyde': [1642], '27': [1643], 'nucleosomes': [1647], '28': [1648, 1708], 'overall': [1652, 2101], 'organization': [1653], 'how': [1659], 'it': [1660, 4057, 4226], 'interacts': [1661], 'substrate.': [1663], 'addition': [1665, 4248], 'its': [1667, 1766], 'deubiquitinate': [1670], 'vitro': [1685, 3160], 'ubiquitin-AMC': [1687, 1792], 'K48-linked': [1689, 1806, 1838], '29.': [1691, 2159], 'nucleosome': [1700], 'estimated': [1703, 1719, 3781], 'at': [1704, 1720, 1950, 2089, 2481, 3798], 'around': [1705], '2': [1706], 'μM': [1707, 1722, 1886, 3791], 'KM': [1711, 1727], 'model': [1714], 'substrate,': [1715], 'ubiquitin-AMC,': [1716], '24': [1721], '29;': [1723], 'however,': [1724], 'neither': [1725, 3624], 'nor': [1728, 3626], 'known.': [1735], 'order': [1737], 'measure': [1739], 'using': [1749, 1808, 2553, 2743, 3101, 3182, 3610], 'assays,': [1751], 'expressed': [1753, 3319, 3345, 3382, 3410, 3821], 'purified': [1755], 'versions': [1758], 'C146,': [1770], 'substituted': [1771, 2070, 2583, 3113, 3695, 3935], '(C146S)': [1775], '(C146A).': [1778], 'first': [1788, 2968], 'verified': [1789, 2969], 'assay': [1794, 1958, 2985, 3105], '(Fig': [1795, 1869, 2157, 2238, 2633, 2689, 2986, 3010, 3106, 3147, 3446, 3461, 3527, 3560, 3938, 3978], 'EV1).': [1796, 2987], 'measured': [1798, 1852, 2549, 2608, 2739, 2812, 2999, 3088, 3178], 'complexes': [1804], 'isothermal': [1809], 'titration': [1810, 1967], 'calorimetry': [1811, 1968], '(ITC;': [1812], 'Fig': [1813, 2098, 2563], '1E': [1814], 'F).': [1816], 'Ubp8C146S': [1821, 1878], 'K48': [1824, 1976, 2005, 2011], 'Kd': [1828, 1842, 1883, 1902, 2018, 2566, 3125], '4.6': [1830], 'μM,': [1831, 1845, 1889, 3128], '0.47': [1844], 'representing': [1846], '10-fold': [1847], 'reaction': [1857], 'product,': [1858], 'monoubiquitin,': [1859], '1A–C).': [1870], '13.9': [1885], '12.8': [1888], 'respectively,': [1890], '~30-fold': [1895], 'tightly': [1897, 3812], '0.43': [1904], 'μM.': [1905], 'Click': [1906, 2458, 2784, 4001], 'expand': [1909, 2461, 2787, 4004], 'figure.': [1911, 2463, 2789, 4006], 'Figure': [1912, 1964, 2380, 2464, 2726, 2790, 3149, 3633, 4007], 'EV1.': [1913], 'Catalytic': [1914], 'DUBm-Ubp8': [1917, 1983], 'mutantsProgress': [1918], 'curve': [1919], 'Ub-AMC': [1921, 2983], '125': [1924], 'nM': [1925, 2596, 2762], 'DUBm-Ubp8WT': [1926, 2439], 'mutants.': [1928], 'experiment': [1930, 3209, 3234, 3667], 'performed': [1934, 1955], 'once.': [1935], 'C146A': [1937, 2041, 2139], 'C146S': [1939], 'lack': [1945, 3842, 4066], 'any': [1946], 'least': [1951, 2024], 'two': [1952, 2177, 2871, 3211, 3388, 3669], 'experiments': [1953, 3826], 'each': [1954], 'methods.': [1959], 'Download': [1960, 1962, 2035, 2037, 2454, 2456, 2483, 2485, 2780, 2782, 2875, 2877, 3239, 3241, 3672, 3674, 4070, 4072], 'figure': [1961, 2036, 2455, 2484, 2781, 2876, 3240, 3673, 4071], 'PowerPoint': [1963, 2038, 2457, 2486, 2783, 2878, 3242, 3675, 4073], 'Isothermal': [1966], 'assays': [1969, 3706, 4100], 'Binding': [1980, 1986, 1991, 1996, 2001, 2007, 2792, 3635], 'monoubiquitin.': [1985, 1990, 1995, 2000, 2746], 'DUBmUbp8C146A': [1988], 'DUBm-Ubp8C146S': [1993, 2009], 'DUBm-Ubp8C146R': [1998], 'DUBm-Ubp8C146A': [2003, 2390, 2449, 2469], 'diubiquitin.': [2006, 2012], 'Data': [2013, 2857], 'information:': [2014, 2858], 'Error': [2015, 2770, 3194], 'ranges': [2016], 'values': [2019], 'were': [2020, 3227, 3418, 3501, 3519, 3645], 'determined': [2021], 'nonlinear': [2023], 'squares': [2025], 'fitting': [2026], 'data': [2029, 2291, 3205, 4177], 'one-site': [2032], 'model.': [2034], 'enables': [2043], 'bonding': [2045, 2243, 2410], 'To': [2050, 2954, 3377], 'determine': [2051], 'marked': [2057], 'when': [2064, 2258, 3315, 3336, 3820], 'solved': [2074], 'crystal': [2076, 2383], 'resolution': [2091], '2.1': [2093], 'Å': [2094, 2132], '(Table': [2095], '1': [2096, 2355, 3734, 3759], '2A).': [2099], 'fold': [2102], 'contacts': [2104, 2411], 'virtually': [2108, 2142], 'identical': [2109, 2143], 'those': [2111], 'aldehyde,': [2123], 'superimposing': [2124], 'atoms': [2126, 2371], 'RMSD': [2129], '0.58': [2131], '27.': [2133], 'apoenzyme': [2149], '29,': [2150], 'no': [2152], 'significant': [2153], 'reordering': [2154], '2B)': [2158], 'negatively': [2168, 3074], 'charged': [2169], 'Gly76': [2175, 2237], 'forms': [2176], 'backbone': [2181], 'amides': [2182], 'Thr145': [2186], 'Ala146,': [2188], 'residues,': [2195], 'Asn141': [2196], 'His427': [2198], '(Figs': [2199, 3733, 3758, 4129], '2B': [2200], 'EV2).': [2202], 'Importantly,': [2203], 'observed': [2205, 2245, 2708, 3577], 'position': [2206], 'would': [2211, 2229, 2904, 3961, 4242], 'compatible': [2214], 'presence': [2217], 'residue,': [2223], 'Cys146,': [2224], 'sulfhydryl': [2227], 'group': [2228, 2337], 'clash': [2230, 3965], 'residue': [2234], '2C).': [2239], 'multiple': [2241], 'interactions': [2244, 3926, 4208], 'occur': [2257], 'Cys146': [2261], 'smaller': [2266], 'side': [2268, 2949, 4160, 4203, 4234, 4261, 4271], 'chain,': [2269], 'explaining': [2271], 'module-Ubp8C146A': [2277], 'compared': [2282, 2951, 3430, 3556], 'Table': [2287], 'X-ray': [2289, 2382], 'crystallographic': [2290], 'refinement': [2293], 'statistics': [2294, 2335], 'Wavelength': [2295], '(Å)': [2296, 2299, 2341, 2364], '0.979': [2297], 'Resolution': [2298], '2.10': [2300], 'Unique': [2301], 'reflections': [2302], '54,195': [2303], 'Redundancy': [2304], '5.7': [2305], '(5.7)': [2306], 'Completeness': [2307], '(%)': [2308, 2357, 2360], '99.2': [2309], '(99.7)': [2310], 'Average': [2311, 2376], 'I/σ': [2312], '(I)': [2313], '13.3': [2314], '(3.0)': [2315], 'R': [2316, 2320, 2324], 'merge': [2317], '0.093': [2318], '(0.572)': [2319], 'meas': [2321], '0.103': [2322], '(0.630)': [2323], 'pim': [2325], '0.043': [2326], '(0.259)': [2327], 'CC1/2': [2328], '0.998': [2329], '(0.857)': [2330], 'CC*': [2331], '0.999': [2332], '(0.961)': [2333], 'Refinement': [2334], 'Space': [2336], 'P212121': [2338], 'Unit': [2339], 'cell': [2340, 3215, 3416, 3788], '=': [2343, 2346, 2349], '78.8,': [2344], 'b': [2345], '103.2,': [2347], 'c': [2348], '112.8': [2350], 'Molecules': [2351], 'per': [2352, 2778, 2873, 3204], 'asymmetric': [2353], 'unit': [2354], 'Rwork': [2356], '20.1': [2358], 'Rfree': [2359], '24.9': [2361], 'Rmsd': [2362, 2366], '0.0198': [2365], 'angles': [2367], '(°)': [2368], '1.855': [2369], 'Protein': [2370], '6,302': [2372], 'Zinc': [2373], 'ions': [2374], '8': [2375], 'B': [2377], '(Å2)': [2378], '40.3': [2379], '2.': [2381], 'Overall': [2394], 'showing': [2398], '(green)': [2400], '(yellow)': [2403], 'domain.': [2408], 'Hydrogen': [2409], 'Ubp8.': [2419, 2725], 'blue': [2421], 'spheres,': [2422], 'van': [2423], 'der': [2424], 'Waals': [2425], 'radii': [2426], 'C146': [2428], 'A146': [2430], 'proximity': [2433], '(yellow).': [2438], 'teal': [2444], '(PDB': [2445, 4032, 4040, 4051], 'ID': [2446, 4033, 4041, 4052], '3MHH)': [2447], 'green.': [2453], 'EV2.': [2465], 'monoubiquitinDensity': [2472], 'rendered': [2474], '2Fo–Fc': [2477], 'map': [2478], 'contoured': [2480], '2σ.': [2482], 'Mutating': [2497], 'DUB,': [2516, 3750], 'USP4,': [2517, 3726], 'regulates': [2522, 3075], 'broad': [2524], 'pathways,': [2528], 'TGF-β': [2530, 3070], 'NF-κB': [2532], 'splicing': [2537], '26,': [2538], '30,': [2539], '31.': [2540], 'fluorescence': [2551, 2610, 2741, 2815, 2830, 3103, 3180], 'polarization': [2552, 2611, 2742, 3104, 3181], 'labeled': [2555, 3098], 'fluorophore.': [2559], '92': [2574, 2759], '±': [2575, 2594, 2760, 2766], '21': [2576, 2761], 'nM,': [2577, 2768], 'whereas': [2578], 'C311,': [2589], 'binds': [2590, 2683, 3120], '0.60': [2593, 2765], '0.17': [2595, 2767], 'affinity,': [2597], '~150-fold': [2599], 'difference': [2600, 3870], '32.': [2601, 2653], 'pre-steady-state': [2603], 'kinetics': [2604, 2793, 2803, 2818], 'dissociation': [2607, 2637, 2748, 3764], 'stopped-flow': [2614, 2814, 2829], 'device': [2615], 'shows': [2616], 'greater': [2619], 'USP4C311A': [2623, 2688], 'decrease': [2630], 'off-rate': [2632], 'EV3A).': [2634], 'Interestingly,': [2635], 'promoted': [2643], 'USP4N-terminal': [2645], 'DUSP-Ubl': [2646], 'regulate': [2650, 3051], 'unique': [2664], 'C-terminus,': [2670], 'conjugated': [2673, 2839, 2849], '18-mer': [2677, 2852], 'fluorophore': [2681], 'EV3C': [2690], 'D).': [2692], 'Since': [2693, 3280, 4294], 'sites': [2696, 3743], 'highly': [2702], 'conserved,': [2703], 'speculate': [2705, 4134], 'relief': [2716], 'clash,': [2719], 'case': [2723], '3.': [2727], 'Equilibrium': [2728, 2832, 2842, 3167], 'WT': [2732, 2755, 2796, 2806, 2821], 'C311A': [2734, 2757, 2798, 2808, 2823, 2836, 2846], 'TAMRA-labeled': [2736, 2745], 'monoubiquitinBinding': [2737], 'N-terminally': [2744], 'constants': [2749, 3765], '32': [2763], 'respectively.': [2769], 'bars': [2771, 2861, 3195], 's.d.': [2773, 2868, 3197], 'calculated': [2774, 2869], 'five': [2776], 'measurements': [2777, 2872, 3203], 'point.': [2779, 2874, 3206], 'EV3.': [2791], 'Dissociation': [2802], 'TAMRA-monoubiquitin,': [2811], 'polarization.': [2816, 2831], 'Association': [2817], 'TAMRA-monoubiquitin.': [2826], 'Measured': [2827], 'TAMRA-ubiquitin': [2838, 2848], 'lysine.': [2841], 'derived': [2854], 'SMAD4.': [2856], 'error': [2860], 'panels': [2863], '(C)': [2864], '(D)': [2866], 'Substitution': [2879, 3012], 'disrupts': [2886], 'class': [2893, 3749, 3889], 'sought': [2896], 'identify': [2898], 'abrogate': [2905], 'reduce': [2911], 'reasoned': [2924], 'bulky': [2945, 4275], 'nature': [2946], 'chain': [2950, 3301, 4161, 4204], 'cysteine.': [2953], 'test': [2955, 3378, 4221], 'hypothesis,': [2957], 'mutated': [2959], 'Ubp8C146R': [2977, 2995], 'ITC': [3001], 'comparable': [3003], '1D).': [3011], 'similarly': [3019, 3962, 4243], 'reduces': [3020], 'member,': [3030], 'OTUD1,': [3031, 3405, 3751, 4104], 'protease.': [3037], 'preferentially': [3040], 'cleaves': [3041], 'K63-linked': [3042, 3099, 3121, 3145, 3175, 3184, 3444, 3459], '20,': [3045], 'nuclear': [3053], 'localization': [3054], 'YAP': [3061], 'oncoprotein': [3062], '33,': [3063], 'represses': [3064], 'metastasis': [3065], 'SMAD7': [3068], 'during': [3069, 3080], '34,': [3072], 'RIG-I-like': [3076], 'receptor': [3077, 3511, 3651], '(RLR)': [3078], 'viral': [3081], 'infection': [3082], 'Smurf1': [3085], '35.': [3086], 'OTUD1': [3095, 3109, 3154, 3170, 3222, 3390], 'fluorescently': [3097, 3192], '4A).': [3107, 3148, 3761], 'While': [3108, 4217], '(OTUD1C320A)': [3119], '~40': [3127], 'substitution,': [3131], 'OTUD1C320R,': [3132], 'completely': [3140], 'abolished': [3141], 'detectable': [3142], '4.': [3150], 'Enhanced': [3151], 'C320A': [3155, 3171, 3226], 'K63': [3157, 3162], 'C320R': [3173], 'FlAsH-tagged': [3183], 'proximal': [3189], 'labeled.': [3193], 'indicate': [3196], 'three': [3202, 3236], 'One': [3207, 3232, 3665], 'shown.': [3213, 3238, 3671], 'Whole': [3214], 'lysates': [3216, 3417], 'HEK293': [3218, 3412, 3504], 'HA-tagged': [3221, 3403, 3487], 'WT,': [3223], 'C320R,': [3224], 'immunoblotted': [3228], 'indicated': [3230, 4179], 'antibodies.': [3231], 'overcome': [3248], 'artifacts': [3249], 'mentioned': [3256], 'above,': [3257], 'markedly': [3263], 'render': [3272], 'less': [3275], 'suitable': [3276], 'studies.': [3279], 'essentially': [3285], 'proteins,': [3288], 'stabilize': [3296], 'modified': [3297], 'preferred': [3300], 'types': [3302], 'protecting': [3304], 'them': [3305, 3597], 'digestion': [3307], 'proteases.': [3312], 'For': [3313], 'example,': [3314], 'C129A': [3317], 'there': [3322, 3832], 'Met1-linked': [3328], 'linear': [3329], 'seen': [3335], 'abrogates': [3340], 'binding,': [3342, 4246], 'L259E,': [3343], 'hypothesized': [3348], 'general': [3360], 'inactivating': [3366, 4250], 'preventing': [3372, 4095], 'idea,': [3380], 'cysteine-to-arginine': [3385], 'DUBs,': [3389, 3723], 'USP14,': [3392, 3473], 'probed': [3396, 3524], 'OTUD1C320A,': [3406], 'OTUD1C320R': [3408, 3452], 'whole': [3415], 'analyzed': [3419], 'immunoblotting': [3421], 'antibody': [3424], 'K63-polyubiquitin': [3427], 'protein,': [3436], 'OTUD1C320A': [3439], 'had': [3440], '4B).': [3447, 3462], 'By': [3448], 'contrast,': [3449], 'did': [3453, 4219], 'enriched': [3456], 'tested': [3465], 'one': [3474], 'chain-trimming': [3477], 'bind': [3480, 3533, 3591, 3811], '26S': [3483, 3654], 'proteasome': [3484, 3514], '36,': [3485], '37.': [3486], 'USP14': [3488, 3531, 3538, 3559, 3637, 3660], 'Cys114,': [3495], 'C114A': [3497, 3532, 3638], 'C114R': [3499, 3539], 'co-expressed': [3502], 'along': [3506], 'FLAG-PSMD4,': [3508, 3648], 'within': [3512], '38.': [3515], 'Proteasome-bound': [3516], 'co-immunoprecipitated': [3520, 3646], 'FLAG-PSMD4': [3522], '5).': [3528, 3561], 'Proteasomes': [3529], 'weight': [3548], 'unable': [3552], 'trimmed': [3555], 'Both': [3562], 'results': [3565, 3604], 'consistent': [3567], 'idea': [3570], 'Our': [3603], 'validate': [3606], 'benefit': [3608], 'Cys': [3612], 'Arg': [3614], 'generate': [3617], 'will': [3623], '5.': [3634], 'cellsPolyubiquitin': [3643], 'proteasome,': [3655], 'wild-type,': [3661], 'C114A,': [3662], 'C114R.': [3664], 'Implications': [3676], 'surprisingly': [3685], 'exhibited': [3690], 'important': [3702, 4214], 'implications': [3703], 'expressed.': [3713], '3).': [3736], 'Similarly,': [3737], 'equilibrium': [3763], 'significantly': [3771, 4238], 'lower': [3772], 'concentrations': [3775], 'substrates,': [3778], 'given': [3779], 'concentration': [3782, 3795], '4–50': [3790], '39': [3792], 'fraction': [3800], '40.': [3803], 'expected': [3809, 4228], 'Particularly': [3824], 'where': [3827], 'overexpressed,': [3831], 'risk': [3835], 'consequences': [3838], 'ascribed': [3839], 'available': [3874], 'ubiquitin-conjugating': [3876], 'enzymes.': [3877], 'likely': [3892], 'extend': [3894], 'UCH': [3901], 'MJD': [3903], 'classes': [3904], 'conserved': [3911], 'architecture': [3914], '14,': [3919], '41': [3920], 'if': [3929], 'EV4A': [3939], 'B).': [3941], 'Although': [3942], 'share': [3948], 'little': [3949], 'homology': [3950], '4-6,': [3957], 'relieve': [3963], 'site,': [3969], 'potentially': [3971], 'increasing': [3972], "DUB's": [3974], 'EV4C).': [3979], 'observations': [3981], 'support': [3982], 'recommendation': [3984], 'should': [3988, 4255, 4310], 'avoided': [3990], 'EV4.': [4008], 'Alignment': [4009, 4023], 'Ubp8C146A+monoUb': [4015, 4025], 'A,': [4021], 'B.': [4022], '(A)': [4029], 'ubiquitin-bound': [4030, 4037], 'UCHL1': [4031], '3KW5)': [4034], '(B)': [4036], 'Ataxin': [4038], '3': [4039], '3O65).': [4042], 'C.': [4043], 'propargyl-bound': [4049], '5JQS)': [4053], 'alone,': [4055], 'does': [4058], 'align': [4060], 'conservation.': [4069], 'presented': [4076], 'equally': [4084], 'effective': [4085], 'abrogating': [4087], 'having': [4091], 'advantage': [4093], 'rendering': [4121], 'detectably': [4128], '1D': [4130], '4).': [4132], 'abolish': [4142], 'domains': [4150], 'explained': [4153], 'partially': [4163], 'occupy': [4164], 'Gly-Gly': [4172], 'Previous': [4176], 'correct': [4182], 'orientation': [4183], 'tail': [4188], 'S1': [4192], 'essential': [4195], 'efficient': [4197], '42,': [4199], '43.': [4200], 'An': [4201], 'mimic': [4206], 'cis,': [4210], 'interactions.': [4216], 'substitutions,': [4225], 'amino': [4231], 'acids': [4232], 'bulkier': [4239], 'block': [4244], 'However,': [4253], 'care': [4254], 'taken': [4257], 'hydrophobic': [4260], 'cause': [4265], 'aggregate,': [4269], 'beta-branched': [4277], 'interfere': [4280], 'proper': [4282], 'folding': [4284], 'clashes': [4288], 'neighboring': [4291], 'backbone.': [4293], 'subject': [4302], 'many': [4304], 'post-translational': [4306], 'modifications,': [4307], 'avoided.': [4313]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2889126774', 'counts_by_year': [{'year': 2024, 'cited_by_count': 8}, {'year': 2023, 'cited_by_count': 8}, {'year': 2022, 'cited_by_count': 7}, {'year': 2021, 'cited_by_count': 5}, {'year': 2020, 'cited_by_count': 8}, {'year': 2019, 'cited_by_count': 10}, {'year': 2018, 'cited_by_count': 3}], 'updated_date': '2024-12-21T18:38:30.479664', 'created_date': '2018-09-07'}
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