Ubiquitin protein ligase

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Line 188: Line 188:
**[[2lc3]] – hUPL helical bundle domain - NMR<br />
**[[2lc3]] – hUPL helical bundle domain - NMR<br />
-
*'''Ubiquitin protein ligase HECW1'''
+
*'''Ubiquitin protein ligase HECW'''
-
**[[3l4h]] – hUPL WW2 and helical box domains <br />
+
**[[3l4h]] – hUPL 1 WW2 and helical box domains <br />
-
 
+
**[[2lfe]] – hUPL 2 N terminal - NMR<br />
-
*'''Ubiquitin protein ligase HECW2'''
+
-
 
+
-
**[[2lfe]] – hUPL N terminal - NMR<br />
+
*'''Ubiquitin protein ligase HERC'''
*'''Ubiquitin protein ligase HERC'''
Line 232: Line 229:
**[[3vqf]] – mUPL 2rd PDZ domain <br />
**[[3vqf]] – mUPL 2rd PDZ domain <br />
-
**[[3b76]] – hUPL 3rd PDZ domain <br />
 
**[[3vqg]] – mUPL 2rd PDZ domain + peptide<br />
**[[3vqg]] – mUPL 2rd PDZ domain + peptide<br />
 +
**[[3b76]] – hUPL 3rd PDZ domain <br />
 +
**[[5h7r]] – hUPL residues 11-138 <br />
 +
**[[5h7s]] – hUPL residues 11-138 + ubiquitin conjugating enzyme E2 N + ubiquitin <br />
*'''Ubiquitin protein ligase LUBX'''
*'''Ubiquitin protein ligase LUBX'''
Line 259: Line 258:
**[[3gbw]] – mUPL 1st PHR domain <br />
**[[3gbw]] – mUPL 1st PHR domain <br />
**[[3hwj]] – mUPL 2nd PHR domain <br />
**[[3hwj]] – mUPL 2nd PHR domain <br />
 +
**[[5o6c]] – hUPL residues 4379-4638 <br />
*'''Ubiquitin protein ligase MYLIP'''
*'''Ubiquitin protein ligase MYLIP'''
Line 268: Line 268:
**[[1wr3]], [[1wr4]], [[1wr7]] – mUPL WW domain - NMR <br />
**[[1wr3]], [[1wr4]], [[1wr7]] – mUPL WW domain - NMR <br />
-
**[[2oni]] – hUPL catalytic domain <br />
 
**[[3b7y]] – hUPL C2 domain <br />
**[[3b7y]] – hUPL C2 domain <br />
**[[2xbf]] – hUPL HECT domain <br />
**[[2xbf]] – hUPL HECT domain <br />
**[[4be8]] – hUPL HECT domain (mutant) <br />
**[[4be8]] – hUPL HECT domain (mutant) <br />
 +
**[[4n7f]] – hUPL WW3 domain <br />
**[[2n8s]] – rUPL WW1 domain – rat - NMR <br />
**[[2n8s]] – rUPL WW1 domain – rat - NMR <br />
**[[2n8u]] – rUPL WW2 domain - NMR <br />
**[[2n8u]] – rUPL WW2 domain - NMR <br />
Line 280: Line 280:
**[[1i5h]] – rUPL WW3 domain + amiloride-sensitive Na channel β subunit <br />
**[[1i5h]] – rUPL WW3 domain + amiloride-sensitive Na channel β subunit <br />
**[[2n8t]] – rUPL WW2 domain + peptide - NMR <br />
**[[2n8t]] – rUPL WW2 domain + peptide - NMR <br />
-
**[[2ltx]], [[2lty]] – hUPL WW2 domain + peptide - NMR <br />
 
**[[2ez5]] – DmUPL WW3 domain + COMM LPSY peptide - NMR <br />
**[[2ez5]] – DmUPL WW3 domain + COMM LPSY peptide - NMR <br />
**[[2kpz]], [[2kq0]], [[2laj]], [[2ltz]], [[2m3o]] – hUPL WW3 domain + peptide - NMR <br />
**[[2kpz]], [[2kq0]], [[2laj]], [[2ltz]], [[2m3o]] – hUPL WW3 domain + peptide - NMR <br />
**[[4n7h]] – hUPL WW3 domain + arrestin peptide <br />
**[[4n7h]] – hUPL WW3 domain + arrestin peptide <br />
-
**[[2lb2]] – hUPL 2nd domain + peptide - NMR <br />
 
**[[3m7f]] – hUPL C2 domain + growth factor receptor bound protein<br />
**[[3m7f]] – hUPL C2 domain + growth factor receptor bound protein<br />
-
**[[3jvz]], [[3jw0]] – hUPL HECT domain + ubiquitin + ubiquitin-conjugating enzyme<br />
 
**[[5c91]] – hUPL HECT domain + inhibitor <br />
**[[5c91]] – hUPL HECT domain + inhibitor <br />
-
**[[2xbb]], [[5c7j]], [[5hpk]], [[5hpl]] – hUPL HECT domain + ubiquitin <br />
+
**[[2xbb]], [[5c7j]], [[5hpl]] – hUPL HECT domain + ubiquitin <br />
**[[4bbn]] – hUPL HECT domain (mutant) + polyubiquitin <br />
**[[4bbn]] – hUPL HECT domain (mutant) + polyubiquitin <br />
 +
 +
*'''Ubiquitin protein ligase NEDD4-like'''
 +
 +
**[[2oni]] – hUPL catalytic domain <br />
 +
**[[2nsq]] – hUPL C2 domain <br />
 +
**[[2mpt]] – hUPL WW3+PY domain - NMR<br />
 +
**[[4y07]] – hUPL WWP2 domain <br />
 +
**[[2op7]] – hUPL WW4 domain - NMR<br />
 +
**[[5tj8]], [[5tjq]], [[5tj7]] – hUPL WW2+WW3+linker+HECT domain <br />
 +
**[[5hpk]] – hUPL HECT domain + ubiquitin <br />
 +
**[[5hpt]] – hUPL HECT domain + ubiquitin + ubiquitin-conjugating enzyme L3<br />
 +
**[[3jvz]], [[3jw0]] – hUPL HECT domain + ubiquitin + ubiquitin-conjugating enzyme D2<br />
 +
**[[2ltx]], [[2lty]],[[2lb2]] – hUPL WW2 domain + peptide - NMR <br />
 +
**[[2laj]] – hUPL WW3 domain + peptide - NMR <br />
*'''Ubiquitin protein ligase Praja'''
*'''Ubiquitin protein ligase Praja'''
Line 298: Line 309:
**[[4k95]], [[4zyn]] – rUPL <br />
**[[4k95]], [[4zyn]] – rUPL <br />
 +
**[[4k7d]] – rUPL C terminal domain <br />
 +
**[[2knb]] – rUPL + endophilin - NMR <br />
**[[5c1z]], [[5c23]] – hUPL <br />
**[[5c1z]], [[5c23]] – hUPL <br />
**[[5c9v]] – hUPL (mutant)<br />
**[[5c9v]] – hUPL (mutant)<br />
**[[2jmo]] – hUPL IBR domain - NMR <br />
**[[2jmo]] – hUPL IBR domain - NMR <br />
 +
**[[2m48]] – hUPL IBR+RING domain - NMR <br />
 +
**[[5tr5]] – hUPL UBL domain - NMR <br />
**[[2zeq]] – hUPL ubiquitin-like domain <br />
**[[2zeq]] – hUPL ubiquitin-like domain <br />
**[[4bm9]], [[4i1h]] – hUPL catalytic domain <br />
**[[4bm9]], [[4i1h]] – hUPL catalytic domain <br />
**[[4i1f]] – hUPL catalytic domain (mutant)<br />
**[[4i1f]] – hUPL catalytic domain (mutant)<br />
 +
**[[5n2w]], [[6glc]], [[5n38]] – hUPL + polyubiquitin <br />
**[[3b1l]] – mUPL ubiquitin-like domain <br />
**[[3b1l]] – mUPL ubiquitin-like domain <br />
**[[4k7d]] – rUPL C terminal domain <br />
**[[4k7d]] – rUPL C terminal domain <br />
Line 309: Line 325:
**[[5caw]] – UPL + ubiquitin – body louse<br />
**[[5caw]] – UPL + ubiquitin – body louse<br />
-
*'''Ubiquitin protein ligase RAD18'''
+
*'''Ubiquitin protein ligase RAD18''' Domains: RING 1-99; UBZ 198-227; rad6-binding 340-366
**[[2y43]] – hUPL RING domain <br />
**[[2y43]] – hUPL RING domain <br />
-
**[[2mrf]] – hUPL UBZ domain - NMR <br />
+
**[[2mrf]], [[5vf0]] – hUPL UBZ domain - NMR <br />
**[[2mre]] – hUPL UBZ domain + ubiquitin - NMR <br />
**[[2mre]] – hUPL UBZ domain + ubiquitin - NMR <br />
 +
**[[2ybf]] – hUPL rad6-binding domain + ubiqitin-conjugating enzyme E2 B <br />
*'''Ubiquitin protein ligase RBBP6'''
*'''Ubiquitin protein ligase RBBP6'''
Line 321: Line 338:
*'''Ubiquitin protein ligase RBX'''
*'''Ubiquitin protein ligase RBX'''
-
**[[2lgv]] – hUPL residues 5-108 (mutant) - NMR <br />
+
**[[2lgv]] – hUPL 1 (mutant) - NMR <br />
-
**[[3rtr]], [[4f52]] – hUPL residues 5-108 + cullin-1 <br />
+
**[[3rtr]], [[4f52]] – hUPL 1 + cullin-1 <br />
-
**[[4a0k]], [[4a0c]] – hUPL residues 12-108 + cullin-4B + cullin-associated NEDD8-dissociated protein<br />
+
**[[4a0k]], [[4a0c]] – hUPL 1 + cullin-4B + cullin-associated NEDD8-dissociated protein<br />
-
**[[4p5o]] – hUPL + cullin-1 + Ubc12 + DCN1-like protein<br />
+
**[[4p5o]] – hUPL 1 + cullin-1 + Ubc12 + DCN1-like protein<br />
-
**[[4a0l]] – hUPL residues 12-108 + cullin-4B + DNA damage-binding protein + DNA<br />
+
**[[5n4w]] – hUPL 1 + cullin-2 + elongin B + elongin C + VHL<br />
 +
**[[4a0l]] – hUPL 1 + cullin-4B + DNA damage-binding protein + DNA<br />
*'''Ubiquitin protein ligase RING2'''
*'''Ubiquitin protein ligase RING2'''
Line 337: Line 355:
**[[4r8p]] – hUPL + polycomb complex protein BMI-1 + histones + DNA <br />
**[[4r8p]] – hUPL + polycomb complex protein BMI-1 + histones + DNA <br />
-
*'''Ubiquitin protein ligase RNF'''
+
*'''Ubiquitin protein ligase RNF''' Domains: PUB 1-184; catalytic 853-1072;
-
**[[4ppe]] – hUPL RING domain <br />
+
**[[4ppe]], [[3ng2]] – hUPL 4 RING domain <br />
**[[4ap4]], [[5ait]], [[5aiu]] – hUPL 4 RING domain + E2 + ubiquitin<br />
**[[4ap4]], [[5ait]], [[5aiu]] – hUPL 4 RING domain + E2 + ubiquitin<br />
**[[2pie]] – hUPL 8 FHA domain <br />
**[[2pie]] – hUPL 8 FHA domain <br />
Line 356: Line 374:
**[[4p0a]] – hUPL 31 PUB domain + p97 peptide<br />
**[[4p0a]] – hUPL 31 PUB domain + p97 peptide<br />
**[[5ljn]] – hUPL 31 PUB domain + SPATA2 peptide<br />
**[[5ljn]] – hUPL 31 PUB domain + SPATA2 peptide<br />
-
**[[4v3k]], [[4v3l]] – hUPL 38 reidues 439-515 + ubiquitin + E2<br />
+
**[[5x0w]] – hUPL 31 residues 480-639 + Sharpin <br />
 +
**[[5y3t]] – hUPL 31 residues 474-630 + Sharpin + HOIL-7 <br />
 +
**[[4v3k]], [[4v3l]] – hUPL 38 residues 439-515 + polyubiquitin-C + E2 D2<br />
**[[4kng]] – hUPL 43 PA domain + LGR5 + RSPO1<br />
**[[4kng]] – hUPL 43 PA domain + LGR5 + RSPO1<br />
**[[2ma6]] – hUPL 123 RING domain - NMR<br />
**[[2ma6]] – hUPL 123 RING domain - NMR<br />
Line 367: Line 387:
**[[4qpl]] – mUPL 146 RING+WWE domains + E2<br />
**[[4qpl]] – mUPL 146 RING+WWE domains + E2<br />
**[[3l11]], [[4gb0]] – hUPL 168 RING domain <br />
**[[3l11]], [[4gb0]] – hUPL 168 RING domain <br />
 +
**[[5xis]] – hUPL 168 residues 110-188 + diubiquitin <br />
*'''Ubiquitin protein ligase RSP'''
*'''Ubiquitin protein ligase RSP'''
Line 378: Line 399:
**[[4qn1]] – hUPL residues 1000-1418<br />
**[[4qn1]] – hUPL residues 1000-1418<br />
-
*'''Ubiquitin protein ligase SIAH1'''
+
*'''Ubiquitin protein ligase SIAH''' Domains: SINA 93-282
-
 
+
-
**[[4c9z]], [[4ca1]] – hUPL zinc finger+substrate binding domains <br />
+
-
**[[2a25]] – hUPL substrate binding domain + calcyclin-binding protein peptide <br />
+
-
**[[4i7b]], [[4i7d]] – hUPL C terminal + phyllopod peptide <br />
+
-
**[[4i7c]] – hUPL C terminal (mutant) + phyllopod peptide <br />
+
-
**[[4x3g]] – hUPL SINA domain + peptide <br />
+
-
**[[2an6]] – mUPL SINA domain + phyllopod peptide <br />
+
-
 
+
-
*'''Ubiquitin protein ligase SIAH2'''
+
-
**[[5h9m]] – hUPL SBD domain <br />
+
**[[4c9z]], [[4ca1]] – hUPL 1 SINA domain <br />
 +
**[[2a25]] – hUPL 1 SINA domain + calcyclin-binding protein peptide <br />
 +
**[[4x3g]], [[5wzz]] – hUPL 1 SINA domain + peptide <br />
 +
**[[4i7b]], [[4i7d]] – hUPL 1 C terminal + phyllopod peptide <br />
 +
**[[4i7c]] – hUPL 1 C terminal (mutant) + phyllopod peptide <br />
 +
**[[2an6]] – mUPL 1 SINA domain + phyllopod peptide <br />
 +
**[[5h9m]] – hUPL 2 SBD domain <br />
*'''Ubiquitin protein ligase SLRP'''
*'''Ubiquitin protein ligase SLRP'''
Line 397: Line 415:
*'''Ubiquitin protein ligase SMURF'''
*'''Ubiquitin protein ligase SMURF'''
-
**[[2jqz]] – hUPL - NMR <br />
+
**[[2laz]], [[2lb0]], [[2lb1]], [[2ltx]] – hUPL 1 WW + peptide - NMR<br />
-
**[[2kxq]] – hUPL WW2 and WW3 + peptide<br />
+
**[[3pyc]] – hUPL 1 C2 domain <br />
-
**[[2laz]], [[2lb0]], [[2lb1]], [[2ltx]] – hUPL WW + peptide - NMR<br />
+
**[[2jqz]] – hUPL 2 - NMR <br />
-
**[[3pyc]] – hUPL C2 domain <br />
+
**[[2kxq]] – hUPL 2 WW2 and WW3 + peptide<br />
*'''Ubiquitin protein ligase SOPA'''
*'''Ubiquitin protein ligase SOPA'''
-
**[[3sy2]] – SeUPL residues 165-782 + ubiquitin + ubiquitin-conjugating enzyme <br />
+
**[[3sy2]] – SeUPL residues 165-782 + ubiquitin + ubiquitin-conjugating enzyme - ''Salmonella enterica'' <br />
**[[5jw7]] – SeUPL residues 163-425 + TRIM56 <br />
**[[5jw7]] – SeUPL residues 163-425 + TRIM56 <br />
*'''Ubiquitin protein ligase SSPH1'''
*'''Ubiquitin protein ligase SSPH1'''
-
**[[4nkh]] –SeUPL 21 LRR domain <br />
+
**[[4nkh]] – SeUPL 21 LRR domain<br />
-
**[[4nkg]] –SeUPL 21 LRR domain + Ser/Thr protein kinase N1 peptide<br />
+
**[[4nkg]] – SeUPL 21 LRR domain + Ser/Thr protein kinase N1 peptide<br />
*'''Ubiquitin protein ligase TIR1'''
*'''Ubiquitin protein ligase TIR1'''
Line 419: Line 437:
*'''Ubiquitin protein ligase TRIM'''
*'''Ubiquitin protein ligase TRIM'''
-
**[[3zo0]] – mUPL 21 residues 291-470 + IG γ-2A<br />
+
**[[2v0k]] – mUPL 21 PRY-SPRY domain <br />
-
**[[5jpx]] – hUPL 21 B-Box2 - NMR domain <br />
+
**[[3zo0]] – mUPL 21 PRY-SPRY domain + IG γ-2A<br />
 +
**[[5olm]] – hUPL 21 residues 1-129<br />
 +
**[[5jpx]] – hUPL 21 B-Box2 domain - NMR <br />
 +
**[[5vzv]] – hUPL 23 RING domain <br />
 +
**[[5vzw]] – hUPL 23 RING domain + ubiquitin + E2 D2 <br />
 +
**[[5eya]] – hUPL 25 RING domain + ubiquitin + E2 N <br />
 +
**[[5fer]] – hUPL 25 RING domain + ribosomal protein S2 + E2 D1 <br />
**[[4b8e]] – mUPL 25 PRY-SPRY domain <br />
**[[4b8e]] – mUPL 25 PRY-SPRY domain <br />
**[[6flm]] – hUPL 25 PRY-SPRY domain <br />
**[[6flm]] – hUPL 25 PRY-SPRY domain <br />
**[[6fln]] – hUPL 25 PRY-SPRY + coiled-coil domains <br />
**[[6fln]] – hUPL 25 PRY-SPRY + coiled-coil domains <br />
-
**[[4cfg]] – hUPL 25 (mutant)<br />
+
**[[4ltb]] – hUPL 25 coiled-coil <br />
-
**[[5nt2]] – hUPL 25 + nonstructural protein<br />
+
**[[4cfg]] – hUPL 25 coiled-coil (mutant)<br />
-
**[[5fey]] – hUPL 32<br />
+
**[[5nt2]], [[5nt1]] – hUPL 25 coiled-coil + nonstructural protein<br />
 +
**[[2yjs]], [[2ysl]] – hUPL 31 RING domain - NMR <br />
 +
**[[5fey]] – hUPL 32 RING domain<br />
 +
**[[2ct2]] – hUPL 32 RING domain - NMR<br />
**[[3u5m]] – hUPL 33 PHD+Bromo domains <br />
**[[3u5m]] – hUPL 33 PHD+Bromo domains <br />
-
**[[3u5n]], [[3u5o]], [[3u5p]] – hUPL 33 PHD+Bromo domain + H3-histone peptide <br />
+
**[[3u5n]], [[3u5o]], [[3u5p]], [[5mr8]] – hUPL 33 PHD+Bromo domain + H3-histone peptide <br />
**[[3ddt]] – hUPL 37 B2-box <br />
**[[3ddt]] – hUPL 37 B2-box <br />
**[[4m3l]] – hUPL 63 coiled-coil domain <br />
**[[4m3l]] – hUPL 63 coiled-coil domain <br />
**[[4nqj]] – hUPL 69 coiled-coil domain <br />
**[[4nqj]] – hUPL 69 coiled-coil domain <br />
 +
**[[3kb5]] – hUPL 72 PRY-SPRY domain <br />
*'''Ubiquitin protein ligase UBR'''
*'''Ubiquitin protein ligase UBR'''

Revision as of 22:57, 3 October 2018

Human UPL HOIP (magenta) complex with ubiquitin (green), imidazole and Zn+2 ion (grey) 4ljo

Drag the structure with the mouse to rotate

3D Structures of ubiquitin protein ligase

Updated on 03-October-2018

References

  1. ↑ Ardley HC, Robinson PA. E3 ubiquitin ligases. Essays Biochem. 2005;41:15-30. PMID:16250895 doi:http://dx.doi.org/10.1042/EB0410015
  2. ↑ Sakemi R, Yano H, Ogasawara S, Akiba J, Nakashima O, Fukahori S, Sata M, Kojiro M. X-linked inhibitor of apoptosis (XIAP) and XIAP-associated factor-1 expressions and their relationship to apoptosis in human hepatocellular carcinoma and non-cancerous liver tissues. Oncol Rep. 2007 Jul;18(1):65-70. PMID:17549347
  3. ↑ Aguilar C, Lenoir C, Lambert N, Begue B, Brousse N, Canioni D, Berrebi D, Roy M, Gerart S, Chapel H, Schwerd T, Siproudhis L, Schappi M, Al-Ahmari A, Mori M, Yamaide A, Galicier L, Neven B, Routes J, Uhlig HH, Koletzko S, Patel S, Kanegane H, Picard C, Fischer A, Bensussan NC, Ruemmele F, Hugot JP, Latour S. Characterization of Crohn disease in X-linked inhibitor of apoptosis-deficient male patients and female symptomatic carriers. J Allergy Clin Immunol. 2014 Nov;134(5):1131-41.e9. doi:, 10.1016/j.jaci.2014.04.031. Epub 2014 Jun 15. PMID:24942515 doi:http://dx.doi.org/10.1016/j.jaci.2014.04.031
  4. ↑ Ardley HC, Robinson PA. The role of ubiquitin-protein ligases in neurodegenerative disease. Neurodegener Dis. 2004;1(2-3):71-87. PMID:16908979 doi:http://dx.doi.org/10.1159/000080048
  5. ↑ Xu G, Jiang X, Jaffrey SR. A mental retardation-linked nonsense mutation in cereblon is rescued by proteasome inhibition. J Biol Chem. 2013 Oct 11;288(41):29573-85. doi: 10.1074/jbc.M113.472092. Epub, 2013 Aug 27. PMID:23983124 doi:http://dx.doi.org/10.1074/jbc.M113.472092
  6. ↑ Lu G, Middleton RE, Sun H, Naniong M, Ott CJ, Mitsiades CS, Wong KK, Bradner JE, Kaelin WG Jr. The myeloma drug lenalidomide promotes the cereblon-dependent destruction of Ikaros proteins. Science. 2014 Jan 17;343(6168):305-9. doi: 10.1126/science.1244917. Epub 2013 Nov, 29. PMID:24292623 doi:http://dx.doi.org/10.1126/science.1244917
  7. ↑ Stieglitz B, Rana RR, Koliopoulos MG, Morris-Davies AC, Schaeffer V, Christodoulou E, Howell S, Brown NR, Dikic I, Rittinger K. Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature. 2013 Oct 20. doi: 10.1038/nature12638. PMID:24141947 doi:http://dx.doi.org/10.1038/nature12638
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