Ubiquitin protein ligase

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*'''Ubiquitin protein ligase LNX'''
*'''Ubiquitin protein ligase LNX'''
-
**[[3vqf]] – mUPL 2rd PDZ domain <br />
 
-
**[[3vqg]] – mUPL 2rd PDZ domain + peptide<br />
 
**[[3b76]] – hUPL 3rd PDZ domain <br />
**[[3b76]] – hUPL 3rd PDZ domain <br />
**[[5h7r]] – hUPL residues 11-138 <br />
**[[5h7r]] – hUPL residues 11-138 <br />
**[[5h7s]] – hUPL residues 11-138 + ubiquitin conjugating enzyme E2 N + ubiquitin <br />
**[[5h7s]] – hUPL residues 11-138 + ubiquitin conjugating enzyme E2 N + ubiquitin <br />
 +
**[[3vqf]] – mUPL 2rd PDZ domain <br />
 +
**[[3vqg]] – mUPL 2rd PDZ domain + peptide<br />
*'''Ubiquitin protein ligase LUBX'''
*'''Ubiquitin protein ligase LUBX'''
Line 262: Line 262:
*'''Ubiquitin protein ligase MYCBP2'''
*'''Ubiquitin protein ligase MYCBP2'''
 +
**[[5o6c]] – hUPL residues 4379-4638 <br />
**[[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'''
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*'''Ubiquitin protein ligase NEDD4'''
*'''Ubiquitin protein ligase NEDD4'''
-
**[[1wr3]], [[1wr4]], [[1wr7]] – mUPL WW domain - NMR <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 />
**[[4n7f]] – hUPL WW3 domain <br />
 +
**[[1wr3]], [[1wr4]], [[1wr7]] – mUPL WW domain - NMR <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 284: Line 284:
*Ubiquitin protein ligase NEDD4 complex
*Ubiquitin protein ligase NEDD4 complex
-
**[[1i5h]] – rUPL WW3 domain + amiloride-sensitive Na channel β subunit <br />
 
-
**[[2n8t]] – rUPL WW2 domain + 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 />
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**[[2xbb]], [[5c7j]], [[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 />
 +
**[[1i5h]] – rUPL WW3 domain + amiloride-sensitive Na channel β subunit <br />
 +
**[[2n8t]] – rUPL WW2 domain + peptide - NMR <br />
 +
**[[2ez5]] – DmUPL WW3 domain + COMM LPSY peptide - NMR <br />
*'''Ubiquitin protein ligase NEDD4-like'''
*'''Ubiquitin protein ligase NEDD4-like'''
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*'''Ubiquitin protein ligase PARKIN'''
*'''Ubiquitin protein ligase PARKIN'''
-
**[[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 />
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**[[5n2w]], [[6glc]], [[5n38]] – hUPL + polyubiquitin <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 />
 +
**[[2knb]] – rUPL + endophilin - NMR <br />
 +
**[[4k95]], [[4zyn]] – rUPL <br />
**[[4k7d]] – rUPL C terminal domain <br />
**[[4k7d]] – rUPL C terminal domain <br />
**[[2knb]] – rUPL + endophilin - NMR <br />
**[[2knb]] – rUPL + endophilin - NMR <br />
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*'''Ubiquitin protein ligase RING2'''
*'''Ubiquitin protein ligase RING2'''
-
**[[2ckl]] – mUPL RING domain + polycomb group ring finger protein 4 <br />
 
-
**[[2h0d]] – mUPL RING domain + B lymphoma MO-MLV insertion region <br />
 
**[[3h8h]] – hUPL C terminal <br />
**[[3h8h]] – hUPL C terminal <br />
**[[3gs2]] – hUPL C terminal + chromobox protein homolog<br />
**[[3gs2]] – hUPL C terminal + chromobox protein homolog<br />
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**[[3rpg]], [[4s3o]] – hUPL + polycomb complex protein BMI-1 + E2 D3 <br />
**[[3rpg]], [[4s3o]] – hUPL + polycomb complex protein BMI-1 + E2 D3 <br />
**[[4r8p]] – hUPL + polycomb complex protein BMI-1 + histones + DNA <br />
**[[4r8p]] – hUPL + polycomb complex protein BMI-1 + histones + DNA <br />
 +
**[[2ckl]] – mUPL RING domain + polycomb group ring finger protein 4 <br />
 +
**[[2h0d]] – mUPL RING domain + B lymphoma MO-MLV insertion region <br />
*'''Ubiquitin protein ligase RNF or ring finger protein''' Domains: PUB 1-184; catalytic 853-1072;
*'''Ubiquitin protein ligase RNF or ring finger protein''' Domains: PUB 1-184; catalytic 853-1072;
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**[[3icu]] – hUPL 128 protease-associated domain <br />
**[[3icu]] – hUPL 128 protease-associated domain <br />
**[[3v3l]] – hUPL 146 WWE domain <br />
**[[3v3l]] – hUPL 146 WWE domain <br />
-
**[[2rsf]] – mUPL 146 WWE domain + ATP<br />
 
-
**[[4qpl]] – mUPL 146 RING+WWE domains + E2<br />
 
**[[5d0i]] – hUPL 165 residues 255-348 <br />
**[[5d0i]] – hUPL 165 residues 255-348 <br />
**[[5d0k]], [[5d0m]], [[5ulh]], [[5ulk]] – hUPL 165 residues 255-348 + ubiquitin + E2 D2 <br />
**[[5d0k]], [[5d0m]], [[5ulh]], [[5ulk]] – hUPL 165 residues 255-348 + ubiquitin + E2 D2 <br />
**[[3l11]], [[4gb0]] – hUPL 168 RING domain <br />
**[[3l11]], [[4gb0]] – hUPL 168 RING domain <br />
**[[5xis]] – hUPL 168 residues 110-188 + diubiquitin <br />
**[[5xis]] – hUPL 168 residues 110-188 + diubiquitin <br />
 +
**[[2rsf]] – mUPL 146 WWE domain + ATP<br />
 +
**[[4qpl]] – mUPL 146 RING+WWE domains + E2<br />
*'''Ubiquitin protein ligase RSP'''
*'''Ubiquitin protein ligase RSP'''
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**[[4x3g]], [[5wzz]] – hUPL 1 SINA domain + peptide <br />
**[[4x3g]], [[5wzz]] – hUPL 1 SINA domain + peptide <br />
**[[4i7b]], [[4i7d]] – hUPL 1 C terminal + phyllopod peptide <br />
**[[4i7b]], [[4i7d]] – hUPL 1 C terminal + phyllopod peptide <br />
-
**[[4i7c]] – hUPL 1 C terminal (mutant) + phyllopod peptide <br />
+
**[[4i7c]] – hUPL 1 C terminal (mutant) + phyllopod pept
**[[2an6]] – mUPL 1 SINA domain + phyllopod peptide <br />
**[[2an6]] – mUPL 1 SINA domain + phyllopod peptide <br />
**[[5h9m]] – hUPL 2 SBD domain <br />
**[[5h9m]] – hUPL 2 SBD domain <br />
 +
**[[2an6]] – mUPL 1 SINA domain + phyllopod peptide <br />
*'''Ubiquitin protein ligase SLRP'''
*'''Ubiquitin protein ligase SLRP'''
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*'''Ubiquitin protein ligase TRIM'''
*'''Ubiquitin protein ligase TRIM'''
-
**[[2v0k]] – mUPL 21 PRY-SPRY domain <br />
 
-
**[[3zo0]] – mUPL 21 PRY-SPRY domain + IG γ-2A<br />
 
**[[5olm]] – hUPL 21 residues 1-129<br />
**[[5olm]] – hUPL 21 residues 1-129<br />
**[[5jpx]] – hUPL 21 B-Box2 domain - NMR <br />
**[[5jpx]] – hUPL 21 B-Box2 domain - NMR <br />
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**[[5eya]] – hUPL 25 RING domain + ubiquitin + E2 N <br />
**[[5eya]] – hUPL 25 RING domain + ubiquitin + E2 N <br />
**[[5fer]] – hUPL 25 RING domain + ribosomal protein S2 + E2 D1 <br />
**[[5fer]] – hUPL 25 RING domain + ribosomal protein S2 + E2 D1 <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 />
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**[[4nqj]] – hUPL 69 coiled-coil domain <br />
**[[4nqj]] – hUPL 69 coiled-coil domain <br />
**[[3kb5]] – hUPL 72 PRY-SPRY domain <br />
**[[3kb5]] – hUPL 72 PRY-SPRY domain <br />
 +
**[[2v0k]] – mUPL 21 PRY-SPRY domain <br />
 +
**[[3zo0]] – mUPL 21 PRY-SPRY domain + IG γ-2A<br />
 +
**[[4b8e]] – mUPL 25 PRY-SPRY domain <br />
*'''Ubiquitin protein ligase UBR'''
*'''Ubiquitin protein ligase UBR'''
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**[[3ny3]] – hUPL 1 UBR-box + N-degron<br />
**[[3ny3]] – hUPL 1 UBR-box + N-degron<br />
**[[5tdc]] – hUPL 1 UBR-box + peptide<br />
**[[5tdc]] – hUPL 1 UBR-box + peptide<br />
-
**[[3nih]], [[3nii]], [[3nij]], [[3nik]], [[3nil]], [[3nim]], [[3nin]] – yUPL 1 UBR-box + peptide <br />
 
-
**[[3nis]], [[3nit]] – yUPL 1 UBR-box <br />
 
**[[5um3]] – hUPL 2 UBR-box (mutant)<br />
**[[5um3]] – hUPL 2 UBR-box (mutant)<br />
**[[5tda]] – hUPL 2 UBR-box + N-degron<br />
**[[5tda]] – hUPL 2 UBR-box + N-degron<br />
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**[[3pt3]] – hUPL 5 C terminal <br />
**[[3pt3]] – hUPL 5 C terminal <br />
**[[3ntw]] – rUPL 5 MLLE domain + peptide <br />
**[[3ntw]] – rUPL 5 MLLE domain + peptide <br />
 +
**[[3nih]], [[3nii]], [[3nij]], [[3nik]], [[3nil]], [[3nim]], [[3nin]] – yUPL 1 UBR-box + peptide - yeast <br />
 +
**[[3nis]], [[3nit]] – yUPL 1 UBR-box <br />
*'''Ubiquitin protein ligase UHRF (Np95)'''
*'''Ubiquitin protein ligase UHRF (Np95)'''
Line 504: Line 505:
**[[3fl2]] – hUPL 1 RING domain <br />
**[[3fl2]] – hUPL 1 RING domain <br />
**[[3bi7]], [[2pb7]], [[3dwh]] – hUPL 1 SRA domain <br />
**[[3bi7]], [[2pb7]], [[3dwh]] – hUPL 1 SRA domain <br />
-
**[[2zkg]] – mUPL 1 SRA domain <br />
 
**[[3oln]] – hUPL 2 SRA domain <br />
**[[3oln]] – hUPL 2 SRA domain <br />
**[[2e6s]] – hUPL 2 PHD finger - NMR <br />
**[[2e6s]] – hUPL 2 PHD finger - NMR <br />
**[[4tvr]] – hUPL 2 TUDOR + PHD domains <br />
**[[4tvr]] – hUPL 2 TUDOR + PHD domains <br />
 +
**[[2zkg]] – mUPL 1 SRA domain <br />
*Ubiquitin protein ligase UHRF complex
*Ubiquitin protein ligase UHRF complex
**[[3clz]], [[2zkd]], [[2zke]], [[2zkf]] – hUPL 1 SRA domain + DNA<br />
**[[3clz]], [[2zkd]], [[2zke]], [[2zkf]] – hUPL 1 SRA domain + DNA<br />
-
**[[2zo0]], [[2zo1]], [[2zo2]], [[3f8i]], [[3f8j]], [[3fde]] – mUPL 1 SRA domain + DNA<br />
 
**[[3sou]], [[3sow]], [[3shb]], [[2lgg]], [[3t6r]], [[3ask]], [[3asl]], [[4gy5]], [[3zvy]] – hUPL 1 PHD finger + histone H3 peptide<br />
**[[3sou]], [[3sow]], [[3shb]], [[2lgg]], [[3t6r]], [[3ask]], [[3asl]], [[4gy5]], [[3zvy]] – hUPL 1 PHD finger + histone H3 peptide<br />
**[[2lgk]] – hUPL 1 PHD finger + histone H3 peptide - NMR<br />
**[[2lgk]] – hUPL 1 PHD finger + histone H3 peptide - NMR<br />
Line 520: Line 520:
**[[5xpi]], [[4qqd]] – hUPL 1 TUDOR domain + inhibitor<br />
**[[5xpi]], [[4qqd]] – hUPL 1 TUDOR domain + inhibitor<br />
**[[4pw5]], [[4pw6]], [[4pw7]] – hUPL 2 SRA domain + DNA<br />
**[[4pw5]], [[4pw6]], [[4pw7]] – hUPL 2 SRA domain + DNA<br />
 +
**[[2zo0]], [[2zo1]], [[2zo2]], [[3f8i]], [[3f8j]], [[3fde]] – mUPL 1 SRA domain + DNA<br />
*'''Ubiquitin protein ligase XIAP or baculoviral IAP repeat containing protein 4''' Domains: BIR1 10-99; BIR2 152-236; BIR3 249-354; UBA 357-449; RING 429-497
*'''Ubiquitin protein ligase XIAP or baculoviral IAP repeat containing protein 4''' Domains: BIR1 10-99; BIR2 152-236; BIR3 249-354; UBA 357-449; RING 429-497
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**[[5ywr]] – hUPL 1 RING domain + E2 N <BR />
**[[5ywr]] – hUPL 1 RING domain + E2 N <BR />
-
**[[4c84]], [[4c85]], [[4c86]], [[4c8a]], [[4c8c]], [[4c8f]] – zUPL 3 ectodomain – zebra fish <br />
+
**[[4ufs]] – hUPL 3 ectodomain + R-spondin + LGR5 <br />
-
**[[4c8p]] – zUPL 3 ectodomain (mutant) <br />
+
-
**[[4c8t]], [[4c8u]] – fUPL 3 ectodomain – frog <br />
+
**[[4cdj]] – mUPL 3 ectodomain <br />
**[[4cdj]] – mUPL 3 ectodomain <br />
**[[4c99]], [[4c9a]], [[4c9e]], [[4c9r]], [[4c9u]], [[4cdk]] – mUPL 3 ectodomain + R-spondin <br />
**[[4c99]], [[4c9a]], [[4c9e]], [[4c9r]], [[4c9u]], [[4cdk]] – mUPL 3 ectodomain + R-spondin <br />
-
**[[4ufs]] – hUPL 3 ectodomain + R-spondin + LGR5 <br />
+
**[[4c8t]], [[4c8u]] – fUPL 3 ectodomain – frog <br />
 +
**[[4c84]], [[4c85]], [[4c86]], [[4c8a]], [[4c8c]], [[4c8f]] – zUPL 3 ectodomain – zebra fish <br />
 +
**[[4c8p]] – zUPL 3 ectodomain (mutant) <br />
*'''Ubiquitin protein ligase ZFP91'''
*'''Ubiquitin protein ligase ZFP91'''

Revision as of 09:21, 21 March 2020

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 21-March-2020

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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