6a3z: Difference between revisions

Latest revision as of 10:35, 14 June 2023

Zinc finger domain from the HRD1 Protein

Structural highlights

6a3z is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYVN1_HUMAN Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation (PubMed:17141218). Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis (PubMed:17170702). Mediates the ubiquitination and subsequent degradation of cytoplasmic NFE2L1 (By similarity).[UniProtKB:Q9DBY1]^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

References

↑ Kaneko M, Ishiguro M, Niinuma Y, Uesugi M, Nomura Y. Human HRD1 protects against ER stress-induced apoptosis through ER-associated degradation. FEBS Lett. 2002 Dec 4;532(1-2):147-52. PMID:12459480
↑ Nadav E, Shmueli A, Barr H, Gonen H, Ciechanover A, Reiss Y. A novel mammalian endoplasmic reticulum ubiquitin ligase homologous to the yeast Hrd1. Biochem Biophys Res Commun. 2003 Mar 28;303(1):91-7. PMID:12646171
↑ Amano T, Yamasaki S, Yagishita N, Tsuchimochi K, Shin H, Kawahara K, Aratani S, Fujita H, Zhang L, Ikeda R, Fujii R, Miura N, Komiya S, Nishioka K, Maruyama I, Fukamizu A, Nakajima T. Synoviolin/Hrd1, an E3 ubiquitin ligase, as a novel pathogenic factor for arthropathy. Genes Dev. 2003 Oct 1;17(19):2436-49. doi: 10.1101/gad.1096603. Epub 2003 Sep 15. PMID:12975321 doi:https://dx.doi.org/10.1101/gad.1096603
↑ Kikkert M, Doolman R, Dai M, Avner R, Hassink G, van Voorden S, Thanedar S, Roitelman J, Chau V, Wiertz E. Human HRD1 is an E3 ubiquitin ligase involved in degradation of proteins from the endoplasmic reticulum. J Biol Chem. 2004 Jan 30;279(5):3525-34. doi: 10.1074/jbc.M307453200. Epub 2003, Oct 30. PMID:14593114 doi:https://dx.doi.org/10.1074/jbc.M307453200
↑ Schulze A, Standera S, Buerger E, Kikkert M, van Voorden S, Wiertz E, Koning F, Kloetzel PM, Seeger M. The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway. J Mol Biol. 2005 Dec 16;354(5):1021-7. Epub 2005 Nov 2. PMID:16289116 doi:https://dx.doi.org/S0022-2836(05)01253-2
↑ Arteaga MF, Wang L, Ravid T, Hochstrasser M, Canessa CM. An amphipathic helix targets serum and glucocorticoid-induced kinase 1 to the endoplasmic reticulum-associated ubiquitin-conjugation machinery. Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11178-83. doi:, 10.1073/pnas.0604816103. Epub 2006 Jul 17. PMID:16847254 doi:https://dx.doi.org/10.1073/pnas.0604816103
↑ Omura T, Kaneko M, Okuma Y, Orba Y, Nagashima K, Takahashi R, Fujitani N, Matsumura S, Hata A, Kubota K, Murahashi K, Uehara T, Nomura Y. A ubiquitin ligase HRD1 promotes the degradation of Pael receptor, a substrate of Parkin. J Neurochem. 2006 Dec;99(6):1456-69. doi: 10.1111/j.1471-4159.2006.04155.x. Epub , 2006 Oct 24. PMID:17059562 doi:https://dx.doi.org/10.1111/j.1471-4159.2006.04155.x
↑ Yang H, Zhong X, Ballar P, Luo S, Shen Y, Rubinsztein DC, Monteiro MJ, Fang S. Ubiquitin ligase Hrd1 enhances the degradation and suppresses the toxicity of polyglutamine-expanded huntingtin. Exp Cell Res. 2007 Feb 1;313(3):538-50. doi: 10.1016/j.yexcr.2006.10.031. Epub, 2006 Nov 3. PMID:17141218 doi:https://dx.doi.org/10.1016/j.yexcr.2006.10.031
↑ Yamasaki S, Yagishita N, Sasaki T, Nakazawa M, Kato Y, Yamadera T, Bae E, Toriyama S, Ikeda R, Zhang L, Fujitani K, Yoo E, Tsuchimochi K, Ohta T, Araya N, Fujita H, Aratani S, Eguchi K, Komiya S, Maruyama I, Higashi N, Sato M, Senoo H, Ochi T, Yokoyama S, Amano T, Kim J, Gay S, Fukamizu A, Nishioka K, Tanaka K, Nakajima T. Cytoplasmic destruction of p53 by the endoplasmic reticulum-resident ubiquitin ligase 'Synoviolin'. EMBO J. 2007 Jan 10;26(1):113-22. Epub 2006 Dec 14. PMID:17170702 doi:https://dx.doi.org/7601490
↑ Sato T, Sako Y, Sho M, Momohara M, Suico MA, Shuto T, Nishitoh H, Okiyoneda T, Kokame K, Kaneko M, Taura M, Miyata M, Chosa K, Koga T, Morino-Koga S, Wada I, Kai H. STT3B-dependent posttranslational N-glycosylation as a surveillance system for secretory protein. Mol Cell. 2012 Jul 13;47(1):99-110. doi: 10.1016/j.molcel.2012.04.015. Epub 2012 , May 17. PMID:22607976 doi:10.1016/j.molcel.2012.04.015
↑ Hosokawa N, Wada I. Association of the SEL1L protein transmembrane domain with HRD1 ubiquitin ligase regulates ERAD-L. FEBS J. 2016 Jan;283(1):157-72. doi: 10.1111/febs.13564. Epub 2015 Nov 6. PMID:26471130 doi:https://dx.doi.org/10.1111/febs.13564

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kaneko M, Ishiguro M, Niinuma Y, Uesugi M, Nomura Y. Human HRD1 protects against ER stress-induced apoptosis through ER-associated degradation. FEBS Lett. 2002 Dec 4;532(1-2):147-52. PMID:12459480

[2] Nadav E, Shmueli A, Barr H, Gonen H, Ciechanover A, Reiss Y. A novel mammalian endoplasmic reticulum ubiquitin ligase homologous to the yeast Hrd1. Biochem Biophys Res Commun. 2003 Mar 28;303(1):91-7. PMID:12646171

[3] Amano T, Yamasaki S, Yagishita N, Tsuchimochi K, Shin H, Kawahara K, Aratani S, Fujita H, Zhang L, Ikeda R, Fujii R, Miura N, Komiya S, Nishioka K, Maruyama I, Fukamizu A, Nakajima T. Synoviolin/Hrd1, an E3 ubiquitin ligase, as a novel pathogenic factor for arthropathy. Genes Dev. 2003 Oct 1;17(19):2436-49. doi: 10.1101/gad.1096603. Epub 2003 Sep 15. PMID:12975321 doi:https://dx.doi.org/10.1101/gad.1096603

[4] Kikkert M, Doolman R, Dai M, Avner R, Hassink G, van Voorden S, Thanedar S, Roitelman J, Chau V, Wiertz E. Human HRD1 is an E3 ubiquitin ligase involved in degradation of proteins from the endoplasmic reticulum. J Biol Chem. 2004 Jan 30;279(5):3525-34. doi: 10.1074/jbc.M307453200. Epub 2003, Oct 30. PMID:14593114 doi:https://dx.doi.org/10.1074/jbc.M307453200

[5] Schulze A, Standera S, Buerger E, Kikkert M, van Voorden S, Wiertz E, Koning F, Kloetzel PM, Seeger M. The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway. J Mol Biol. 2005 Dec 16;354(5):1021-7. Epub 2005 Nov 2. PMID:16289116 doi:https://dx.doi.org/S0022-2836(05)01253-2

[6] Arteaga MF, Wang L, Ravid T, Hochstrasser M, Canessa CM. An amphipathic helix targets serum and glucocorticoid-induced kinase 1 to the endoplasmic reticulum-associated ubiquitin-conjugation machinery. Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11178-83. doi:, 10.1073/pnas.0604816103. Epub 2006 Jul 17. PMID:16847254 doi:https://dx.doi.org/10.1073/pnas.0604816103

[7] Omura T, Kaneko M, Okuma Y, Orba Y, Nagashima K, Takahashi R, Fujitani N, Matsumura S, Hata A, Kubota K, Murahashi K, Uehara T, Nomura Y. A ubiquitin ligase HRD1 promotes the degradation of Pael receptor, a substrate of Parkin. J Neurochem. 2006 Dec;99(6):1456-69. doi: 10.1111/j.1471-4159.2006.04155.x. Epub , 2006 Oct 24. PMID:17059562 doi:https://dx.doi.org/10.1111/j.1471-4159.2006.04155.x

[8] Yang H, Zhong X, Ballar P, Luo S, Shen Y, Rubinsztein DC, Monteiro MJ, Fang S. Ubiquitin ligase Hrd1 enhances the degradation and suppresses the toxicity of polyglutamine-expanded huntingtin. Exp Cell Res. 2007 Feb 1;313(3):538-50. doi: 10.1016/j.yexcr.2006.10.031. Epub, 2006 Nov 3. PMID:17141218 doi:https://dx.doi.org/10.1016/j.yexcr.2006.10.031

[9] Yamasaki S, Yagishita N, Sasaki T, Nakazawa M, Kato Y, Yamadera T, Bae E, Toriyama S, Ikeda R, Zhang L, Fujitani K, Yoo E, Tsuchimochi K, Ohta T, Araya N, Fujita H, Aratani S, Eguchi K, Komiya S, Maruyama I, Higashi N, Sato M, Senoo H, Ochi T, Yokoyama S, Amano T, Kim J, Gay S, Fukamizu A, Nishioka K, Tanaka K, Nakajima T. Cytoplasmic destruction of p53 by the endoplasmic reticulum-resident ubiquitin ligase 'Synoviolin'. EMBO J. 2007 Jan 10;26(1):113-22. Epub 2006 Dec 14. PMID:17170702 doi:https://dx.doi.org/7601490

[10] Sato T, Sako Y, Sho M, Momohara M, Suico MA, Shuto T, Nishitoh H, Okiyoneda T, Kokame K, Kaneko M, Taura M, Miyata M, Chosa K, Koga T, Morino-Koga S, Wada I, Kai H. STT3B-dependent posttranslational N-glycosylation as a surveillance system for secretory protein. Mol Cell. 2012 Jul 13;47(1):99-110. doi: 10.1016/j.molcel.2012.04.015. Epub 2012 , May 17. PMID:22607976 doi:10.1016/j.molcel.2012.04.015

[11] Hosokawa N, Wada I. Association of the SEL1L protein transmembrane domain with HRD1 ubiquitin ligase regulates ERAD-L. FEBS J. 2016 Jan;283(1):157-72. doi: 10.1111/febs.13564. Epub 2015 Nov 6. PMID:26471130 doi:https://dx.doi.org/10.1111/febs.13564

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@@ Line 1: / Line 1: @@
 ==Zinc finger domain from the HRD1 Protein==
-<StructureSection load='6a3z' size='340' side='right'caption='[[6a3z]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='6a3z' size='340' side='right'caption='[[6a3z]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a3z]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A3Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A3Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a3z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A3Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A3Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6a3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a3z OCA], [https://pdbe.org/6a3z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a3z RCSB], [https://www.ebi.ac.uk/pdbsum/6a3z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a3z ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6a3z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a3z OCA], [http://pdbe.org/6a3z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a3z RCSB], [http://www.ebi.ac.uk/pdbsum/6a3z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a3z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SYVN1_HUMAN SYVN1_HUMAN]] Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation (PubMed:17141218). Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis (PubMed:17170702). Mediates the ubiquitination and subsequent degradation of cytoplasmic NFE2L1 (By similarity).[UniProtKB:Q9DBY1]<ref>PMID:12459480</ref> <ref>PMID:12646171</ref> <ref>PMID:12975321</ref> <ref>PMID:14593114</ref> <ref>PMID:16289116</ref> <ref>PMID:16847254</ref> <ref>PMID:17059562</ref> <ref>PMID:17141218</ref> <ref>PMID:17170702</ref> <ref>PMID:22607976</ref> <ref>PMID:26471130</ref>
+[https://www.uniprot.org/uniprot/SYVN1_HUMAN SYVN1_HUMAN] Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation (PubMed:17141218). Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis (PubMed:17170702). Mediates the ubiquitination and subsequent degradation of cytoplasmic NFE2L1 (By similarity).[UniProtKB:Q9DBY1]<ref>PMID:12459480</ref> <ref>PMID:12646171</ref> <ref>PMID:12975321</ref> <ref>PMID:14593114</ref> <ref>PMID:16289116</ref> <ref>PMID:16847254</ref> <ref>PMID:17059562</ref> <ref>PMID:17141218</ref> <ref>PMID:17170702</ref> <ref>PMID:22607976</ref> <ref>PMID:26471130</ref>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: RING-type E3 ubiquitin transferase]]
+[[Category: Miyamoto K]]
-[[Category: Miyamoto, K]]
-[[Category: Hrd1]]
-[[Category: Metal binding protein]]

6a3z: Difference between revisions

Latest revision as of 10:35, 14 June 2023

Zinc finger domain from the HRD1 Protein

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