2lxp: Difference between revisions

Revision as of 13:18, 22 February 2023

NMR structure of two domains in ubiquitin ligase gp78, RING and G2BR, bound to its conjugating enzyme Ube2g

Structural highlights

2lxp is a 3 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

UB2G2_HUMAN Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Involved in endoplasmic reticulum-associated degradation (ERAD).^[1] ^[2]

Publication Abstract from PubMed

RING finger proteins constitute the large majority of ubiquitin ligases (E3s) and function by interacting with ubiquitin-conjugating enzymes (E2s) charged with ubiquitin. How low-affinity RING-E2 interactions result in highly processive substrate ubiquitination is largely unknown. The RING E3, gp78, represents an excellent model to study this process. gp78 includes a high-affinity secondary binding region for its cognate E2, Ube2g2, the G2BR. The G2BR allosterically enhances RING:Ube2g2 binding and ubiquitination. Structural analysis of the RING:Ube2g2:G2BR complex reveals that a G2BR-induced conformational effect at the RING:Ube2g2 interface is necessary for enhanced binding of RING to Ube2g2 or Ube2g2 conjugated to Ub. This conformational effect and a key ternary interaction with conjugated ubiquitin are required for ubiquitin transfer. Moreover, RING:Ube2g2 binding induces a second allosteric effect, disrupting Ube2g2:G2BR contacts, decreasing affinity and facilitating E2 exchange. Thus, gp78 is a ubiquitination machine where multiple E2-binding sites coordinately facilitate processive ubiquitination.

Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.,Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA EMBO J. 2013 Aug 13. doi: 10.1038/emboj.2013.174. PMID:23942235^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ David Y, Ziv T, Admon A, Navon A. The E2 ubiquitin conjugating enzymes direct polyubiquitination to preferred lysines. J Biol Chem. 2010 Jan 8. PMID:20061386 doi:M109.089003
↑ 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
↑ Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA. Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J. 2013 Aug 13. doi: 10.1038/emboj.2013.174. PMID:23942235 doi:10.1038/emboj.2013.174

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] David Y, Ziv T, Admon A, Navon A. The E2 ubiquitin conjugating enzymes direct polyubiquitination to preferred lysines. J Biol Chem. 2010 Jan 8. PMID:20061386 doi:M109.089003

[2] 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

[3] Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA. Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J. 2013 Aug 13. doi: 10.1038/emboj.2013.174. PMID:23942235 doi:10.1038/emboj.2013.174

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==NMR structure of two domains in ubiquitin ligase gp78, RING and G2BR, bound to its conjugating enzyme Ube2g==
-<StructureSection load='2lxp' size='340' side='right'caption='[[2lxp]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2lxp' size='340' side='right'caption='[[2lxp]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2lxp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LXP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2lxp]] is a 3 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=2LXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LXP FirstGlance]. <br>
 </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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBE2G2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), AMFR, RNF45 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </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=2lxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lxp OCA], [https://pdbe.org/2lxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lxp RCSB], [https://www.ebi.ac.uk/pdbsum/2lxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lxp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/UB2G2_HUMAN UB2G2_HUMAN]] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Involved in endoplasmic reticulum-associated degradation (ERAD).<ref>PMID:20061386</ref> <ref>PMID:22607976</ref>  [[https://www.uniprot.org/uniprot/AMFR_HUMAN AMFR_HUMAN]] E3 ubiquitin-protein ligase that mediates the polyubiquitination of a number of proteins such as CD3D, CYP3A4, CFTR and APOB for proteasomal degradation. Component of a VCP/p97-AMFR/gp78 complex that participates in the final step of endoplasmic reticulum-associated degradation (ERAD). The VCP/p97-AMFR/gp78 complex is involved in the sterol-accelerated ERAD degradation of HMGCR through binding to the HMGCR-INSIG complex at the ER membrane and initiating ubiquitination of HMGCR. The ubiquitinated HMGCR is then released from the ER by the complex into the cytosol for subsequent destruction. Also acts as a scaffold protein to assemble a complex that couples ubiquitination, retranslocation and deglycosylation. Mediates tumor invasion and metastasis as a receptor for the GPI/autocrine motility factor.<ref>PMID:10456327</ref> <ref>PMID:11724934</ref> <ref>PMID:16168377</ref> <ref>PMID:19103148</ref>
+[https://www.uniprot.org/uniprot/UB2G2_HUMAN UB2G2_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Involved in endoplasmic reticulum-associated degradation (ERAD).<ref>PMID:20061386</ref> <ref>PMID:22607976</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Byrd R]]
-[[Category: Byrd, R]]
+[[Category: Das R]]
-[[Category: Das, R]]
+[[Category: Huang T]]
-[[Category: Huang, T]]
+[[Category: Ji X]]
-[[Category: Ji, X]]
+[[Category: King A]]
-[[Category: King, A]]
+[[Category: Li J]]
-[[Category: Li, J]]
+[[Category: Linag Y]]
-[[Category: Linag, Y]]
+[[Category: Mariano J]]
-[[Category: Mariano, J]]
+[[Category: Weissman A]]
-[[Category: Weissman, A]]
-[[Category: Ligase]]
-[[Category: Ring domain]]
-[[Category: Ubiquitin]]

2lxp: Difference between revisions

Revision as of 13:18, 22 February 2023

NMR structure of two domains in ubiquitin ligase gp78, RING and G2BR, bound to its conjugating enzyme Ube2g

Structural highlights

Function

Publication Abstract from PubMed

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References

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