5d1m: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5d1m is ON HOLD  until Paper Publication
+==Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)==
+<StructureSection load='5d1m' size='340' side='right'caption='[[5d1m]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5d1m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D1M FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.581&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5d1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d1m OCA], [https://pdbe.org/5d1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d1m RCSB], [https://www.ebi.ac.uk/pdbsum/5d1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d1m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNF25_HUMAN RNF25_HUMAN] E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of NKD2 (By similarity). Stimulates transcription mediated by NF-kappa-B.<ref>PMID:12748188</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RING proteins constitute the largest class of E3 ubiquitin ligases. Unlike most RINGs, AO7 (RNF25) binds the E2 ubiquitin-conjugating enzyme, UbcH5B (UBE2D2), with strikingly high affinity. We have defined, by co-crystallization, the distinctive means by which AO7 binds UbcH5B. AO7 contains a structurally unique UbcH5B binding region (U5BR) that is connected by an 11-amino acid linker to its RING domain, forming a clamp surrounding the E2. The U5BR interacts extensively with a region of UbcH5B that is distinct from both the active site and the RING-interacting region, referred to as the backside of the E2. An apparent paradox is that the high-affinity binding of the AO7 clamp to UbcH5B, which is dependent on the U5BR, decreases the rate of ubiquitination. We establish that this is a consequence of blocking the stimulatory, non-covalent, binding of ubiquitin to the backside of UbcH5B. Interestingly, when non-covalent backside ubiquitin binding cannot occur, the AO7 clamp now enhances the rate of ubiquitination. The high-affinity binding of the AO7 clamp to UbcH5B has also allowed for the co-crystallization of previously described and functionally important RING mutants at the RING-E2 interface. We show that mutations having marked effects on function only minimally affect the intermolecular interactions between the AO7 RING and UbcH5B, establishing a high degree of complexity in activation through the RING-E2 interface.
-Authors: Liang, Y.-H., Li, S., Weissman, A.M., Ji, X.
+Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B.,Li S, Liang YH, Mariano J, Metzger MB, Stringer DK, Hristova VA, Li J, Randazzo PA, Tsai YC, Ji X, Weissman AM J Biol Chem. 2015 Dec 18;290(51):30225-39. doi: 10.1074/jbc.M115.685867. Epub, 2015 Oct 16. PMID:26475854<ref>PMID:26475854</ref>
-Description: Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Li, S]]
+<div class="pdbe-citations 5d1m" style="background-color:#fffaf0;"></div>
-[[Category: Liang, Y.-H]]
-[[Category: Ji, X]]
+==See Also==
-[[Category: Weissman, A.M]]
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
+*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Ji X]]
+[[Category: Li S]]
+[[Category: Liang Y-H]]
+[[Category: Weissman AM]]