9quf: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 9quf is ~~ON HOLD until sometime~~ in the ~~future~~

==Structure of a fungal Ube2O==

== Structural highlights ==

<table><tr><td colspan='2'>[[9quf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrenophora_tritici-repentis Pyrenophora tritici-repentis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QUF 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]] 3Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=9quf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9quf OCA], [https://pdbe.org/9quf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9quf RCSB], [https://www.ebi.ac.uk/pdbsum/9quf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9quf ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A922SUA0_9PLEO A0A922SUA0_9PLEO]

== Publication Abstract from PubMed ==

UBE2O is a promiscuous ubiquitin ligase involved in cellular quality control pathways. Along with BIRC6, UBE2O is one of only two E2 enzymes that can ubiquitinate substrates in an E3-independent manner. The E2/E3 hybrid targets and multi-monoubiquitinates a multitude of orphan proteins; however, the mechanisms underlying substrate specificity and ubiquitin transfer remain poorly understood. By combining structural and biochemical approaches, we show that substrate binding by UBE2O occurs through a conserved acidic pocket formed by the N-terminal SH3-like domains and that this platform allows the recruitment of a broad range of proteins. Furthermore, we identified specific residues in the catalytic UBC domain that position ubiquitin in a closed state, confirming its confirmation, and priming it for nucleophilic attack by the incoming substrate. Importantly, the activated E2 approximately Ub conjugate is protected by a tryptophan residue, avoiding premature hydrolysis. By incorporating these findings into the UBC domain of BIRC6 our data provide the molecular basis of how specialized E2/E3 hybrid proteins function as potent ubiquitination enzymes reminiscent of the catalytic principle of RING E3 ligases.

~~Authors:~~ Kordic, D., Williams, ~~T.L., Luiza~~ Deszcz, L., Ehrmann~~, J.~~, Arnese, R~~., Meinhart~~, A., Clausen, T.

Structural basis for substrate recruitment and catalytic ubiquitin transfer by the E2/E3 hybrid enzyme UBE2O.,Kordic D, Williams TL, Deszcz L, Ehrmann JF, Arnese R, Schleiffer A, Clausen T, Meinhart A J Biol Chem. 2025 Dec 17;302(2):111073. doi: 10.1016/j.jbc.2025.111073. PMID:41419192<ref>PMID:41419192</ref>

~~Description~~: ~~To be published~~

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

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Arnese, R~~]]

[[Category: ~~Kordic, D~~]]

== References ==

[[Category: Clausen, T]]

[[Category: Ehrmann, J]]

__TOC__

[[Category: Luiza Deszcz, L]]

</StructureSection>

[[Category: Meinhart, A]]

[[Category: Large Structures]]

[[Category: Williams~~, T.L~~]]

[[Category: Pyrenophora tritici-repentis]]

[[Category: Arnese R]]

[[Category: Clausen T]]

[[Category: Ehrmann J]]

[[Category: Kordic D]]

[[Category: Luiza Deszcz L]]

[[Category: Meinhart A]]

[[Category: Williams TL]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9quf is ON HOLD  until sometime in the future
+==Structure of a fungal Ube2O==
+<StructureSection load='9quf' size='340' side='right'caption='[[9quf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9quf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrenophora_tritici-repentis Pyrenophora tritici-repentis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QUF 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]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=9quf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9quf OCA], [https://pdbe.org/9quf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9quf RCSB], [https://www.ebi.ac.uk/pdbsum/9quf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9quf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A922SUA0_9PLEO A0A922SUA0_9PLEO]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+UBE2O is a promiscuous ubiquitin ligase involved in cellular quality control pathways. Along with BIRC6, UBE2O is one of only two E2 enzymes that can ubiquitinate substrates in an E3-independent manner. The E2/E3 hybrid targets and multi-monoubiquitinates a multitude of orphan proteins; however, the mechanisms underlying substrate specificity and ubiquitin transfer remain poorly understood. By combining structural and biochemical approaches, we show that substrate binding by UBE2O occurs through a conserved acidic pocket formed by the N-terminal SH3-like domains and that this platform allows the recruitment of a broad range of proteins. Furthermore, we identified specific residues in the catalytic UBC domain that position ubiquitin in a closed state, confirming its confirmation, and priming it for nucleophilic attack by the incoming substrate. Importantly, the activated E2 approximately Ub conjugate is protected by a tryptophan residue, avoiding premature hydrolysis. By incorporating these findings into the UBC domain of BIRC6 our data provide the molecular basis of how specialized E2/E3 hybrid proteins function as potent ubiquitination enzymes reminiscent of the catalytic principle of RING E3 ligases.
-Authors: Kordic, D., Williams, T.L., Luiza Deszcz, L., Ehrmann, J., Arnese, R., Meinhart, A., Clausen, T.
+Structural basis for substrate recruitment and catalytic ubiquitin transfer by the E2/E3 hybrid enzyme UBE2O.,Kordic D, Williams TL, Deszcz L, Ehrmann JF, Arnese R, Schleiffer A, Clausen T, Meinhart A J Biol Chem. 2025 Dec 17;302(2):111073. doi: 10.1016/j.jbc.2025.111073. PMID:41419192<ref>PMID:41419192</ref>
-Description: To be published
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Arnese, R]]
+<div class="pdbe-citations 9quf" style="background-color:#fffaf0;"></div>
-[[Category: Kordic, D]]
+== References ==
-[[Category: Clausen, T]]
+<references/>
-[[Category: Ehrmann, J]]
+__TOC__
-[[Category: Luiza Deszcz, L]]
+</StructureSection>
-[[Category: Meinhart, A]]
+[[Category: Large Structures]]
-[[Category: Williams, T.L]]
+[[Category: Pyrenophora tritici-repentis]]
+[[Category: Arnese R]]
+[[Category: Clausen T]]
+[[Category: Ehrmann J]]
+[[Category: Kordic D]]
+[[Category: Luiza Deszcz L]]
+[[Category: Meinhart A]]
+[[Category: Williams TL]]