8cms

From Proteopedia

(Difference between revisions)

Current revision

OTUB2 in covalent complex with LN5P45

Structural highlights

8cms is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.77Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OTUB2_HUMAN Hydrolase that can remove conjugated ubiquitin from proteins in vitro and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, with a preference for 'Lys-63'-linked polyubiquitin chains.^[1] ^[2]

Publication Abstract from PubMed

Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.

Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2.,Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP ACS Chem Biol. 2023 Sep 15;18(9):2003-2013. doi: 10.1021/acschembio.3c00227. Epub , 2023 Aug 29. PMID:37642399^[3]

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

References

↑ Balakirev MY, Tcherniuk SO, Jaquinod M, Chroboczek J. Otubains: a new family of cysteine proteases in the ubiquitin pathway. EMBO Rep. 2003 May;4(5):517-22. PMID:12704427 doi:10.1038/sj.embor.embor824
↑ Edelmann MJ, Iphofer A, Akutsu M, Altun M, di Gleria K, Kramer HB, Fiebiger E, Dhe-Paganon S, Kessler BM. Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem J. 2009 Mar 1;418(2):379-90. PMID:18954305 doi:10.1042/BJ20081318
↑ Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP. Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2. ACS Chem Biol. 2023 Sep 15;18(9):2003-2013. PMID:37642399 doi:10.1021/acschembio.3c00227

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8cms"

Categories: Homo sapiens | Large Structures | Gan J | De Vries J

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8cms is ON HOLD  until Paper Publication
+==OTUB2 in covalent complex with LN5P45==
+<StructureSection load='8cms' size='340' side='right'caption='[[8cms]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8cms]] is a 1 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=8CMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CMS 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]] 1.77&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=V2X:(1~{S},2~{S})-~{N}-ethanoyl-2-(3-methylphenyl)cyclopropane-1-carbohydrazide'>V2X</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=8cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8cms OCA], [https://pdbe.org/8cms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8cms RCSB], [https://www.ebi.ac.uk/pdbsum/8cms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8cms ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OTUB2_HUMAN OTUB2_HUMAN] Hydrolase that can remove conjugated ubiquitin from proteins in vitro and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, with a preference for 'Lys-63'-linked polyubiquitin chains.<ref>PMID:12704427</ref> <ref>PMID:18954305</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.
-Authors: Gan, J., de Vries, J.
+Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2.,Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP ACS Chem Biol. 2023 Sep 15;18(9):2003-2013. doi: 10.1021/acschembio.3c00227. Epub , 2023 Aug 29. PMID:37642399<ref>PMID:37642399</ref>
-Description: OTUB2 in covalent complex with LN5P45
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Gan, J]]
+<div class="pdbe-citations 8cms" style="background-color:#fffaf0;"></div>
-[[Category: De Vries, J]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Gan J]]
+[[Category: De Vries J]]

8cms

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Current revision

OTUB2 in covalent complex with LN5P45

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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