8oyp

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

Structural highlights

8oyp is a 4 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 2.44Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q1D4U9_MYXXD UBP11_HUMAN Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains. Inhibits the degradation of target proteins by the proteasome. Plays a role in the regulation of pathways leading to NF-kappa-B activation. Plays a role in the regulation of DNA repair after double-stranded DNA breaks.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Ubiquitin specific proteases (USPs) are crucial for controlling cellular proteostasis and signaling pathways but how deubiquitination is selective remains poorly understood, in particular between paralogues. Here, we developed a fusion tag method by mining the Protein Data Bank and trapped USP11, a key regulator of DNA double-strand break repair, in complex with a novel engineered substrate mimetic. Together, this enabled structure determination of USP11 as a Michaelis-like complex that revealed key S1 and S1' binding site interactions with a substrate. Combined mutational, enzymatic, and binding experiments identified Met(77) in linear di-ubiquitin as a significant residue that leads to substrate discrimination. We identified an aspartate 'gatekeeper' residue in the S1' site of USP11 as a contributing feature for discriminating against linear di-ubiquitin. When mutated to a glycine, the corresponding residue in paralogue USP15, USP11 acquired elevated activity towards linear di-ubiquitin in gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralogue-specific differences impacting di-ubiquitin cleavage rates. The results advance our understanding of the molecular basis for the higher selectivity of USP11 compared to USP15 and may aid targeted inhibitor development. Moreover, the reported carrier-based crystallization strategy may be applicable to other challenging targets.

Ubiquitin specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity.,Maurer SK, Mayer MP, Ward SJ, Boudjema S, Halawa M, Zhang J, Caulton SG, Emsley J, Dreveny I J Biol Chem. 2023 Sep 28:105300. doi: 10.1016/j.jbc.2023.105300. PMID:37777157^[6]

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

References

↑ Schoenfeld AR, Apgar S, Dolios G, Wang R, Aaronson SA. BRCA2 is ubiquitinated in vivo and interacts with USP11, a deubiquitinating enzyme that exhibits prosurvival function in the cellular response to DNA damage. Mol Cell Biol. 2004 Sep;24(17):7444-55. PMID:15314155 doi:http://dx.doi.org/10.1128/MCB.24.17.7444-7455.2004
↑ Yamaguchi T, Kimura J, Miki Y, Yoshida K. The deubiquitinating enzyme USP11 controls an IkappaB kinase alpha (IKKalpha)-p53 signaling pathway in response to tumor necrosis factor alpha (TNFalpha). J Biol Chem. 2007 Nov 23;282(47):33943-8. Epub 2007 Sep 26. PMID:17897950 doi:http://dx.doi.org/10.1074/jbc.M706282200
↑ Lin CH, Chang HS, Yu WC. USP11 stabilizes HPV-16E7 and further modulates the E7 biological activity. J Biol Chem. 2008 Jun 6;283(23):15681-8. doi: 10.1074/jbc.M708278200. Epub 2008, Apr 11. PMID:18408009 doi:http://dx.doi.org/10.1074/jbc.M708278200
↑ Sun W, Tan X, Shi Y, Xu G, Mao R, Gu X, Fan Y, Yu Y, Burlingame S, Zhang H, Rednam SP, Lu X, Zhang T, Fu S, Cao G, Qin J, Yang J. USP11 negatively regulates TNFalpha-induced NF-kappaB activation by targeting on IkappaBalpha. Cell Signal. 2010 Mar;22(3):386-94. doi: 10.1016/j.cellsig.2009.10.008. Epub . PMID:19874889 doi:http://dx.doi.org/10.1016/j.cellsig.2009.10.008
↑ Wiltshire TD, Lovejoy CA, Wang T, Xia F, O'Connor MJ, Cortez D. Sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition identifies ubiquitin-specific peptidase 11 (USP11) as a regulator of DNA double-strand break repair. J Biol Chem. 2010 May 7;285(19):14565-71. doi: 10.1074/jbc.M110.104745. Epub 2010, Mar 15. PMID:20233726 doi:http://dx.doi.org/10.1074/jbc.M110.104745
↑ Maurer SK, Mayer MP, Ward SJ, Boudjema S, Halawa M, Zhang J, Caulton SG, Emsley J, Dreveny I. Ubiquitin specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity. J Biol Chem. 2023 Sep 28:105300. PMID:37777157 doi:10.1016/j.jbc.2023.105300

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/8oyp"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8oyp is ON HOLD
+==Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic==
+<StructureSection load='8oyp' size='340' side='right'caption='[[8oyp]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8oyp]] is a 4 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=8OYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8OYP 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]] 2.44&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSU:CYSTEINE-S-SULFONIC+ACID'>CSU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=8oyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8oyp OCA], [https://pdbe.org/8oyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8oyp RCSB], [https://www.ebi.ac.uk/pdbsum/8oyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8oyp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q1D4U9_MYXXD Q1D4U9_MYXXD] [https://www.uniprot.org/uniprot/UBP11_HUMAN UBP11_HUMAN] Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains. Inhibits the degradation of target proteins by the proteasome. Plays a role in the regulation of pathways leading to NF-kappa-B activation. Plays a role in the regulation of DNA repair after double-stranded DNA breaks.<ref>PMID:15314155</ref> <ref>PMID:17897950</ref> <ref>PMID:18408009</ref> <ref>PMID:19874889</ref> <ref>PMID:20233726</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ubiquitin specific proteases (USPs) are crucial for controlling cellular proteostasis and signaling pathways but how deubiquitination is selective remains poorly understood, in particular between paralogues. Here, we developed a fusion tag method by mining the Protein Data Bank and trapped USP11, a key regulator of DNA double-strand break repair, in complex with a novel engineered substrate mimetic. Together, this enabled structure determination of USP11 as a Michaelis-like complex that revealed key S1 and S1' binding site interactions with a substrate. Combined mutational, enzymatic, and binding experiments identified Met(77) in linear di-ubiquitin as a significant residue that leads to substrate discrimination. We identified an aspartate 'gatekeeper' residue in the S1' site of USP11 as a contributing feature for discriminating against linear di-ubiquitin. When mutated to a glycine, the corresponding residue in paralogue USP15, USP11 acquired elevated activity towards linear di-ubiquitin in gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralogue-specific differences impacting di-ubiquitin cleavage rates. The results advance our understanding of the molecular basis for the higher selectivity of USP11 compared to USP15 and may aid targeted inhibitor development. Moreover, the reported carrier-based crystallization strategy may be applicable to other challenging targets.
-Authors:
+Ubiquitin specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity.,Maurer SK, Mayer MP, Ward SJ, Boudjema S, Halawa M, Zhang J, Caulton SG, Emsley J, Dreveny I J Biol Chem. 2023 Sep 28:105300. doi: 10.1016/j.jbc.2023.105300. PMID:37777157<ref>PMID:37777157</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8oyp" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Caulton SG]]
+[[Category: Dreveny I]]
+[[Category: Emsley J]]
+[[Category: Maurer SK]]
+[[Category: Ward SJ]]

8oyp

From Proteopedia

Current revision

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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