{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T16:12:09Z","timestamp":1788970329172,"version":"build-2803163510"},"reference-count":53,"publisher":"American Chemical Society (ACS)","issue":"35","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019180","name":"HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["101003289Ubl-tool to K.L."],"award-info":[{"award-number":["101003289Ubl-tool to K.L."]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003006","name":"Eidgen?ssische Technische Hochschule Z?rich","doi-asserted-by":"publisher","award":["to K.L."],"award-info":[{"award-number":["to K.L."]}],"id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015754","name":"Stiftung der Deutschen Wirtschaft","doi-asserted-by":"publisher","award":["to A.H."],"award-info":[{"award-number":["to A.H."]}],"id":[{"id":"10.13039\/501100015754","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Research Council (DFG)","award":["SFB 1309-325871075 to M.G."],"award-info":[{"award-number":["SFB 1309-325871075 to M.G."]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Activity-based probes (ABPs) have become powerful tools for profiling enzymes that write and erase ubiquitin (Ub) and ubiquitin-like modifier (Ubl) signals. Extending this strategy to small ubiquitin-like modifier (SUMO)-specific proteases in defined substrate contexts remains challenging, because site-specific SUMO attachment must be combined with precise electrophile placement near the scissile isopeptide linkage. Here, we introduce a sortase-enabled chemoenzymatic platform for generating SUMO ABPs ranging from monoSUMO probes to native-like SUMO-substrate conjugates. The engineered sortase Srt2A ligates SUMO variants to glycine-bearing electrophiles, providing facile access to monoSUMO probes that trap deSUMOylases in vitro, in cellular lysates, and in living cells. To generate SUMO-substrate probes, we develop AzGVAisoK, a genetically encodable bifunctional lysine derivative containing both an azide-protected sortase handle and a vinyl amide electrophile. An engineered pyrrolysyl-tRNA synthetase\/tRNA pair enables its site-specific incorporation into target proteins. Subsequent on-protein Staudinger reduction and sortase-mediated SUMOylation furnish defined SUMO-substrate ABPs under mild aqueous conditions. Applying this platform to PCNA and K11-linked diSUMO conjugates revealed distinct deSUMOylase trapping profiles governed by SUMO paralog and acceptor-substrate contexts. This work establishes a modular route to native-like SUMO probes and provides a general strategy for interrogating context-dependent enzyme recognition in Ubl signaling.<\/jats:p>","DOI":"10.1021\/jacs.6c10081","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T18:02:09Z","timestamp":1786557729000},"page":"38092-38101","source":"Crossref","is-referenced-by-count":0,"title":["A Genetically Encoded\nElectrophilic Lysine Derivative\nEnables Sortase-Mediated Assembly of SUMO Activity-Based Probes"],"prefix":"10.1021","volume":"148","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-3280-4129","authenticated-orcid":true,"given":"Vera","family":"Wanka","sequence":"first","affiliation":[{"name":"ETH Zurich , , ,","place":["Zurich, Switzerland, 8093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denys","family":"Kvasha","sequence":"additional","affiliation":[{"name":"ETH Zurich , , ,","place":["Zurich, Switzerland, 8093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1861-7968","authenticated-orcid":true,"given":"Marko","family":"Cigler","sequence":"additional","affiliation":[{"name":"Technical University of Munich , , ,","place":["Garching, Germany, 85748"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristina","family":"Heymes-Krauskopf","sequence":"additional","affiliation":[{"name":"ETH Zurich , , ,","place":["Zurich, Switzerland, 8093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Ruckgaber","sequence":"additional","affiliation":[{"name":"ETH Zurich , , ,","place":["Zurich, Switzerland, 8093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Heider","sequence":"additional","affiliation":[{"name":"Technical University of Munich , , ,","place":["Garching, Germany, 85748"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8628-183X","authenticated-orcid":true,"given":"Maximilian","family":"Fottner","sequence":"additional","affiliation":[{"name":"ETH Zurich , , ,","place":["Zurich, Switzerland, 8093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1660-340X","authenticated-orcid":true,"given":"Michael","family":"Groll","sequence":"additional","affiliation":[{"name":"Technical University of Munich , , ,","place":["Garching, Germany, 85748"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1318-6567","authenticated-orcid":true,"given":"Kathrin","family":"Lang","sequence":"additional","affiliation":[{"name":"ETH Zurich , , ,","place":["Zurich, Switzerland, 8093"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"2026090910093384300_cit1","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1146\/annurev-biochem-060310-170328","article-title":"The Ubiquitin Code","volume":"81","author":"Komander","year":"2012","journal-title":"Annu. Rev. Biochem."},{"key":"2026090910093384300_cit2","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1021\/acs.chemrev.6b00737","article-title":"Ubiquitin-Like Protein\nConjugation: Structures, Chemistry,\nand Mechanism","volume":"118","author":"Cappadocia","year":"2018","journal-title":"Chem. Rev."},{"key":"2026090910093384300_cit3","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nrm.2016.81","article-title":"A Comprehensive\nCompilation of Sumo Proteomics","volume":"17","author":"Hendriks","year":"2016","journal-title":"Nat. Rev. Mol.\nCell Biol."},{"key":"2026090910093384300_cit4","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1038\/s41580-022-00500-y","article-title":"Signalling\nMechanisms and Cellular Functions of Sumo","volume":"23","author":"Vertegaal","year":"2022","journal-title":"Nat.\nRev. Mol. Cell Biol."},{"key":"2026090910093384300_cit5","doi-asserted-by":"publisher","first-page":"6043","DOI":"10.1093\/nar\/gkab280","article-title":"Histone Sumoylation and Chromatin\nDynamics","volume":"49","author":"Ryu","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2026090910093384300_cit6","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1146\/annurev-biochem-061909-093311","article-title":"Sumoylation: A Regulatory\nProtein Modification in Health\nand Disease","volume":"82","author":"Flotho","year":"2013","journal-title":"Annu. Rev. Biochem."},{"key":"2026090910093384300_cit7","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1074\/mcp.M700173-MCP200","article-title":"In Vivo\nIdentification of Human Small Ubiquitin-Like\nModifier Polymerization Sites by High Accuracy Mass Spectrometry and\nan in Vitro to in Vivo Strategy","volume":"7","author":"Matic","year":"2008","journal-title":"Mol. Cell Proteomics"},{"key":"2026090910093384300_cit8","doi-asserted-by":"publisher","first-page":"3678","DOI":"10.1038\/s41467-019-11549-3","article-title":"Arkadia\/Rnf111 Is\na Sumo-Targeted Ubiquitin Ligase with Preference for Substrates Marked\nwith Sumo1-Capped Sumo2\/3 Chain","volume":"10","author":"Sriramachandran","year":"2019","journal-title":"Nat. Commun."},{"key":"2026090910093384300_cit9","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1186\/s13059-014-0422-2","article-title":"Sumo-Specific Proteases\/Isopeptidases:\nSenps and Beyond","volume":"15","author":"Nayak","year":"2014","journal-title":"Genome Biol."},{"key":"2026090910093384300_cit10","doi-asserted-by":"publisher","first-page":"jcs211904","DOI":"10.1242\/jcs.211904","article-title":"Sumo-Specific\nProteases and Isopeptidases\nof the Senp Family at a Glance","volume":"131","author":"Kunz","year":"2018","journal-title":"J. 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Soc. Rev."},{"key":"2026090910093384300_cit15","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1021\/acschembio.9b00402","article-title":"Chemical Tools and\nBiochemical Assays for Sumo Specific Proteases (Senps)","volume":"14","author":"Jia","year":"2019","journal-title":"ACS Chem. Biol."},{"key":"2026090910093384300_cit16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.21775\/cimb.037.001","article-title":"Cracking the Ubiquitin\nCode: The\nUbiquitin Toolbox","volume":"37","author":"Mulder","year":"2020","journal-title":"Curr. Issues Mol. Biol."},{"key":"2026090910093384300_cit17","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1111\/febs.14039","article-title":"Activity-Based Probes\nfor the Ubiquitin Conjugation-Deconjugation Machinery: New Chemistries,\nNew Tools, and New Insights","volume":"284","author":"Hewings","year":"2017","journal-title":"FEBS J."},{"key":"2026090910093384300_cit18","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1042\/BJ20151195","article-title":"Chemical Ubiquitination\nfor Decrypting a Cellular Code","volume":"473","author":"Stanley","year":"2016","journal-title":"Biochem. 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Sci."},{"key":"2026090910093384300_cit22","doi-asserted-by":"publisher","first-page":"756","DOI":"10.1021\/acscentsci.2c00203","article-title":"Facile\nPreparation of Ufmylation Activity-Based Probes by Chemoselective\nInstallation of Electrophiles at the C-Terminus of Recombinant Ufm1","volume":"8","author":"Tolmachova","year":"2022","journal-title":"ACS Cent Sci."},{"key":"2026090910093384300_cit23","doi-asserted-by":"publisher","first-page":"14164","DOI":"10.1002\/anie.201809232","article-title":"Generation\nof the Ufm1 Toolkit for Profiling Ufm1-Specific Proteases and Ligases","volume":"57","author":"Witting","year":"2018","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026090910093384300_cit24","doi-asserted-by":"publisher","first-page":"10148","DOI":"10.1039\/C9OB02127B","article-title":"Total Chemical\nSynthesis of Murine Isg15 and an Activity-Based Probe with Physiological\nBinding Properties","volume":"17","author":"Xin","year":"2019","journal-title":"Org. Biomol Chem."},{"key":"2026090910093384300_cit25","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1002\/cbic.201402012","article-title":"A Native Chemical Ligation\nHandle That Enables the Synthesis of Advanced Activity-Based Probes:\nDiubiquitin as a Case Study","volume":"15","author":"Mulder","year":"2014","journal-title":"Chembiochem"},{"key":"2026090910093384300_cit26","doi-asserted-by":"publisher","first-page":"5645","DOI":"10.1002\/anie.201800032","article-title":"Activity-Based Probes\nDeveloped by Applying a Sequential Dehydroalanine Formation Strategy\nto Expressed Proteins Reveal a Potential Alpha-Globin-Modulating Deubiquitinase","volume":"57","author":"Meledin","year":"2018","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026090910093384300_cit27","doi-asserted-by":"publisher","first-page":"7859","DOI":"10.1039\/C8SC01573B","article-title":"Activity-Based Ubiquitin-Protein Probes Reveal Target\nProtein Specificity of Deubiquitinating Enzymes","volume":"9","author":"Gong","year":"2018","journal-title":"Chem. Sci."},{"key":"2026090910093384300_cit28","doi-asserted-by":"publisher","first-page":"e03578","DOI":"10.1002\/chem.202503578","article-title":"Chemical\nSynthesis of Ubiquitinated Proteins and Ubiquitin\nProbes for Biochemical and Functional Analysis","volume":"32","author":"Li","year":"2026","journal-title":"Chemistry"},{"key":"2026090910093384300_cit29","doi-asserted-by":"publisher","first-page":"e03597","DOI":"10.1002\/chem.202503597","article-title":"Synthetic Strategies\nfor Activity-Based\nProbes to Decode Ubiquitin-Like Modifiers","author":"Chanda","year":"2026","journal-title":"Chemistry"},{"key":"2026090910093384300_cit30","doi-asserted-by":"publisher","first-page":"13343","DOI":"10.1073\/pnas.1411179111","article-title":"Reprogramming\nthe Specificity of Sortase Enzymes","volume":"111","author":"Dorr","year":"2014","journal-title":"Proc. Natl.\nAcad. Sci. U.S.A."},{"key":"2026090910093384300_cit31","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41589-019-0227-4","article-title":"Site-Specific\nUbiquitylation and Sumoylation Using Genetic-Code Expansion and Sortase","volume":"15","author":"Fottner","year":"2019","journal-title":"Nat. Chem. Biol."},{"key":"2026090910093384300_cit32","doi-asserted-by":"publisher","first-page":"6515","DOI":"10.1038\/s41467-021-26812-9","article-title":"A Modular Toolbox to\nGenerate Complex Polymeric Ubiquitin Architectures\nUsing Orthogonal Sortase Enzymes","volume":"12","author":"Fottner","year":"2021","journal-title":"Nat. Commun."},{"key":"2026090910093384300_cit33","doi-asserted-by":"publisher","first-page":"2867","DOI":"10.1021\/ja309802n","article-title":"On Terminal Alkynes\nThat Can React with Active-Site Cysteine Nucleophiles in Proteases","volume":"135","author":"Ekkebus","year":"2013","journal-title":"J. Am. Chem. Soc."},{"key":"2026090910093384300_cit34","doi-asserted-by":"publisher","first-page":"8958","DOI":"10.1002\/anie.201803483","article-title":"Total Chemical Synthesis of Sumo\nand Sumo-Based Probes for Profiling the Activity of Sumo-Specific\nProteases","volume":"57","author":"Mulder","year":"2018","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026090910093384300_cit35","doi-asserted-by":"publisher","first-page":"1416","DOI":"10.1002\/cbic.201200261","article-title":"Profiling\nUbiquitin Linkage Specificities of Deubiquitinating\nEnzymes with Branched Ubiquitin Isopeptide Probes","volume":"13","author":"Ipho\u0308fer","year":"2012","journal-title":"Chembiochem"},{"key":"2026090910093384300_cit36","doi-asserted-by":"publisher","first-page":"592","DOI":"10.3389\/fchem.2019.00592","article-title":"Comprehensive Landscape of Active Deubiquitinating\nEnzymes Profiled by Advanced Chemoproteomics","volume":"7","author":"Pinto-Ferna\u0301ndez","year":"2019","journal-title":"Front. Chem."},{"key":"2026090910093384300_cit37","doi-asserted-by":"publisher","first-page":"32045","DOI":"10.1074\/jbc.M805655200","article-title":"Structure of the Human\nSenp7 Catalytic Domain and Poly-Sumo\nDeconjugation Activities for Senp6 and Senp7","volume":"283","author":"Lima","year":"2008","journal-title":"J. Biol. Chem."},{"key":"2026090910093384300_cit38","doi-asserted-by":"publisher","first-page":"3987","DOI":"10.1038\/s41467-019-11773-x","article-title":"The\nPoly-Sumo2\/3 Protease Senp6 Enables Assembly of the Constitutive Centromere-Associated\nNetwork by Group Desumoylation","volume":"10","author":"Liebelt","year":"2019","journal-title":"Nat. Commun."},{"key":"2026090910093384300_cit39","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1042\/BJ20100504","article-title":"Distribution\nand Paralogue Specificity of Mammalian Desumoylating Enzymes","volume":"430","author":"Kolli","year":"2010","journal-title":"Biochem. J."},{"key":"2026090910093384300_cit40","doi-asserted-by":"publisher","first-page":"1819","DOI":"10.1038\/s41467-022-29485-0","article-title":"Structural Basis for the Sumo Protease\nActivity of the Atypical Ubiquitin-Specific Protease Uspl1","volume":"13","author":"Li","year":"2022","journal-title":"Nat. Commun."},{"key":"2026090910093384300_cit41","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/embor.2012.3","article-title":"Desumoylating\nIsopeptidase: A Second\nClass of Sumo Protease","volume":"13","author":"Shin","year":"2012","journal-title":"EMBO Rep."},{"key":"2026090910093384300_cit42","doi-asserted-by":"publisher","first-page":"112701","DOI":"10.1016\/j.cclet.2026.112701","article-title":"Cellular\nSynthesis of Ubiquitin-Based Probes for Compartment-Specific Deubiquitinase\nProfiling","author":"Chen","year":"2026","journal-title":"Chin. Chem. Lett."},{"key":"2026090910093384300_cit43","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/s41586-025-09576-w","article-title":"Hijacking a Bacterial\nAbc Transporter for Genetic Code Expansion","volume":"647","author":"Iype","year":"2025","journal-title":"Nature"},{"key":"2026090910093384300_cit44","doi-asserted-by":"publisher","first-page":"2706","DOI":"10.1038\/s41467-018-05236-y","article-title":"Sumo2 Conjugation\nof Pcna Facilitates Chromatin Remodeling to Resolve Transcription-Replication\nConflicts","volume":"9","author":"Li","year":"2018","journal-title":"Nat. Commun."},{"key":"2026090910093384300_cit45","doi-asserted-by":"publisher","first-page":"6049","DOI":"10.1093\/nar\/gks256","article-title":"Role of Sumo Modification\nof Human PCNA at Stalled Replication Fork","volume":"40","author":"Gali","year":"2012","journal-title":"Nucleic\nAcids Res."},{"key":"2026090910093384300_cit46","doi-asserted-by":"publisher","first-page":"5893","DOI":"10.1038\/s41467-023-41623-w","article-title":"Senp6\nRegulates Localization and Nuclear Condensation of DNA Damage Response\nProteins by Group Desumoylation","volume":"14","author":"Claessens","year":"2023","journal-title":"Nat. Commun."},{"key":"2026090910093384300_cit47","doi-asserted-by":"publisher","first-page":"2306","DOI":"10.1093\/hmg\/ddy135","article-title":"Sumoylation\nof Xrcc1 Activated by\nPoly (ADP-ribosyl)ation Regulates DNA Repair","volume":"27","author":"Hu","year":"2018","journal-title":"Hum. Mol. Genet."},{"key":"2026090910093384300_cit48","doi-asserted-by":"publisher","first-page":"EMBJ201899242","DOI":"10.15252\/embj.201899242","article-title":"Sumoylation Coordinates Berosome\nAssembly in Active DNA Demethylation During Cell Differentiation","volume":"38","author":"Steinacher","year":"2019","journal-title":"EMBO J."},{"key":"2026090910093384300_cit49","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1042\/BST20230862","article-title":"Sumo and the DNA Damage Response","volume":"52","author":"Bhachoo","year":"2024","journal-title":"Biochem. Soc. Trans."},{"key":"2026090910093384300_cit50","doi-asserted-by":"publisher","first-page":"13118","DOI":"10.1021\/jacs.2c02191","article-title":"Site-Specific Protein Labeling and\nGeneration of Defined Ubiquitin-Protein Conjugates Using an Asparaginyl\nEndopeptidase","volume":"144","author":"Fottner","year":"2022","journal-title":"J. Am. Chem. Soc."},{"key":"2026090910093384300_cit51","doi-asserted-by":"publisher","first-page":"11399","DOI":"10.1073\/pnas.1101046108","article-title":"A General\nStrategy for the Evolution\nof Bond-Forming Enzymes Using Yeast Display","volume":"108","author":"Chen","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026090910093384300_cit52","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/s41589-020-00706-1","article-title":"Laboratory\nEvolution of a Sortase Enzyme That Modifies Amyloid-Beta Protein","volume":"17","author":"Podracky","year":"2021","journal-title":"Nat. Chem. Biol."},{"key":"2026090910093384300_cit53","doi-asserted-by":"publisher","first-page":"17536","DOI":"10.1021\/ja205630g","article-title":"Directed Evolution\nof Sortase a Mutants\nwith Altered Substrate Selectivity Profiles","volume":"133","author":"Piotukh","year":"2011","journal-title":"J. Am. Chem. Soc."}],"container-title":["Journal of the American\nChemical Society"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jacs.6c10081","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jacsat\/article-pdf\/148\/35\/38092\/66516761\/jacs.6c10081.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jacsat\/article-pdf\/148\/35\/38092\/66516761\/jacs.6c10081.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T15:28:08Z","timestamp":1788967688000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jacsat\/article\/148\/35\/38092\/5253731\/A-Genetically-Encoded-Electrophilic-Lysine"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,12]]},"references-count":53,"journal-issue":{"issue":"35","published-online":{"date-parts":[[2026,8,12]]},"published-print":{"date-parts":[[2026,9,9]]}},"URL":"https:\/\/doi.org\/10.1021\/jacs.6c10081","relation":{},"ISSN":["0002-7863","1520-5126"],"issn-type":[{"value":"0002-7863","type":"print"},{"value":"1520-5126","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,12]]}}}