Mechanism and regulation of the Lys6-selective deubiquitinase USP30
Structural and biochemical analyses of human USP30 explain the basis of Lys6-linkage preference and regulation by PINK1 and Parkin, shedding light onto how USP30 can act as a brake on mitophagy. Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein...
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| Veröffentlicht in: | Nature structural & molecular biology 2017-11, Vol.24 (11), p.920-930 |
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| creator | Gersch, Malte Gladkova, Christina Schubert, Alexander F Michel, Martin A Maslen, Sarah Komander, David |
| description | Structural and biochemical analyses of human USP30 explain the basis of Lys6-linkage preference and regulation by PINK1 and Parkin, shedding light onto how USP30 can act as a brake on mitophagy.
Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes. |
| doi_str_mv | 10.1038/nsmb.3475 |
| format | Article |
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Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.</description><identifier>ISSN: 1545-9993</identifier><identifier>EISSN: 1545-9985</identifier><identifier>DOI: 10.1038/nsmb.3475</identifier><identifier>PMID: 28945249</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>101/58 ; 631/45/612/1240 ; 631/45/612/645 ; 631/535/1266 ; 631/80/39 ; Autophagy ; Biochemistry ; Biological Microscopy ; Chains ; Crystal structure ; Deubiquitinating Enzymes - chemistry ; Deubiquitinating Enzymes - metabolism ; Dismantling ; Drug development ; Genetic regulation ; Humans ; Interfaces ; Kinases ; Life Sciences ; Membrane Biology ; Mitochondria ; Mitochondrial Proteins - chemistry ; Mitochondrial Proteins - metabolism ; Parkin protein ; Phagocytosis ; Protein Binding ; Protein kinase ; Protein Kinases - metabolism ; Protein Structure ; Proteins ; PTEN-induced putative kinase ; Substrate Specificity ; Substrates ; Thiolester Hydrolases - chemistry ; Thiolester Hydrolases - metabolism ; Ubiquitin ; Ubiquitin - chemistry ; Ubiquitin - metabolism ; Ubiquitin-protein ligase ; Ubiquitin-Protein Ligases - metabolism ; Ubiquitin-specific proteinase ; Ubiquitination</subject><ispartof>Nature structural & molecular biology, 2017-11, Vol.24 (11), p.920-930</ispartof><rights>Springer Nature America, Inc. 2017</rights><rights>COPYRIGHT 2017 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Nov 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c605t-829ecd4c34daf0cd01ba297bdb55183be3c312ff863d025bc8b555ce07eecec93</citedby><cites>FETCH-LOGICAL-c605t-829ecd4c34daf0cd01ba297bdb55183be3c312ff863d025bc8b555ce07eecec93</cites><orcidid>0000-0002-8092-4320 ; 0000-0003-2767-9589</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28945249$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gersch, Malte</creatorcontrib><creatorcontrib>Gladkova, Christina</creatorcontrib><creatorcontrib>Schubert, Alexander F</creatorcontrib><creatorcontrib>Michel, Martin A</creatorcontrib><creatorcontrib>Maslen, Sarah</creatorcontrib><creatorcontrib>Komander, David</creatorcontrib><title>Mechanism and regulation of the Lys6-selective deubiquitinase USP30</title><title>Nature structural & molecular biology</title><addtitle>Nat Struct Mol Biol</addtitle><addtitle>Nat Struct Mol Biol</addtitle><description>Structural and biochemical analyses of human USP30 explain the basis of Lys6-linkage preference and regulation by PINK1 and Parkin, shedding light onto how USP30 can act as a brake on mitophagy.
Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.</description><subject>101/58</subject><subject>631/45/612/1240</subject><subject>631/45/612/645</subject><subject>631/535/1266</subject><subject>631/80/39</subject><subject>Autophagy</subject><subject>Biochemistry</subject><subject>Biological Microscopy</subject><subject>Chains</subject><subject>Crystal structure</subject><subject>Deubiquitinating Enzymes - chemistry</subject><subject>Deubiquitinating Enzymes - metabolism</subject><subject>Dismantling</subject><subject>Drug development</subject><subject>Genetic regulation</subject><subject>Humans</subject><subject>Interfaces</subject><subject>Kinases</subject><subject>Life Sciences</subject><subject>Membrane Biology</subject><subject>Mitochondria</subject><subject>Mitochondrial Proteins - chemistry</subject><subject>Mitochondrial Proteins - metabolism</subject><subject>Parkin protein</subject><subject>Phagocytosis</subject><subject>Protein Binding</subject><subject>Protein kinase</subject><subject>Protein Kinases - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature structural & molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gersch, Malte</au><au>Gladkova, Christina</au><au>Schubert, Alexander F</au><au>Michel, Martin A</au><au>Maslen, Sarah</au><au>Komander, David</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mechanism and regulation of the Lys6-selective deubiquitinase USP30</atitle><jtitle>Nature structural & molecular biology</jtitle><stitle>Nat Struct Mol Biol</stitle><addtitle>Nat Struct Mol Biol</addtitle><date>2017-11-01</date><risdate>2017</risdate><volume>24</volume><issue>11</issue><spage>920</spage><epage>930</epage><pages>920-930</pages><issn>1545-9993</issn><eissn>1545-9985</eissn><abstract>Structural and biochemical analyses of human USP30 explain the basis of Lys6-linkage preference and regulation by PINK1 and Parkin, shedding light onto how USP30 can act as a brake on mitophagy.
Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>28945249</pmid><doi>10.1038/nsmb.3475</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-8092-4320</orcidid><orcidid>https://orcid.org/0000-0003-2767-9589</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 101/58 631/45/612/1240 631/45/612/645 631/535/1266 631/80/39 Autophagy Biochemistry Biological Microscopy Chains Crystal structure Deubiquitinating Enzymes - chemistry Deubiquitinating Enzymes - metabolism Dismantling Drug development Genetic regulation Humans Interfaces Kinases Life Sciences Membrane Biology Mitochondria Mitochondrial Proteins - chemistry Mitochondrial Proteins - metabolism Parkin protein Phagocytosis Protein Binding Protein kinase Protein Kinases - metabolism Protein Structure Proteins PTEN-induced putative kinase Substrate Specificity Substrates Thiolester Hydrolases - chemistry Thiolester Hydrolases - metabolism Ubiquitin Ubiquitin - chemistry Ubiquitin - metabolism Ubiquitin-protein ligase Ubiquitin-Protein Ligases - metabolism Ubiquitin-specific proteinase Ubiquitination |
| title | Mechanism and regulation of the Lys6-selective deubiquitinase USP30 |
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