Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10
Abstract Doa10 (MARCHF6 in metazoans) is a large polytopic membrane-embedded E3 ubiquitin ligase in the endoplasmic reticulum (ER) that plays an important role in quality control of cytosolic and ER proteins. Although Doa10 is highly conserved across eukaryotes, it is not understood how Doa10 recogn...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-46409-2 |
| _version_ | 1797259175312490496 |
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| author | Kevin Wu Samuel Itskanov Diane L. Lynch Yuanyuan Chen Aasha Turner James C. Gumbart Eunyong Park |
| author_facet | Kevin Wu Samuel Itskanov Diane L. Lynch Yuanyuan Chen Aasha Turner James C. Gumbart Eunyong Park |
| author_sort | Kevin Wu |
| collection | DOAJ |
| description | Abstract Doa10 (MARCHF6 in metazoans) is a large polytopic membrane-embedded E3 ubiquitin ligase in the endoplasmic reticulum (ER) that plays an important role in quality control of cytosolic and ER proteins. Although Doa10 is highly conserved across eukaryotes, it is not understood how Doa10 recognizes its substrates. Here, we define the substrate recognition mechanism of Doa10 by structural and functional analyses on Saccharomyces cerevisiae Doa10 and its model substrates. Cryo-EM analysis shows that Doa10 has unusual architecture with a large lipid-filled central cavity, and its conserved middle domain forms an additional water-filled lateral tunnel open to the cytosol. Our biochemical data and molecular dynamics simulations suggest that the entrance of the substrate’s degron peptide into the lateral tunnel is required for efficient polyubiquitination. The N- and C-terminal membrane domains of Doa10 seem to form fence-like features to restrict polyubiquitination to those proteins that can access the central cavity and lateral tunnel. Our study reveals how extended hydrophobic sequences at the termini of substrate proteins are recognized by Doa10 as a signal for quality control. |
| first_indexed | 2024-04-24T23:05:15Z |
| format | Article |
| id | doaj.art-be2e86f1e3154106b7a2c1e7f41a8492 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T23:05:15Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-be2e86f1e3154106b7a2c1e7f41a84922024-03-17T12:31:16ZengNature PortfolioNature Communications2041-17232024-03-0115111810.1038/s41467-024-46409-2Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10Kevin Wu0Samuel Itskanov1Diane L. Lynch2Yuanyuan Chen3Aasha Turner4James C. Gumbart5Eunyong Park6Department of Molecular and Cell Biology, University of CaliforniaBiophysics Graduate Program, University of CaliforniaSchool of Physics and School of Chemistry and Biochemistry, Georgia Institute of TechnologyDepartment of Molecular and Cell Biology, University of CaliforniaDepartment of Molecular and Cell Biology, University of CaliforniaSchool of Physics and School of Chemistry and Biochemistry, Georgia Institute of TechnologyDepartment of Molecular and Cell Biology, University of CaliforniaAbstract Doa10 (MARCHF6 in metazoans) is a large polytopic membrane-embedded E3 ubiquitin ligase in the endoplasmic reticulum (ER) that plays an important role in quality control of cytosolic and ER proteins. Although Doa10 is highly conserved across eukaryotes, it is not understood how Doa10 recognizes its substrates. Here, we define the substrate recognition mechanism of Doa10 by structural and functional analyses on Saccharomyces cerevisiae Doa10 and its model substrates. Cryo-EM analysis shows that Doa10 has unusual architecture with a large lipid-filled central cavity, and its conserved middle domain forms an additional water-filled lateral tunnel open to the cytosol. Our biochemical data and molecular dynamics simulations suggest that the entrance of the substrate’s degron peptide into the lateral tunnel is required for efficient polyubiquitination. The N- and C-terminal membrane domains of Doa10 seem to form fence-like features to restrict polyubiquitination to those proteins that can access the central cavity and lateral tunnel. Our study reveals how extended hydrophobic sequences at the termini of substrate proteins are recognized by Doa10 as a signal for quality control.https://doi.org/10.1038/s41467-024-46409-2 |
| spellingShingle | Kevin Wu Samuel Itskanov Diane L. Lynch Yuanyuan Chen Aasha Turner James C. Gumbart Eunyong Park Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10 Nature Communications |
| title | Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10 |
| title_full | Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10 |
| title_fullStr | Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10 |
| title_full_unstemmed | Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10 |
| title_short | Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10 |
| title_sort | substrate recognition mechanism of the endoplasmic reticulum associated ubiquitin ligase doa10 |
| url | https://doi.org/10.1038/s41467-024-46409-2 |
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