Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA
Abstract Pupylation, a post-translational modification found in Mycobacterium tuberculosis and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-40807-8 |
| _version_ | 1797558227631603712 |
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| author | Matthias F. Block Cyrille L. Delley Lena M. L. Keller Timo T. Stuehlinger Eilika Weber-Ban |
| author_facet | Matthias F. Block Cyrille L. Delley Lena M. L. Keller Timo T. Stuehlinger Eilika Weber-Ban |
| author_sort | Matthias F. Block |
| collection | DOAJ |
| description | Abstract Pupylation, a post-translational modification found in Mycobacterium tuberculosis and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like ubiquitinated proteins in eukaryotes, are recruited for proteasomal degradation. Proteomic studies suggest that hundreds of potential pupylation targets are modified by the sole existing ligase PafA. This raises intriguing questions regarding the selectivity of this enzyme towards a diverse range of substrates. Here, we show that the availability of surface lysines alone is not sufficient for interaction between PafA and target proteins. By identifying the interacting residues at the pupylation site, we demonstrate that PafA recognizes authentic substrates via a structural recognition motif centered around exposed lysines. Through a combination of computational analysis, examination of available structures and pupylated proteomes, and biochemical experiments, we elucidate the mechanism by which PafA achieves recognition of a wide array of substrates while retaining selective protein turnover. |
| first_indexed | 2024-03-10T17:27:21Z |
| format | Article |
| id | doaj.art-5ea4dc9d802c4ca89e88933c0012a0d6 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-10T17:27:21Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-5ea4dc9d802c4ca89e88933c0012a0d62023-11-20T10:07:54ZengNature PortfolioNature Communications2041-17232023-08-0114111310.1038/s41467-023-40807-8Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafAMatthias F. Block0Cyrille L. Delley1Lena M. L. Keller2Timo T. Stuehlinger3Eilika Weber-Ban4ETH Zurich, Institute of Molecular Biology & BiophysicsETH Zurich, Institute of Molecular Biology & BiophysicsETH Zurich, Institute of Molecular Biology & BiophysicsETH Zurich, Institute of Molecular Biology & BiophysicsETH Zurich, Institute of Molecular Biology & BiophysicsAbstract Pupylation, a post-translational modification found in Mycobacterium tuberculosis and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like ubiquitinated proteins in eukaryotes, are recruited for proteasomal degradation. Proteomic studies suggest that hundreds of potential pupylation targets are modified by the sole existing ligase PafA. This raises intriguing questions regarding the selectivity of this enzyme towards a diverse range of substrates. Here, we show that the availability of surface lysines alone is not sufficient for interaction between PafA and target proteins. By identifying the interacting residues at the pupylation site, we demonstrate that PafA recognizes authentic substrates via a structural recognition motif centered around exposed lysines. Through a combination of computational analysis, examination of available structures and pupylated proteomes, and biochemical experiments, we elucidate the mechanism by which PafA achieves recognition of a wide array of substrates while retaining selective protein turnover.https://doi.org/10.1038/s41467-023-40807-8 |
| spellingShingle | Matthias F. Block Cyrille L. Delley Lena M. L. Keller Timo T. Stuehlinger Eilika Weber-Ban Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA Nature Communications |
| title | Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA |
| title_full | Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA |
| title_fullStr | Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA |
| title_full_unstemmed | Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA |
| title_short | Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA |
| title_sort | electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin like protein ligase pafa |
| url | https://doi.org/10.1038/s41467-023-40807-8 |
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