Structural insights into the RNA methyltransferase domain of METTL16
Abstract N 6-methyladenosine (m6A) is an abundant modification in messenger RNA and noncoding RNAs that affects RNA metabolism. Methyltransferase-like protein 16 (METTL16) is a recently confirmed m6A RNA methyltransferase that methylates U6 spliceosomal RNA and interacts with the 3′-terminal RNA tri...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2018-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-018-23608-8 |
| _version_ | 1818998767619145728 |
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| author | Agnieszka Ruszkowska Milosz Ruszkowski Zbigniew Dauter Jessica A. Brown |
| author_facet | Agnieszka Ruszkowska Milosz Ruszkowski Zbigniew Dauter Jessica A. Brown |
| author_sort | Agnieszka Ruszkowska |
| collection | DOAJ |
| description | Abstract N 6-methyladenosine (m6A) is an abundant modification in messenger RNA and noncoding RNAs that affects RNA metabolism. Methyltransferase-like protein 16 (METTL16) is a recently confirmed m6A RNA methyltransferase that methylates U6 spliceosomal RNA and interacts with the 3′-terminal RNA triple helix of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). Here, we present two X-ray crystal structures of the N-terminal methyltransferase domain (residues 1–291) of human METTL16 (METTL16_291): an apo structure at 1.9 Å resolution and a post-catalytic S-adenosylhomocysteine-bound complex at 2.1 Å resolution. The structures revealed a highly conserved Rossmann fold that is characteristic of Class I S-adenosylmethionine-dependent methyltransferases and a large, positively charged groove. This groove likely represents the RNA-binding site and it includes structural elements unique to METTL16. In-depth analysis of the active site led to a model of the methyl transfer reaction catalyzed by METTL16. In contrast to the major m6A methyltransferase heterodimer METTL3/METTL14, full-length METTL16 forms a homodimer and METTL16_291 exists as a monomer based on size-exclusion chromatography. A native gel-shift assay shows that METTL16 binds to the MALAT1 RNA triple helix, but monomeric METTL16_291 does not. Our results provide insights into the molecular structure of METTL16, which is distinct from METTL3/METTL14. |
| first_indexed | 2024-12-20T22:06:46Z |
| format | Article |
| id | doaj.art-c432554ac8cf4b92918adc32a9762164 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-20T22:06:46Z |
| publishDate | 2018-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-c432554ac8cf4b92918adc32a97621642022-12-21T19:25:15ZengNature PortfolioScientific Reports2045-23222018-03-018111310.1038/s41598-018-23608-8Structural insights into the RNA methyltransferase domain of METTL16Agnieszka Ruszkowska0Milosz Ruszkowski1Zbigniew Dauter2Jessica A. Brown3Department of Chemistry and Biochemistry, University of Notre DameSynchrotron Radiation Research Section of MCL, National Cancer InstituteSynchrotron Radiation Research Section of MCL, National Cancer InstituteDepartment of Chemistry and Biochemistry, University of Notre DameAbstract N 6-methyladenosine (m6A) is an abundant modification in messenger RNA and noncoding RNAs that affects RNA metabolism. Methyltransferase-like protein 16 (METTL16) is a recently confirmed m6A RNA methyltransferase that methylates U6 spliceosomal RNA and interacts with the 3′-terminal RNA triple helix of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). Here, we present two X-ray crystal structures of the N-terminal methyltransferase domain (residues 1–291) of human METTL16 (METTL16_291): an apo structure at 1.9 Å resolution and a post-catalytic S-adenosylhomocysteine-bound complex at 2.1 Å resolution. The structures revealed a highly conserved Rossmann fold that is characteristic of Class I S-adenosylmethionine-dependent methyltransferases and a large, positively charged groove. This groove likely represents the RNA-binding site and it includes structural elements unique to METTL16. In-depth analysis of the active site led to a model of the methyl transfer reaction catalyzed by METTL16. In contrast to the major m6A methyltransferase heterodimer METTL3/METTL14, full-length METTL16 forms a homodimer and METTL16_291 exists as a monomer based on size-exclusion chromatography. A native gel-shift assay shows that METTL16 binds to the MALAT1 RNA triple helix, but monomeric METTL16_291 does not. Our results provide insights into the molecular structure of METTL16, which is distinct from METTL3/METTL14.https://doi.org/10.1038/s41598-018-23608-8 |
| spellingShingle | Agnieszka Ruszkowska Milosz Ruszkowski Zbigniew Dauter Jessica A. Brown Structural insights into the RNA methyltransferase domain of METTL16 Scientific Reports |
| title | Structural insights into the RNA methyltransferase domain of METTL16 |
| title_full | Structural insights into the RNA methyltransferase domain of METTL16 |
| title_fullStr | Structural insights into the RNA methyltransferase domain of METTL16 |
| title_full_unstemmed | Structural insights into the RNA methyltransferase domain of METTL16 |
| title_short | Structural insights into the RNA methyltransferase domain of METTL16 |
| title_sort | structural insights into the rna methyltransferase domain of mettl16 |
| url | https://doi.org/10.1038/s41598-018-23608-8 |
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