Structural insights into the RNA methyltransferase domain of METTL16

Ruszkowska, Agnieszka; Ruszkowski, Milosz; Dauter, Zbigniew; Brown, Jessica A.

doi:10.1038/s41598-018-23608-8

Title: Structural insights into the RNA methyltransferase domain of METTL16

Journal Article · Wed Mar 28 00:00:00 EDT 2018 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-018-23608-8· OSTI ID:1431367

Ruszkowska, Agnieszka ^[1]; Ruszkowski, Milosz ^[2]; Dauter, Zbigniew ^[2]; Brown, Jessica A. ^[1]

Univ. of Notre Dame, IN (United States)
National Cancer Inst. (NCI), Argonne, IL (United States). Macromolecular Crystallography Lab., Synchrotron Radiation Research Section

N⁶-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-adenosylhomocysteinebound 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); Henry Luce Foundation; National Cancer Institute (NCI); USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institute of General Medical Sciences (NIGMS)

Grant/Contract Number:: R00GM111430; W-31-109-Eng-38; AC02-06CH11357; 9 P41 GM103622; 1S10OD018090-01

OSTI ID:: 1431367

Journal Information:: Scientific Reports, Vol. 8, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 72 works

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