Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules
| Autor: | Hiroyuki Hori, Toshihiro Tamura, Akira Hirata, Ayano Yamauchi, Seiji Nishiyama |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
S-Adenosylmethionine Biology Crystallography X-Ray Methylation Site 03 medical and health sciences RNA Transfer Genetics Transferase Amino Acid Sequence Binding site tRNA Methyltransferases Binding Sites Guanosine 030102 biochemistry & molecular biology Nucleic Acid Enzymes TRNA Methyltransferase RNA DNA Methylation biology.organism_classification TRNA Methyltransferases Thermococcus kodakarensis Molecular Docking Simulation Thermococcus 030104 developmental biology Biochemistry Transfer RNA RNA-Binding Motifs Sequence Alignment |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | N(2)-methylguanosine is one of the most universal modified nucleosides required for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species, a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase (MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the apo-form, and of its complex with SAM. The structures show that TkoTrm11 consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP domain and Rossmann-fold MTase (RFM) domain. A linker region connects the THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of other tRNA MTases containing an RFM domain. Furthermore, the conformation of NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying enzymes specifically recognizing the tRNA acceptor stem. Our docking model of TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and pre-existing evidence, provides insights into the substrate tRNA recognition mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby causing TkoTrm11 to specifically identify its methylation site. |
| Databáze: | OpenAIRE |
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