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Wang M, Zhu Y, Wang C, Fan X, Jiang X, Ebrahimi M, Qiao Z, Niu L, Teng M, Li X. Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae. Sci Rep 2016; 6:32562. [PMID: 27582183 PMCID: PMC5007650 DOI: 10.1038/srep32562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/09/2016] [Indexed: 01/19/2023] Open
Abstract
The N(1) methylation of adenine at position 58 (m(1)A58) of tRNA is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine tRNAi(Met). In eukaryotes, this modification is performed by the TRM6-TRM61 holoenzyme. To understand the molecular mechanism that underlies the cooperation of TRM6 and TRM61 in the methyl transfer reaction, we determined the crystal structure of TRM6-TRM61 holoenzyme from Saccharomyces cerevisiae in the presence and absence of its methyl donor S-Adenosyl-L-methionine (SAM). In the structures, two TRM6-TRM61 heterodimers assemble as a heterotetramer. Both TRM6 and TRM61 subunits comprise an N-terminal β-barrel domain linked to a C-terminal Rossmann-fold domain. TRM61 functions as the catalytic subunit, containing a methyl donor (SAM) binding pocket. TRM6 diverges from TRM61, lacking the conserved motifs used for binding SAM. However, TRM6 cooperates with TRM61 forming an L-shaped tRNA binding regions. Collectively, our results provide a structural basis for better understanding the m(1)A58 modification of tRNA occurred in Saccharomyces cerevisiae.
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Affiliation(s)
- Mingxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Yuwei Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Xiaojiao Fan
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Xuguang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Mohammad Ebrahimi
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Zhi Qiao
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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