5ERG

Crystal structure of the two-subunit tRNA m1A58 methyltransferase TRM6-TRM61 in complex with SAM

Summary for 5ERG

• Entry DOI: 10.2210/pdb5erg/pdb
• Related: 5EQJ
• Descriptor: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6, tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61, S-ADENOSYLMETHIONINE, ... (4 entities in total)
• Functional Keywords: trna, complex, sam, methylation, transferase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Cellular location: Nucleus : P41814 P46959
• Total number of polymer chains: 2
• Total formula weight: 100106.61

Authors

Zhu, Y.,Wang, M.,Wang, C.,Fan, X.,Jiang, X.,Teng, M.,Li, X. (deposition date: 2015-11-14, release date: 2016-09-14, Last modification date: 2024-03-20)

Primary citation

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, 6:32562-32562, 2016

PubMed 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.

PubMed: 27582183
DOI: 10.1038/srep32562

Experimental method

X-RAY DIFFRACTION (2.202 Å)