PDBsum entry 5erg

Transferase

PDB id: 5erg

Contents

Protein chains

340 a.a.

324 a.a.

Ligands

SAM

Waters ×199

References listed in PDB file

Key reference

• Title: Crystal structure of the two-Subunit tRNA m(1)a58 methyltransferase trm6-Trm61 from saccharomyces cerevisiae.
• Authors: M.Wang, Y.Zhu, C.Wang, X.Fan, X.Jiang, M.Ebrahimi, Z.Qiao, L.Niu, M.Teng, X.Li.
• Ref.: Sci Rep, 2016, 6, 32562.
• PubMed id: 27582183

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.