5E72

Crystal structure of the archaeal tRNA m2G/m22G10 methyltransferase (aTrm11) in complex with S-adenosyl-L-methionine (SAM) from Thermococcus kodakarensis

Summary for 5E72

• Entry DOI: 10.2210/pdb5e72/pdb
• Related: 5E71
• Descriptor: N2, N2-dimethylguanosine tRNA methyltransferase, S-ADENOSYLMETHIONINE (3 entities in total)
• Functional Keywords: trna methyltransferase, sam, transferase
• Biological source: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
• Total number of polymer chains: 1
• Total formula weight: 39698.57

Authors

Hirata, A. (deposition date: 2015-10-11, release date: 2016-07-06, Last modification date: 2024-10-23)

Primary citation

Hirata, A.,Nishiyama, S.,Tamura, T.,Yamauchi, A.,Hori, H.
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.
Nucleic Acids Res., 2016

PubMed Abstract: 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.

PubMed: 27325738
DOI: 10.1093/nar/gkw561

Experimental method

X-RAY DIFFRACTION (1.739 Å)