6JP6

The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs

Summary for 6JP6

• Entry DOI: 10.2210/pdb6jp6/pdb
• Descriptor: tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734, tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase, SULFATE ION, ... (5 entities in total)
• Functional Keywords: trna methyltransferase, trna maturation, transferase
• Biological source: Saccharomyces cerevisiae S288c (Baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 306737.48

Authors

Hirata, A.,Okada, K.,Yoshii, K.,Shiraisi, H.,Saijo, S.,Yonezawa, K.,Sihimzu, N.,Hori, H. (deposition date: 2019-03-26, release date: 2019-10-02, Last modification date: 2024-03-27)

Primary citation

Hirata, A.,Okada, K.,Yoshii, K.,Shiraishi, H.,Saijo, S.,Yonezawa, K.,Shimizu, N.,Hori, H.
Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
Nucleic Acids Res., 47:10942-10955, 2019

PubMed Abstract: The complex between Trm7 and Trm734 (Trm7-Trm734) from Saccharomyces cerevisiae catalyzes 2'-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7-Trm734 complex. Purified recombinant Trm7-Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7-Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7-Trm734. Small angle X-ray scattering reveals that Trm7-Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7-Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.

PubMed: 31586407
DOI: 10.1093/nar/gkz856

Experimental method

X-RAY DIFFRACTION (2.699 Å)