Evidence map›Paper›PMID 31586407›Full record

ArticleNucleic acids research2019

Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.

Akira Hirata, Keisuke Okada, Kazuaki Yoshii, Hiroyuki Shiraishi, Shinya Saijo, Kento Yonezawa, Nobutaka Shimizu, Hiroyuki Hori

Open access · goldAbstract read
In one paragraph

Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
1.1field-weighted citation impact, top 22% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed, 26 citations in OpenAlex.

  1. Article
  2. Review
  3. Optimized tRNA structure-seq reveals robust tRNA secondary structures inbioRxiv : the preprint server for biology · 2026
    Article
  4. Article
  5. Article
  6. Article
  7. Transcriptional Reprogramming ofJournal of fungi (Basel, Switzerland) · 2023
    Article
  8. The life and times of a tRNA.RNA (New York, N.Y.) · 2023
    Review
  9. Article
  10. Review
  11. Article
  12. Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine-International journal of molecular sciences · 2022
    Article
  13. Review
  14. Review
  15. Review
  16. Article
  17. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 2 institutions in 1 country.

Akira HirataDepartment of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
Keisuke OkadaDepartment of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
Kazuaki YoshiiDepartment of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
Hiroyuki ShiraishiDepartment of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
Shinya SaijoPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Kento YonezawaPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Nobutaka ShimizuPhoton Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Hiroyuki HoriDepartment of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
Ehime University · JPHigh Energy Accelerator Research Organization · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Catalytic DomainHydrogen BondingMethylationModels, MolecularMutant ProteinsProtein BindingProtein SubunitsPyrimidinesRecombinant ProteinsRNA, TransferSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsS-AdenosylmethionineSubstrate SpecificitytRNA MethyltransferasesVesicular Transport ProteinsMutant ProteinsProtein SubunitspyrimidinePyrimidinesRecombinant ProteinsRNA, TransferRTT10 protein, S cerevisiaeSaccharomyces cerevisiae ProteinsS-AdenosylmethionineTrm7 protein, S cerevisiaetRNA MethyltransferasesVesicular Transport Proteins

Identifiers

PMID31586407
PMCPMC6847430
OpenAlexW2977680906

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.