ArticleNucleic acids research2004
Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 117 citations in OpenAlex.
- Emerging roles of tRNA modification-mediated codon-specific translational reprogramming in cancer biology.Cell death & disease · 2026Review
- NSUN7 is a catalytically inactive RNA mNature communications · 2025Article
- RNA methylation modifications in neurodegenerative diseases: Focus on their enzyme system.Journal of advanced research · 2025Review
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- Transfer RNA Aspartic Acid Methyltransferase 1 (TRDMT1/DNMT2) Regulates Plant Development and Gene Expression in the Moss Physcomitrium patens.Molecular genetics and genomics : MGG · 2025Article
- The functions and modifications of tRNA-derived small RNAs in cancer biology.Cancer metastasis reviews · 2025Review
- Epitranscriptomic mechanisms and implications of RNA mTheranostics · 2025Review
- The role of m5C, m1A and m7G modifications in tumors of urinary system.Frontiers in cell and developmental biology · 2025Review
- The role of RNA methylation in glioma progression: mechanisms, diagnostic implications, and therapeutic value.Frontiers in immunology · 2025Review
- A novelProceedings of the National Academy of Sciences of the United States of America · 2024Article
- A robust deep learning approach for identification of RNA 5-methyluridine sites.Scientific reports · 2024Article
- The Quiet Giant: Identification, Effectors, Molecular Mechanism, Physiological and Pathological Function in mRNA 5-methylcytosine Modification.International journal of biological sciences · 2024Review
- The role of RNA modification in urological cancers: mechanisms and clinical potential.Discover oncology · 2023Review
- Insights into the regulatory role of RNA methylation modifications in glioma.Journal of translational medicine · 2023Review
- Investigations of Single-Subunit tRNA Methyltransferases from Yeast.Journal of fungi (Basel, Switzerland) · 2023Review
- Small RNA modifications: regulatory molecules and potential applications.Journal of hematology & oncology · 2023Review
- A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical PlantGenes · 2023Article
- m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation.BMC biology · 2023Article
- The diverse role of RNA methylation in esophageal cancer.Acta biochimica et biophysica Sinica · 2023Review
- Review
8 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three types of methyltransferases (MTases) generate 5-methylpyrimidine in nucleic acids, forming m5U in RNA, m5C in RNA and m5C in DNA. The DNA:m5C MTases have been extensively studied by crystallographic, biophysical, biochemical and computational methods. On the other hand, the sequence-structure-function relationships of RNA:m5C MTases remain obscure, as do the potential evolutionary relationships between the three types of 5-methylpyrimidine-generating enzymes. Sequence analyses and homology modeling of the yeast tRNA:m5C MTase Trm4p (also called Ncl1p) provided a structural and evolutionary platform for identification of catalytic residues and modeling of the architecture of the RNA:m5C MTase active site. The analysis led to the identification of two invariant residues that are important for Trm4p activity in addition to the conserved Cys residues in motif IV and motif VI that were previously found to be critical. The newly identified residues include a Lys residue in motif I and an Asp in motif IV. A conserved Gln found in motif X was found to be dispensable for MTase activity. Locations of essential residues in the model of Trm4p are in very good agreement with the X-ray structure of an RNA:m5C MTase homolog PH1374. Theoretical and experimental analyses revealed that RNA:m5C MTases share a number of features with either RNA:m5U MTases or DNA:m5C MTases, which suggested a tentative phylogenetic model of relationships between these three classes of 5-methylpyrimidine MTases. We infer that RNA:m5C MTases evolved from RNA:m5U MTases by acquiring an additional Cys residue in motif IV, which was adapted to function as the nucleophilic catalyst only later in DNA:m5C MTases, accompanied by loss of the original Cys from motif VI, transfer of a conserved carboxylate from motif IV to motif VI and sequence permutation.
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