ArticleRNA (New York, N.Y.)2009
Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 13 citations in OpenAlex.
- Deciphering the influence of the [4Fe-4S] cluster of tRNA thiolation enzymes on tRNA binding.RNA (New York, N.Y.) · 2025Article
- Review
- 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 research · 2016Article
- Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.Nature methods · 2015Article
- Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.Nucleic acids research · 2014Article
- Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase-RNA complex.Acta crystallographica. Section F, Structural biology and crystallization communications · 2013Article
- Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis.The Journal of biological chemistry · 2012Article
- Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity.Nucleic acids research · 2012Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ThiI catalyzes the thio-introduction reaction to tRNA, and a truncated tRNA consisting of 39 nucleotides, TPHE39A, is the minimal RNA substrate for modification by ThiI from Escherichia coli. To examine the molecular basis of the tRNA recognition by ThiI, we have solved the crystal structure of TPHE39A, which showed that base pairs in the T-stem were almost completely disrupted, although those in the acceptor-stem were preserved. Gel shift assays and isothermal titration calorimetry experiments showed that ThiI can efficiently bind with not only tRNA(Phe) but also TPHE39A. Binding assays using truncated ThiI, i.e., N- and C-terminal domains of ThiI, showed that the N-domain can bind with both tRNA(Phe) and TPHE39A, whereas the C-domain cannot. These results indicated that the N-domain of ThiI recognizes the acceptor-stem region. Thermodynamic analysis indicated that the C-domain also affects RNA binding by its enthalpically favorable, but entropically unfavorable, contribution. In addition, circular dichroism spectra showed that the C-domain induced a conformation change in tRNA(Phe). Based on these results, a possible RNA binding mechanism of ThiI in which the N-terminal domain recognizes the acceptor-stem region and the C-terminal region causes a conformational change of RNA is proposed.
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