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Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site

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Abstract

2′-O-ribose methylation is one of the most common posttranscriptional modifications in RNA. Methylations at different positions are introduced by enzymes from at least two unrelated superfamilies. Recently, a new family of eukaryotic RNA methyltransferases (MTases) has been identified, and its representative from yeast (Yol125w, renamed as Trm13p) has been shown to 2′-O-methylate position 4 of tRNA. Trm13 is conserved in Eukaryota, but exhibits no sequence similarity to other known MTases. Here, I present the results of bioinformatics analysis which suggest that Trm13 is a strongly diverged member of the Rossmann-fold MTase (RFM) superfamily, and therefore is evolutionarily related to 2′-O-MTases such as Trm7 and fibrillarin. However, the character of conserved residues in the predicted active site of the Trm13 family suggests it may use a different mechanism of ribose methylation than its relatives. A molecular model of the Trm13p structure has been constructed and evaluated for potential accuracy using model quality assessment methods. The predicted structure will facilitate experimental analyses of the Trm13p mechanism of action.

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Abbreviations

aa:

Amino acid(s)

e:

Expectation

MTase:

Methyltransferase

RFM:

Rossmann-fold MTase

SAM:

AdoMet, S-adenosyl-L-methionine

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Acknowledgments

KLT was supported by two grants from the Polish Ministry of Science (grant number N301 2396 33 and doctoral grant number N301 105 32/3599) and the START fellowship from Foundation for Polish Science. KLT would like to thank Dr. Janusz M. Bujnicki for the discussions and comments concerning the presented material and this manuscript.

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  1. Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland

    Karolina L. Tkaczuk

  2. Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924, Lodz, Poland

    Karolina L. Tkaczuk

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Correspondence to Karolina L. Tkaczuk.

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Tkaczuk, K.L. Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site. J Mol Model 16, 599–606 (2010). https://doi.org/10.1007/s00894-009-0570-6

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  • DOI: https://doi.org/10.1007/s00894-009-0570-6

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