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Nucleic Acids Research Advance Access published online on July 24, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn437
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity

Hélène Walbott1, Nicolas Leulliot2, Henri Grosjean1 and Béatrice Golinelli-Pimpaneau1,*

1Enzymology and Structural Biochemistry Laboratory, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette and 2Institute of Molecular and Cellular Biochemistry and Biophysics, University Paris-South 11, 91400 Orsay, France

*To whom correspondence should be addressed. Tel: 33 1 69 82 42 35; Fax: 33 1 69 82 31 29; Email: beatrice.golinelli{at}lebs.cnrs-gif.fr

Received April 2, 2008. Revised May 25, 2008. Accepted June 25, 2008.

The 5-methyluridine is invariably found at position 54 in the T{Psi}C loop of tRNAs of most organisms. In Pyrococcus abyssi, its formation is catalyzed by the S-adenosyl-L-methionine-dependent tRNA (uracil-54, C5)-methyltransferase (PabTrmU54), an enzyme that emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea. The crystal structure of PabTrmU54 in complex with S-adenosyl-L-homocysteine at 1.9 Å resolution shows the protein organized into three domains like Escherichia coli RumA, which catalyzes the same reaction at position 1939 of 23S rRNA. A positively charged groove at the interface between the three domains probably locates part of the tRNA-binding site of PabTrmU54. We show that a mini-tRNA lacking both the D and anticodon stem-loops is recognized by PabTrmU54. These results were used to model yeast tRNAAsp in the PabTrmU54 structure to get further insights into the different RNA specificities of RumA and PabTrmU54. Interestingly, the presence of two flexible loops in the central domain, unique to PabTrmU54, may explain the different substrate selectivities of both enzymes. We also predict that a large T{Psi}C loop conformational change has to occur for the flipping of the target uridine into the PabTrmU54 active site during catalysis.

Present addresses: Hélène Walbott, Institute of Molecular and Cellular Biochemistry and Biophysics, University Paris-South 11, 91400 Orsay, France

Henri Grosjean, Institute of Genetics and Microbiology, University Paris-South 11, 91400 Orsay, France


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