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Nucleic Acids Research 2006 34(9):2483-2494; doi:10.1093/nar/gkl145
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Published online 10 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain

Guillaume Gabant1, Sylvie Auxilien2, Irina Tuszynska3, Marie Locard2, Michal J. Gajda3,4, Guylaine Chaussinand1, Bernard Fernandez1, Alain Dedieu1, Henri Grosjean2, Béatrice Golinelli-Pimpaneau2, Janusz M. Bujnicki3 and Jean Armengaud1,*

1 CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie Nucléaire F-30207 Bagnols-sur-Cèze, France 2 Laboratoire d'Enzymologie et Biochimie Structurales, CNRS Bld 34, avenue de la Terrasse 1, F-91198 Gif-sur-Yvette, France 3 Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Trojdena 4, 02-109, Warsaw, Poland 4 Faculty of Mathematics and Information Science, Warsaw University of Technology Warsaw, Poland

*To whom correspondence should be addressed at CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie Nucléaire, Marcoule, BP 17171, F-30207 Bagnols-sur-Cèze cedex, France. Tel: 33 4 66 79 68 02; Fax: 33 4 66 79 19 05; Email: armengaud{at}cea.fr

Received January 13, 2006. Revised February 13, 2006. Accepted March 16, 2006.

The tRNA:m22G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N2,N2-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)—containing N-terminal domain [1–152] and C-terminal catalytic domain [157–329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed. The N-terminal domain was then produced as a standalone protein (THUMP{alpha}) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMP{alpha} and a putative RNA-recognition module observed in the crystal structure of another THUMP-containing protein (ThiI thiolase of Bacillus anthracis). A comparative model of THUMP{alpha} structure was generated, which fulfills experimentally defined restraints, i.e. chemical modification of surface exposed residues assessed by mass spectrometry, and identification of an intramolecular disulfide bridge. A model of the whole PAB1283 enzyme docked onto its tRNAAsp substrate suggests that the THUMP module specifically takes support on the co-axially stacked helices of T-arm and acceptor stem of tRNA and, together with the catalytic domain, screw-clamp structured tRNA. We propose that this mode of interactions may be common to other THUMP-containing enzymes that specifically modify nucleotides in the 3D-core of tRNA.


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