THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain
Identifieur interne : 000165 ( France/Analysis ); précédent : 000164; suivant : 000166THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain
Auteurs : Guillaume Gabant [France] ; Sylvie Auxilien [France] ; Irina Tuszynska [Pologne] ; Marie Locard [France] ; Michal J. Gajda [Pologne] ; Guylaine Chaussinand [France] ; Bernard Fernandez [France] ; Alain Dedieu [France] ; Henri Grosjean [France] ; Be Atrice Golinelli-Pimpaneau [France] ; Janusz M. Bujnicki [Pologne] ; Jean Armengaud [France]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2006.
Abstract
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 (THUMPα) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMPα 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 THUMPα 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.
Url:
DOI: 10.1093/nar/gkl145
Affiliations:
- France, Pologne
- Languedoc-Roussillon, Occitanie (région administrative), Île-de-France
- Bagnols-sur-Cèze, Gif-sur-Yvette
Links toward previous steps (curation, corpus...)
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- to stream Main, to step Merge: 001618
- to stream Main, to step Curation: 001610
- to stream Main, to step Exploration: 001610
- to stream France, to step Extraction: 000165
Links to Exploration step
ISTEX:96BE1E343DB400DB831EE7298BD31A6BF0D24A2ELe document en format XML
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Bujnicki</name><affiliation wicri:level="1"><country xml:lang="fr">Pologne</country><wicri:regionArea>Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Trojdena 4, 02-109, Warsaw</wicri:regionArea><wicri:noRegion>Warsaw</wicri:noRegion></affiliation></author><author><name sortKey="Armengaud, Jean" sort="Armengaud, Jean" uniqKey="Armengaud J" first="Jean" last="Armengaud">Jean Armengaud</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>CEA VALRHO, DSV-DIEP—SBTN, Service de Biochimie post-génomique & Toxicologie Nucléaire F-30207 Bagnols-sur-Cèze</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region><settlement type="city">Bagnols-sur-Cèze</settlement></placeName></affiliation><affiliation wicri:level="3"><country wicri:rule="url">France</country><wicri:regionArea>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</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region><settlement type="city">Bagnols-sur-Cèze</settlement></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2006">2006</date><biblScope unit="volume">34</biblScope><biblScope unit="issue">9</biblScope><biblScope unit="page" from="2483">2483</biblScope><biblScope unit="page" to="2494">2494</biblScope></imprint><idno type="ISSN">0305-1048</idno></series><idno type="istex">96BE1E343DB400DB831EE7298BD31A6BF0D24A2E</idno><idno type="DOI">10.1093/nar/gkl145</idno><idno type="local">gkl145</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 (THUMPα) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMPα 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 THUMPα 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.</div></front></TEI><affiliations><list><country><li>France</li><li>Pologne</li></country><region><li>Languedoc-Roussillon</li><li>Occitanie (région administrative)</li><li>Île-de-France</li></region><settlement><li>Bagnols-sur-Cèze</li><li>Gif-sur-Yvette</li></settlement></list><tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Gabant, Guillaume" sort="Gabant, Guillaume" uniqKey="Gabant G" first="Guillaume" last="Gabant">Guillaume Gabant</name></region><name sortKey="Armengaud, Jean" sort="Armengaud, Jean" uniqKey="Armengaud J" first="Jean" last="Armengaud">Jean Armengaud</name><name sortKey="Armengaud, Jean" sort="Armengaud, Jean" uniqKey="Armengaud J" first="Jean" last="Armengaud">Jean Armengaud</name><name sortKey="Auxilien, Sylvie" sort="Auxilien, Sylvie" uniqKey="Auxilien S" first="Sylvie" last="Auxilien">Sylvie Auxilien</name><name sortKey="Chaussinand, Guylaine" sort="Chaussinand, Guylaine" uniqKey="Chaussinand G" first="Guylaine" last="Chaussinand">Guylaine Chaussinand</name><name sortKey="Dedieu, Alain" sort="Dedieu, Alain" uniqKey="Dedieu A" first="Alain" last="Dedieu">Alain Dedieu</name><name sortKey="Fernandez, Bernard" sort="Fernandez, Bernard" uniqKey="Fernandez B" first="Bernard" last="Fernandez">Bernard Fernandez</name><name sortKey="Golinelli Pimpaneau, Be Atrice" sort="Golinelli Pimpaneau, Be Atrice" uniqKey="Golinelli Pimpaneau B" first="Be Atrice" last="Golinelli-Pimpaneau">Be Atrice Golinelli-Pimpaneau</name><name sortKey="Grosjean, Henri" sort="Grosjean, Henri" uniqKey="Grosjean H" first="Henri" last="Grosjean">Henri Grosjean</name><name sortKey="Locard, Marie" sort="Locard, Marie" uniqKey="Locard M" first="Marie" last="Locard">Marie Locard</name></country><country name="Pologne"><noRegion><name sortKey="Tuszynska, Irina" sort="Tuszynska, Irina" uniqKey="Tuszynska I" first="Irina" last="Tuszynska">Irina Tuszynska</name></noRegion><name sortKey="Bujnicki, Janusz M" sort="Bujnicki, Janusz M" uniqKey="Bujnicki J" first="Janusz M." last="Bujnicki">Janusz M. Bujnicki</name><name sortKey="Gajda, Michal J" sort="Gajda, Michal J" uniqKey="Gajda M" first="Michal J." last="Gajda">Michal J. Gajda</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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