Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major i...
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| Veröffentlicht in: | RNA (Cambridge) 2003-01, Vol.9 (1), p.100 |
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| creator | Fukai, Shuya Nureki, Osamu Sekine, Shun-Ichi Shimada, Atsushi Vassylyev, Dmitry G Yokoyama, Shigeyuki |
| description | The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction. |
| doi_str_mv | 10.1261/rna.2760703 |
| format | Article |
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In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.</description><identifier>ISSN: 1355-8382</identifier><identifier>DOI: 10.1261/rna.2760703</identifier><identifier>PMID: 12554880</identifier><language>eng</language><publisher>United States</publisher><subject>Anticodon ; Hydrogen Bonding ; Kinetics ; Models, Molecular ; Protein Conformation ; RNA, Transfer, Val - metabolism ; Thermus thermophilus - enzymology ; Valine-tRNA Ligase - chemistry ; Valine-tRNA Ligase - metabolism</subject><ispartof>RNA (Cambridge), 2003-01, Vol.9 (1), p.100</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12554880$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fukai, Shuya</creatorcontrib><creatorcontrib>Nureki, Osamu</creatorcontrib><creatorcontrib>Sekine, Shun-Ichi</creatorcontrib><creatorcontrib>Shimada, Atsushi</creatorcontrib><creatorcontrib>Vassylyev, Dmitry G</creatorcontrib><creatorcontrib>Yokoyama, Shigeyuki</creatorcontrib><title>Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase</title><title>RNA (Cambridge)</title><addtitle>RNA</addtitle><description>The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.</description><subject>Anticodon</subject><subject>Hydrogen Bonding</subject><subject>Kinetics</subject><subject>Models, Molecular</subject><subject>Protein Conformation</subject><subject>RNA, Transfer, Val - metabolism</subject><subject>Thermus thermophilus - enzymology</subject><subject>Valine-tRNA Ligase - chemistry</subject><subject>Valine-tRNA Ligase - metabolism</subject><issn>1355-8382</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo1j01LAzEYhHNQbK2evEuOetia5M3XHkvxC6qCaK8lGxO7ks2WJBX237tFPc0wDzMwCF1QMqdM0psUzZwpSRSBIzSlIESlQbMJOs35ixAKlMsTNKFMCK41maL1k7NbE9vc4d7jrg_O7oNJuI3FJWNL28eMfZ9weX1eXK1NuMbJ2f4ztgeEmwF_mzCE6oBxHmLZumKyO0PH3oTszv90ht7vbt-WD9Xq5f5xuVhVO0ZUqXgtai0t1NZ7B8zXoE0jKLfcg2J6NJJLSa0aPxCox4gZAdQpM1YEaWCGLn93d_umcx-bXWo7k4bN_0H4AQ5tT1M</recordid><startdate>200301</startdate><enddate>200301</enddate><creator>Fukai, Shuya</creator><creator>Nureki, Osamu</creator><creator>Sekine, Shun-Ichi</creator><creator>Shimada, Atsushi</creator><creator>Vassylyev, Dmitry G</creator><creator>Yokoyama, Shigeyuki</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope></search><sort><creationdate>200301</creationdate><title>Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase</title><author>Fukai, Shuya ; Nureki, Osamu ; Sekine, Shun-Ichi ; Shimada, Atsushi ; Vassylyev, Dmitry G ; Yokoyama, Shigeyuki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p207t-495986c39cffe32f938ab514c4f372814c64661c73820397282a531e7a39c50b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Anticodon</topic><topic>Hydrogen Bonding</topic><topic>Kinetics</topic><topic>Models, Molecular</topic><topic>Protein Conformation</topic><topic>RNA, Transfer, Val - metabolism</topic><topic>Thermus thermophilus - enzymology</topic><topic>Valine-tRNA Ligase - chemistry</topic><topic>Valine-tRNA Ligase - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fukai, Shuya</creatorcontrib><creatorcontrib>Nureki, Osamu</creatorcontrib><creatorcontrib>Sekine, Shun-Ichi</creatorcontrib><creatorcontrib>Shimada, Atsushi</creatorcontrib><creatorcontrib>Vassylyev, Dmitry G</creatorcontrib><creatorcontrib>Yokoyama, Shigeyuki</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><jtitle>RNA (Cambridge)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fukai, Shuya</au><au>Nureki, Osamu</au><au>Sekine, Shun-Ichi</au><au>Shimada, Atsushi</au><au>Vassylyev, Dmitry G</au><au>Yokoyama, Shigeyuki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase</atitle><jtitle>RNA (Cambridge)</jtitle><addtitle>RNA</addtitle><date>2003-01</date><risdate>2003</risdate><volume>9</volume><issue>1</issue><spage>100</spage><pages>100-</pages><issn>1355-8382</issn><abstract>The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.</abstract><cop>United States</cop><pmid>12554880</pmid><doi>10.1261/rna.2760703</doi><oa>free_for_read</oa></addata></record> |
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| ispartof | RNA (Cambridge), 2003-01, Vol.9 (1), p.100 |
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| source | MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Anticodon Hydrogen Bonding Kinetics Models, Molecular Protein Conformation RNA, Transfer, Val - metabolism Thermus thermophilus - enzymology Valine-tRNA Ligase - chemistry Valine-tRNA Ligase - metabolism |
| title | Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase |
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