Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine
In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we...
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| Veröffentlicht in: | Structure (London) 2007-12, Vol.15 (12), p.1642-1653 |
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| creator | Kuratani, Mitsuo Yoshikawa, Yuka Bessho, Yoshitaka Higashijima, Kyoko Ishii, Takeshi Shibata, Rie Takahashi, Seizo Yutani, Katsuhide Yokoyama, Shigeyuki |
| description | In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex. |
| doi_str_mv | 10.1016/j.str.2007.09.020 |
| format | Article |
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Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex.</description><identifier>ISSN: 0969-2126</identifier><identifier>DOI: 10.1016/j.str.2007.09.020</identifier><identifier>PMID: 18073113</identifier><language>eng</language><publisher>United States</publisher><subject>Adenosine Triphosphate - chemistry ; Adenosine Triphosphate - metabolism ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases - chemistry ; Amino Acyl-tRNA Synthetases - metabolism ; Lysine - chemistry ; Lysine - metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid</subject><ispartof>Structure (London), 2007-12, Vol.15 (12), p.1642-1653</ispartof><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,778,782,27907,27908</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18073113$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kuratani, Mitsuo</creatorcontrib><creatorcontrib>Yoshikawa, Yuka</creatorcontrib><creatorcontrib>Bessho, Yoshitaka</creatorcontrib><creatorcontrib>Higashijima, Kyoko</creatorcontrib><creatorcontrib>Ishii, Takeshi</creatorcontrib><creatorcontrib>Shibata, Rie</creatorcontrib><creatorcontrib>Takahashi, Seizo</creatorcontrib><creatorcontrib>Yutani, Katsuhide</creatorcontrib><creatorcontrib>Yokoyama, Shigeyuki</creatorcontrib><title>Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine</title><title>Structure (London)</title><addtitle>Structure</addtitle><description>In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. 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In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex.</description><subject>Adenosine Triphosphate - chemistry</subject><subject>Adenosine Triphosphate - metabolism</subject><subject>Amino Acid Sequence</subject><subject>Amino Acyl-tRNA Synthetases - chemistry</subject><subject>Amino Acyl-tRNA Synthetases - metabolism</subject><subject>Lysine - chemistry</subject><subject>Lysine - metabolism</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Sequence Homology, Amino Acid</subject><issn>0969-2126</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo10L1OwzAUhmEPIFoKF8CCPCEYEo6dOLbHquKnUgWIljlynBPqyk1L7Aj17mmhTEd69egbDiFXDFIGrLhfpSF2KQeQKegUOJyQIehCJ5zxYkDOQ1gBABcAZ2TAFMiMsWxI7Dx2vY19ZzytTHCBbhoal0hd66I7RNfWrv38ze8v49upxzvqd8HtK9Kwa_c4moB04fycfru4pOPFGzVtTWfJwbV4QU4b4wNeHu-IfDw-LCbPyez1aToZz5ItBx2TRimLFmupi0owXQnLEISpGlnYnHMuc-Q5NEKAsDnLhGBMKpUzpjCrpFHZiNz87W67zVePIZZrFyx6b1rc9KEsNAgtVL6H10fYV2usy23n1qbblf9vyX4A5GNiMg</recordid><startdate>20071201</startdate><enddate>20071201</enddate><creator>Kuratani, Mitsuo</creator><creator>Yoshikawa, Yuka</creator><creator>Bessho, Yoshitaka</creator><creator>Higashijima, Kyoko</creator><creator>Ishii, Takeshi</creator><creator>Shibata, Rie</creator><creator>Takahashi, Seizo</creator><creator>Yutani, Katsuhide</creator><creator>Yokoyama, Shigeyuki</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7X8</scope></search><sort><creationdate>20071201</creationdate><title>Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine</title><author>Kuratani, Mitsuo ; Yoshikawa, Yuka ; Bessho, Yoshitaka ; Higashijima, Kyoko ; Ishii, Takeshi ; Shibata, Rie ; Takahashi, Seizo ; Yutani, Katsuhide ; Yokoyama, Shigeyuki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p209t-f88ceced796b519b5c1e05abf76c422274e240f5505c41355117884118e3b7a83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Adenosine Triphosphate - chemistry</topic><topic>Adenosine Triphosphate - metabolism</topic><topic>Amino Acid Sequence</topic><topic>Amino Acyl-tRNA Synthetases - chemistry</topic><topic>Amino Acyl-tRNA Synthetases - metabolism</topic><topic>Lysine - chemistry</topic><topic>Lysine - metabolism</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Protein Binding</topic><topic>Protein Conformation</topic><topic>Sequence Homology, Amino Acid</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kuratani, Mitsuo</creatorcontrib><creatorcontrib>Yoshikawa, Yuka</creatorcontrib><creatorcontrib>Bessho, Yoshitaka</creatorcontrib><creatorcontrib>Higashijima, Kyoko</creatorcontrib><creatorcontrib>Ishii, Takeshi</creatorcontrib><creatorcontrib>Shibata, Rie</creatorcontrib><creatorcontrib>Takahashi, Seizo</creatorcontrib><creatorcontrib>Yutani, Katsuhide</creatorcontrib><creatorcontrib>Yokoyama, Shigeyuki</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>MEDLINE - Academic</collection><jtitle>Structure (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kuratani, Mitsuo</au><au>Yoshikawa, Yuka</au><au>Bessho, Yoshitaka</au><au>Higashijima, Kyoko</au><au>Ishii, Takeshi</au><au>Shibata, Rie</au><au>Takahashi, Seizo</au><au>Yutani, Katsuhide</au><au>Yokoyama, Shigeyuki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine</atitle><jtitle>Structure (London)</jtitle><addtitle>Structure</addtitle><date>2007-12-01</date><risdate>2007</risdate><volume>15</volume><issue>12</issue><spage>1642</spage><epage>1653</epage><pages>1642-1653</pages><issn>0969-2126</issn><abstract>In the bacterial genetic-code system, the codon AUA is decoded as isoleucine by tRNA(Ile)(2) with the lysidine residue at the wobble position. Lysidine is derived from cytidine, with ATP and L-lysine, by tRNA(Ile) lysidine synthetase (TilS), which is an N-type ATP pyrophosphatase. In this study, we determined the crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex.</abstract><cop>United States</cop><pmid>18073113</pmid><doi>10.1016/j.str.2007.09.020</doi><tpages>12</tpages></addata></record> |
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| source | Elsevier ScienceDirect Journals Complete - AutoHoldings; MEDLINE; Cell Press Free Archives; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Free Full-Text Journals in Chemistry |
| subjects | Adenosine Triphosphate - chemistry Adenosine Triphosphate - metabolism Amino Acid Sequence Amino Acyl-tRNA Synthetases - chemistry Amino Acyl-tRNA Synthetases - metabolism Lysine - chemistry Lysine - metabolism Models, Molecular Molecular Sequence Data Protein Binding Protein Conformation Sequence Homology, Amino Acid |
| title | Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine |
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