{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T22:26:08Z","timestamp":1787005568952,"version":"build-2736575974"},"reference-count":26,"publisher":"National Academy of Sciences","issue":"5","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2005,2]]},"abstract":"<jats:p>\n                    The genetic code in a eukaryotic system has been expanded by the engineering of\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo-\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine rather than\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine. In the present study, we determined the 3-iodo-\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine- and\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine-bound structures of the 37V195C mutant of the\n                    <jats:italic>E. coli<\/jats:italic>\n                    TyrRS catalytic domain at 2.0-\u00c5 resolution. The \u03b3-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo-\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo-\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosyladenylate analogue was also solved, indicating that the 3-iodo-\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine and\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-\n                    <jats:sc>l<\/jats:sc>\n                    -tyrosine recognition.\n                  <\/jats:p>","DOI":"10.1073\/pnas.0407039102","type":"journal-article","created":{"date-parts":[[2005,1,25]],"date-time":"2005-01-25T22:43:38Z","timestamp":1106693018000},"page":"1366-1371","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":36,"title":["Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion"],"prefix":"10.1073","volume":"102","author":[{"given":"Takatsugu","family":"Kobayashi","sequence":"first","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kensaku","family":"Sakamoto","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetsuo","family":"Takimura","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryo","family":"Sekine","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Vincent","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenji","family":"Kamata","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susumu","family":"Nishimura","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shigeyuki","family":"Yokoyama","sequence":"additional","affiliation":[{"name":"Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Tsukuba Research Institute, Banyu Pharmaceuticals, 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan; and RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2005,1,25]]},"reference":[{"key":"e_1_3_2_1_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.85.17.6237"},{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1060077"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.142220099"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf589"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1084772"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0307029101"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401517101"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt742"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja027007w"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.172226299"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1089509"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja012307j"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(87)90376-7"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(89)90090-9"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.18001"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.242611799"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/cdf373"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb934"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.11.034"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(97)76066-X"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889897006766"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444994003112"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00355047"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444998003254"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0108767390010224"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00235a007"}],"updated-by":[{"DOI":"10.1073\/pnas.0505010102","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2005,7,8]],"date-time":"2005-07-08T00:00:00Z","timestamp":1120780800000}}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.0407039102","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T08:21:10Z","timestamp":1649751670000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.0407039102"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,1,25]]},"references-count":26,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2005,2]]}},"alternative-id":["10.1073\/pnas.0407039102"],"URL":"https:\/\/doi.org\/10.1073\/pnas.0407039102","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,1,25]]},"assertion":[{"value":"2004-09-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2004-12-21","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2005-01-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}