Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography
Genetically encoded caged amino acids can be used to control the dynamics of protein activities and cellular localization in response to external cues. In the present study, we revealed the structural basis for the recognition of <i>O</i>-(2-nitrobenzyl)-L-tyrosine (<i>o</i>N...
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MDPI AG
2022-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/18/10399 |
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| author | Toshiaki Hosaka Kazushige Katsura Yoshiko Ishizuka-Katsura Kazuharu Hanada Kaori Ito Yuri Tomabechi Mio Inoue Ryogo Akasaka Chie Takemoto Mikako Shirouzu |
| author_facet | Toshiaki Hosaka Kazushige Katsura Yoshiko Ishizuka-Katsura Kazuharu Hanada Kaori Ito Yuri Tomabechi Mio Inoue Ryogo Akasaka Chie Takemoto Mikako Shirouzu |
| author_sort | Toshiaki Hosaka |
| collection | DOAJ |
| description | Genetically encoded caged amino acids can be used to control the dynamics of protein activities and cellular localization in response to external cues. In the present study, we revealed the structural basis for the recognition of <i>O</i>-(2-nitrobenzyl)-L-tyrosine (<i>o</i>NBTyr) by its specific variant of <i>Methanocaldococcus jannaschii</i> tyrosyl-tRNA synthetase (<i>o</i>NBTyrRS), and then demonstrated its potential availability for time-resolved X-ray crystallography. The substrate-bound crystal structure of <i>o</i>NBTyrRS at a 2.79 Å resolution indicated that the replacement of tyrosine and leucine at positions 32 and 65 by glycine (Tyr32Gly and Leu65Gly, respectively) and Asp158Ser created sufficient space for entry of the bulky substitute into the amino acid binding pocket, while Glu in place of Leu162 formed a hydrogen bond with the nitro moiety of <i>o</i>NBTyr. We also produced an <i>o</i>NBTyr-containing lysozyme through a cell-free protein synthesis system derived from the <i>Escherichia coli</i> B95. ΔA strain with the UAG codon reassigned to the nonnatural amino acid. Another crystallographic study of the caged protein showed that the site-specifically incorporated <i>o</i>NBTyr was degraded to tyrosine by light irradiation of the crystals. Thus, cell-free protein synthesis of caged proteins with <i>o</i>NBTyr could facilitate time-resolved structural analysis of proteins, including medically important membrane proteins. |
| first_indexed | 2024-03-09T23:47:25Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:47:25Z |
| publishDate | 2022-09-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1b21cd4106cd40cea6fb37e78572ec8c2023-11-23T16:40:54ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123181039910.3390/ijms231810399Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray CrystallographyToshiaki Hosaka0Kazushige Katsura1Yoshiko Ishizuka-Katsura2Kazuharu Hanada3Kaori Ito4Yuri Tomabechi5Mio Inoue6Ryogo Akasaka7Chie Takemoto8Mikako Shirouzu9Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, JapanGenetically encoded caged amino acids can be used to control the dynamics of protein activities and cellular localization in response to external cues. In the present study, we revealed the structural basis for the recognition of <i>O</i>-(2-nitrobenzyl)-L-tyrosine (<i>o</i>NBTyr) by its specific variant of <i>Methanocaldococcus jannaschii</i> tyrosyl-tRNA synthetase (<i>o</i>NBTyrRS), and then demonstrated its potential availability for time-resolved X-ray crystallography. The substrate-bound crystal structure of <i>o</i>NBTyrRS at a 2.79 Å resolution indicated that the replacement of tyrosine and leucine at positions 32 and 65 by glycine (Tyr32Gly and Leu65Gly, respectively) and Asp158Ser created sufficient space for entry of the bulky substitute into the amino acid binding pocket, while Glu in place of Leu162 formed a hydrogen bond with the nitro moiety of <i>o</i>NBTyr. We also produced an <i>o</i>NBTyr-containing lysozyme through a cell-free protein synthesis system derived from the <i>Escherichia coli</i> B95. ΔA strain with the UAG codon reassigned to the nonnatural amino acid. Another crystallographic study of the caged protein showed that the site-specifically incorporated <i>o</i>NBTyr was degraded to tyrosine by light irradiation of the crystals. Thus, cell-free protein synthesis of caged proteins with <i>o</i>NBTyr could facilitate time-resolved structural analysis of proteins, including medically important membrane proteins.https://www.mdpi.com/1422-0067/23/18/10399nonnatural amino acidcell-free protein synthesisX-ray crystallographycaged amino acid<i>O</i>-(2-nitrobenzyl)-L-tyrosine |
| spellingShingle | Toshiaki Hosaka Kazushige Katsura Yoshiko Ishizuka-Katsura Kazuharu Hanada Kaori Ito Yuri Tomabechi Mio Inoue Ryogo Akasaka Chie Takemoto Mikako Shirouzu Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography International Journal of Molecular Sciences nonnatural amino acid cell-free protein synthesis X-ray crystallography caged amino acid <i>O</i>-(2-nitrobenzyl)-L-tyrosine |
| title | Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography |
| title_full | Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography |
| title_fullStr | Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography |
| title_full_unstemmed | Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography |
| title_short | Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography |
| title_sort | crystal structure of an archaeal tyrosyl trna synthetase bound to photocaged l tyrosine and its potential application to time resolved x ray crystallography |
| topic | nonnatural amino acid cell-free protein synthesis X-ray crystallography caged amino acid <i>O</i>-(2-nitrobenzyl)-L-tyrosine |
| url | https://www.mdpi.com/1422-0067/23/18/10399 |
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