Serial femtosecond X‐ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase
The mechanisms by which enzymes promote catalytic reactions efficiently through their structural changes remain to be fully elucidated. Recent progress in serial femtosecond X‐ray crystallography (SFX) using X‐ray free‐electron lasers (XFELs) has made it possible to address these issues. In particul...
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| Veröffentlicht in: | Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2022-12, Vol.78 (12), p.1428-1438 |
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| container_title | Acta crystallographica. Section D, Biological crystallography. |
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| creator | Murakawa, Takeshi Suzuki, Mamoru Fukui, Kenji Masuda, Tetsuya Sugahara, Michihiro Tono, Kensuke Tanaka, Tomoyuki Iwata, So Nango, Eriko Yano, Takato Tanizawa, Katsuyuki Okajima, Toshihide |
| description | The mechanisms by which enzymes promote catalytic reactions efficiently through their structural changes remain to be fully elucidated. Recent progress in serial femtosecond X‐ray crystallography (SFX) using X‐ray free‐electron lasers (XFELs) has made it possible to address these issues. In particular, mix‐and‐inject serial crystallography (MISC) is promising for the direct observation of structural changes associated with ongoing enzymic reactions. In this study, SFX measurements using a liquid‐jet system were performed on microcrystals of bacterial copper amine oxidase anaerobically premixed with a substrate amine solution. The structure determined at 1.94 Å resolution indicated that the peptidyl quinone cofactor is in equilibrium between the aminoresorcinol and semiquinone radical intermediates, which accumulate only under anaerobic single‐turnover conditions. These results show that anaerobic conditions were well maintained throughout the liquid‐jet SFX measurements, preventing the catalytic intermediates from reacting with dioxygen. These results also provide a necessary framework for performing time‐resolved MISC to study enzymic reaction mechanisms under anaerobic conditions.
Serial femtosecond X‐ray crystallography was performed using a liquid‐jet system on bacterial copper amine oxidase microcrystals anaerobically premixed with an amine substrate. The structure determined at 1.94 Å resolution revealed catalytic intermediates in two reduced forms, confirming that anaerobic conditions were well maintained throughout the measurements. |
| doi_str_mv | 10.1107/S2059798322010385 |
| format | Article |
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Serial femtosecond X‐ray crystallography was performed using a liquid‐jet system on bacterial copper amine oxidase microcrystals anaerobically premixed with an amine substrate. The structure determined at 1.94 Å resolution revealed catalytic intermediates in two reduced forms, confirming that anaerobic conditions were well maintained throughout the measurements.</description><identifier>ISSN: 2059-7983</identifier><identifier>ISSN: 0907-4449</identifier><identifier>EISSN: 2059-7983</identifier><identifier>EISSN: 1399-0047</identifier><identifier>DOI: 10.1107/S2059798322010385</identifier><language>eng</language><publisher>5 Abbey Square, Chester, Cheshire CH1 2HU, England: International Union of Crystallography</publisher><subject>Anaerobic conditions ; catalytic intermediates ; Copper ; copper amine oxidases ; Crystallography ; Intermediates ; Microcrystals ; mix‐and‐inject method ; Oxidase ; peptidyl quinone cofactor ; Quinones ; Reaction mechanisms ; serial femtosecond X‐ray crystallography ; Substrates</subject><ispartof>Acta crystallographica. Section D, Biological crystallography., 2022-12, Vol.78 (12), p.1428-1438</ispartof><rights>2022 Takeshi Murakawa et al. published by IUCr Journals.</rights><rights>Copyright Wiley Subscription Services, Inc. Dec 2022</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4223-702856c0df6cc7718534af15d390a593800a4efbe1441febf211cb4ae757251f3</citedby><cites>FETCH-LOGICAL-c4223-702856c0df6cc7718534af15d390a593800a4efbe1441febf211cb4ae757251f3</cites><orcidid>0000-0003-1218-3759 ; 0000-0001-5905-532X ; 0000-0002-0617-4429 ; 0000-0001-5857-5753 ; 0000-0003-1735-2937</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1107%2FS2059798322010385$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1107%2FS2059798322010385$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,778,782,1414,27907,27908,45557,45558</link.rule.ids></links><search><creatorcontrib>Murakawa, Takeshi</creatorcontrib><creatorcontrib>Suzuki, Mamoru</creatorcontrib><creatorcontrib>Fukui, Kenji</creatorcontrib><creatorcontrib>Masuda, Tetsuya</creatorcontrib><creatorcontrib>Sugahara, Michihiro</creatorcontrib><creatorcontrib>Tono, Kensuke</creatorcontrib><creatorcontrib>Tanaka, Tomoyuki</creatorcontrib><creatorcontrib>Iwata, So</creatorcontrib><creatorcontrib>Nango, Eriko</creatorcontrib><creatorcontrib>Yano, Takato</creatorcontrib><creatorcontrib>Tanizawa, Katsuyuki</creatorcontrib><creatorcontrib>Okajima, Toshihide</creatorcontrib><title>Serial femtosecond X‐ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase</title><title>Acta crystallographica. Section D, Biological crystallography.</title><description>The mechanisms by which enzymes promote catalytic reactions efficiently through their structural changes remain to be fully elucidated. Recent progress in serial femtosecond X‐ray crystallography (SFX) using X‐ray free‐electron lasers (XFELs) has made it possible to address these issues. In particular, mix‐and‐inject serial crystallography (MISC) is promising for the direct observation of structural changes associated with ongoing enzymic reactions. In this study, SFX measurements using a liquid‐jet system were performed on microcrystals of bacterial copper amine oxidase anaerobically premixed with a substrate amine solution. The structure determined at 1.94 Å resolution indicated that the peptidyl quinone cofactor is in equilibrium between the aminoresorcinol and semiquinone radical intermediates, which accumulate only under anaerobic single‐turnover conditions. These results show that anaerobic conditions were well maintained throughout the liquid‐jet SFX measurements, preventing the catalytic intermediates from reacting with dioxygen. These results also provide a necessary framework for performing time‐resolved MISC to study enzymic reaction mechanisms under anaerobic conditions.
Serial femtosecond X‐ray crystallography was performed using a liquid‐jet system on bacterial copper amine oxidase microcrystals anaerobically premixed with an amine substrate. The structure determined at 1.94 Å resolution revealed catalytic intermediates in two reduced forms, confirming that anaerobic conditions were well maintained throughout the measurements.</description><subject>Anaerobic conditions</subject><subject>catalytic intermediates</subject><subject>Copper</subject><subject>copper amine oxidases</subject><subject>Crystallography</subject><subject>Intermediates</subject><subject>Microcrystals</subject><subject>mix‐and‐inject method</subject><subject>Oxidase</subject><subject>peptidyl quinone cofactor</subject><subject>Quinones</subject><subject>Reaction mechanisms</subject><subject>serial femtosecond X‐ray crystallography</subject><subject>Substrates</subject><issn>2059-7983</issn><issn>0907-4449</issn><issn>2059-7983</issn><issn>1399-0047</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNqFkc1KxEAMx4soKLoP4G3Ai5fV-ey0x8VvWFBQQU8lO83oLG2nznTR3nwEn9EnsWU9iB6EQJJ_fv8QSJLsM3rEGNXHt5yqXOeZ4JwyKjK1keyM0nTUNn_U28kkxiWllKVCMyF3ku4Wg4OKWKw7H9H4piQPn-8fAXpiQh87qCr_FKB97om3BJohAINfODNMemJ9qLEkBgaw75whrulwlBx0ODqMb1sMBGrXDP2bKyHiXrJloYo4-c67yf352d3J5XR-fXF1MptPjeRcTDXlmUoNLW1qjNYsU0KCZaoUOQWVi4xSkGgXyKRkFheWM2YWElArzRWzYjc5XO9tg39ZYeyK2kWDVQUN-lUsuJapyIVWckAPfqFLvwrNcN1ISanzVIuBYmvKBB9jQFu0wdUQ-oLRYnxF8ecVgydfe15dhf3_hmL2eMrnN4qmQnwBlQyNlg</recordid><startdate>202212</startdate><enddate>202212</enddate><creator>Murakawa, Takeshi</creator><creator>Suzuki, Mamoru</creator><creator>Fukui, Kenji</creator><creator>Masuda, Tetsuya</creator><creator>Sugahara, Michihiro</creator><creator>Tono, Kensuke</creator><creator>Tanaka, Tomoyuki</creator><creator>Iwata, So</creator><creator>Nango, Eriko</creator><creator>Yano, Takato</creator><creator>Tanizawa, Katsuyuki</creator><creator>Okajima, Toshihide</creator><general>International Union of Crystallography</general><general>Wiley Subscription Services, Inc</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QP</scope><scope>7SP</scope><scope>7SR</scope><scope>7TK</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>H8D</scope><scope>JG9</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-1218-3759</orcidid><orcidid>https://orcid.org/0000-0001-5905-532X</orcidid><orcidid>https://orcid.org/0000-0002-0617-4429</orcidid><orcidid>https://orcid.org/0000-0001-5857-5753</orcidid><orcidid>https://orcid.org/0000-0003-1735-2937</orcidid></search><sort><creationdate>202212</creationdate><title>Serial femtosecond X‐ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase</title><author>Murakawa, Takeshi ; Suzuki, Mamoru ; Fukui, Kenji ; Masuda, Tetsuya ; Sugahara, Michihiro ; Tono, Kensuke ; Tanaka, Tomoyuki ; Iwata, So ; Nango, Eriko ; Yano, Takato ; Tanizawa, Katsuyuki ; Okajima, Toshihide</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4223-702856c0df6cc7718534af15d390a593800a4efbe1441febf211cb4ae757251f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Anaerobic conditions</topic><topic>catalytic intermediates</topic><topic>Copper</topic><topic>copper amine oxidases</topic><topic>Crystallography</topic><topic>Intermediates</topic><topic>Microcrystals</topic><topic>mix‐and‐inject method</topic><topic>Oxidase</topic><topic>peptidyl quinone cofactor</topic><topic>Quinones</topic><topic>Reaction mechanisms</topic><topic>serial femtosecond X‐ray crystallography</topic><topic>Substrates</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Murakawa, Takeshi</creatorcontrib><creatorcontrib>Suzuki, Mamoru</creatorcontrib><creatorcontrib>Fukui, Kenji</creatorcontrib><creatorcontrib>Masuda, Tetsuya</creatorcontrib><creatorcontrib>Sugahara, Michihiro</creatorcontrib><creatorcontrib>Tono, Kensuke</creatorcontrib><creatorcontrib>Tanaka, Tomoyuki</creatorcontrib><creatorcontrib>Iwata, So</creatorcontrib><creatorcontrib>Nango, Eriko</creatorcontrib><creatorcontrib>Yano, Takato</creatorcontrib><creatorcontrib>Tanizawa, Katsuyuki</creatorcontrib><creatorcontrib>Okajima, Toshihide</creatorcontrib><collection>CrossRef</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Murakawa, Takeshi</au><au>Suzuki, Mamoru</au><au>Fukui, Kenji</au><au>Masuda, Tetsuya</au><au>Sugahara, Michihiro</au><au>Tono, Kensuke</au><au>Tanaka, Tomoyuki</au><au>Iwata, So</au><au>Nango, Eriko</au><au>Yano, Takato</au><au>Tanizawa, Katsuyuki</au><au>Okajima, Toshihide</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Serial femtosecond X‐ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase</atitle><jtitle>Acta crystallographica. Section D, Biological crystallography.</jtitle><date>2022-12</date><risdate>2022</risdate><volume>78</volume><issue>12</issue><spage>1428</spage><epage>1438</epage><pages>1428-1438</pages><issn>2059-7983</issn><issn>0907-4449</issn><eissn>2059-7983</eissn><eissn>1399-0047</eissn><abstract>The mechanisms by which enzymes promote catalytic reactions efficiently through their structural changes remain to be fully elucidated. Recent progress in serial femtosecond X‐ray crystallography (SFX) using X‐ray free‐electron lasers (XFELs) has made it possible to address these issues. In particular, mix‐and‐inject serial crystallography (MISC) is promising for the direct observation of structural changes associated with ongoing enzymic reactions. In this study, SFX measurements using a liquid‐jet system were performed on microcrystals of bacterial copper amine oxidase anaerobically premixed with a substrate amine solution. The structure determined at 1.94 Å resolution indicated that the peptidyl quinone cofactor is in equilibrium between the aminoresorcinol and semiquinone radical intermediates, which accumulate only under anaerobic single‐turnover conditions. These results show that anaerobic conditions were well maintained throughout the liquid‐jet SFX measurements, preventing the catalytic intermediates from reacting with dioxygen. These results also provide a necessary framework for performing time‐resolved MISC to study enzymic reaction mechanisms under anaerobic conditions.
Serial femtosecond X‐ray crystallography was performed using a liquid‐jet system on bacterial copper amine oxidase microcrystals anaerobically premixed with an amine substrate. The structure determined at 1.94 Å resolution revealed catalytic intermediates in two reduced forms, confirming that anaerobic conditions were well maintained throughout the measurements.</abstract><cop>5 Abbey Square, Chester, Cheshire CH1 2HU, England</cop><pub>International Union of Crystallography</pub><doi>10.1107/S2059798322010385</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0003-1218-3759</orcidid><orcidid>https://orcid.org/0000-0001-5905-532X</orcidid><orcidid>https://orcid.org/0000-0002-0617-4429</orcidid><orcidid>https://orcid.org/0000-0001-5857-5753</orcidid><orcidid>https://orcid.org/0000-0003-1735-2937</orcidid></addata></record> |
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| identifier | ISSN: 2059-7983 |
| ispartof | Acta crystallographica. Section D, Biological crystallography., 2022-12, Vol.78 (12), p.1428-1438 |
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| language | eng |
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| source | Wiley Online Library Journals Frontfile Complete; Alma/SFX Local Collection |
| subjects | Anaerobic conditions catalytic intermediates Copper copper amine oxidases Crystallography Intermediates Microcrystals mix‐and‐inject method Oxidase peptidyl quinone cofactor Quinones Reaction mechanisms serial femtosecond X‐ray crystallography Substrates |
| title | Serial femtosecond X‐ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase |
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