Structural Insights into Substrate Specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana
Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6’-hydroxylase (F6’H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6’H...
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| description | Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6’-hydroxylase (F6’H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6’H1 apo enzyme by X-ray crystallography. It is the first reported structure of a 2OGD enzyme involved in coumarin biosynthesis and closely resembles the structure of
Arabidopsis thaliana
anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C2’H) from sweet potato. By comparing these two structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis. |
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Arabidopsis thaliana
anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C2’H) from sweet potato. By comparing these two structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep10355</identifier><identifier>PMID: 25993561</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/45/603 ; 631/535/1266 ; 631/92/173 ; 631/92/607 ; 82 ; 82/80 ; 82/83 ; Amino acids ; Arabidopsis - enzymology ; Arabidopsis Proteins - chemistry ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; BASIC BIOLOGICAL SCIENCES ; Binding Sites ; Biocatalysis ; Biosynthesis ; Catalysis ; Coumarin ; Coumarins - chemistry ; Coumarins - metabolism ; Crystallography ; Crystallography, X-Ray ; Dioxygenase ; Dioxygenases - chemistry ; Dioxygenases - genetics ; Dioxygenases - metabolism ; enzyme mechanisms ; Enzymes ; Homology ; Humanities and Social Sciences ; Hydroxylase ; Ketoglutaric acid ; Metabolites ; Molecular Dynamics Simulation ; multidisciplinary ; Mutagenesis, Site-Directed ; Oxygenases - chemistry ; Oxygenases - metabolism ; Protein Structure, Tertiary ; Science ; Secondary metabolites ; Site-directed mutagenesis ; Substrate Specificity ; Substrates ; X-ray crystallography</subject><ispartof>Scientific reports, 2015-05, Vol.5 (1), p.10355, Article 10355</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group May 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited 2015 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c465t-5afa3a358822644d2f4377ad361154c495e6a8be4282aa23544014b9c45f57763</citedby><cites>FETCH-LOGICAL-c465t-5afa3a358822644d2f4377ad361154c495e6a8be4282aa23544014b9c45f57763</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438608/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438608/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25993561$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1215409$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Xinxiao</creatorcontrib><creatorcontrib>Zhou, Dayong</creatorcontrib><creatorcontrib>Kandavelu, Palani</creatorcontrib><creatorcontrib>Zhang, Hua</creatorcontrib><creatorcontrib>Yuan, Qipeng</creatorcontrib><creatorcontrib>Wang, Bi-Cheng</creatorcontrib><creatorcontrib>Rose, John</creatorcontrib><creatorcontrib>Yan, Yajun</creatorcontrib><creatorcontrib>Argonne National Laboratory (ANL), Argonne, IL (United States)</creatorcontrib><title>Structural Insights into Substrate Specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6’-hydroxylase (F6’H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6’H1 apo enzyme by X-ray crystallography. It is the first reported structure of a 2OGD enzyme involved in coumarin biosynthesis and closely resembles the structure of
Arabidopsis thaliana
anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C2’H) from sweet potato. By comparing these two structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis.</description><subject>631/45/603</subject><subject>631/535/1266</subject><subject>631/92/173</subject><subject>631/92/607</subject><subject>82</subject><subject>82/80</subject><subject>82/83</subject><subject>Amino acids</subject><subject>Arabidopsis - enzymology</subject><subject>Arabidopsis Proteins - chemistry</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - metabolism</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Binding Sites</subject><subject>Biocatalysis</subject><subject>Biosynthesis</subject><subject>Catalysis</subject><subject>Coumarin</subject><subject>Coumarins - chemistry</subject><subject>Coumarins - metabolism</subject><subject>Crystallography</subject><subject>Crystallography, X-Ray</subject><subject>Dioxygenase</subject><subject>Dioxygenases - chemistry</subject><subject>Dioxygenases - genetics</subject><subject>Dioxygenases - metabolism</subject><subject>enzyme mechanisms</subject><subject>Enzymes</subject><subject>Homology</subject><subject>Humanities and Social Sciences</subject><subject>Hydroxylase</subject><subject>Ketoglutaric acid</subject><subject>Metabolites</subject><subject>Molecular Dynamics Simulation</subject><subject>multidisciplinary</subject><subject>Mutagenesis, Site-Directed</subject><subject>Oxygenases - chemistry</subject><subject>Oxygenases - metabolism</subject><subject>Protein Structure, Tertiary</subject><subject>Science</subject><subject>Secondary metabolites</subject><subject>Site-directed mutagenesis</subject><subject>Substrate Specificity</subject><subject>Substrates</subject><subject>X-ray crystallography</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNplkd9qFDEUxoMottRe-AIS9MrCtJN_s8mNsCzWFgq9WL0OZzKZ3ZTZZEwy4tz5Gr6eT2LK1mWLucmB8-M738eH0FtSX5KayasU7VgGIV6gU1pzUVFG6cuj-QSdp_RQlyeo4kS9RidUKMVEQ06RW-c4mTxFGPCtT26zzQk7nwNeT23KEbLF69Ea1zvj8oxDj69tnIYwD9UqLHHz59fv6mbuYvg5D5As7mPY4WWE1nVhTC7hvIXBgYc36FUPQ7LnT_8Z-nb9-evqprq7_3K7Wt5VhjciVwJ6YMCElJQ2nHe052yxgI41hAhuuBK2AdlaTiUFoExwXhPeKsNFLxaLhp2hT3vdcWp3tjPWlxSDHqPbQZx1AKefb7zb6k34oTlnsqllEXi_FwgpO51KbGu2JnhvTdaEFhe1KtCHpysxfJ9syvohTNGXYJpIpYSQRNFCfdxTJoZUiuoPNkitH9vTh_YK--7Y94H811UBLvZAKiu_sfHo5H9qfwEslKT-</recordid><startdate>20150520</startdate><enddate>20150520</enddate><creator>Sun, Xinxiao</creator><creator>Zhou, Dayong</creator><creator>Kandavelu, Palani</creator><creator>Zhang, Hua</creator><creator>Yuan, Qipeng</creator><creator>Wang, Bi-Cheng</creator><creator>Rose, John</creator><creator>Yan, Yajun</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20150520</creationdate><title>Structural Insights into Substrate Specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana</title><author>Sun, Xinxiao ; Zhou, Dayong ; Kandavelu, Palani ; Zhang, Hua ; Yuan, Qipeng ; Wang, Bi-Cheng ; Rose, John ; Yan, Yajun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c465t-5afa3a358822644d2f4377ad361154c495e6a8be4282aa23544014b9c45f57763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/45/603</topic><topic>631/535/1266</topic><topic>631/92/173</topic><topic>631/92/607</topic><topic>82</topic><topic>82/80</topic><topic>82/83</topic><topic>Amino acids</topic><topic>Arabidopsis - enzymology</topic><topic>Arabidopsis Proteins - chemistry</topic><topic>Arabidopsis Proteins - genetics</topic><topic>Arabidopsis Proteins - metabolism</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Binding Sites</topic><topic>Biocatalysis</topic><topic>Biosynthesis</topic><topic>Catalysis</topic><topic>Coumarin</topic><topic>Coumarins - chemistry</topic><topic>Coumarins - metabolism</topic><topic>Crystallography</topic><topic>Crystallography, X-Ray</topic><topic>Dioxygenase</topic><topic>Dioxygenases - chemistry</topic><topic>Dioxygenases - genetics</topic><topic>Dioxygenases - metabolism</topic><topic>enzyme mechanisms</topic><topic>Enzymes</topic><topic>Homology</topic><topic>Humanities and Social Sciences</topic><topic>Hydroxylase</topic><topic>Ketoglutaric acid</topic><topic>Metabolites</topic><topic>Molecular Dynamics Simulation</topic><topic>multidisciplinary</topic><topic>Mutagenesis, Site-Directed</topic><topic>Oxygenases - chemistry</topic><topic>Oxygenases - metabolism</topic><topic>Protein Structure, Tertiary</topic><topic>Science</topic><topic>Secondary metabolites</topic><topic>Site-directed mutagenesis</topic><topic>Substrate Specificity</topic><topic>Substrates</topic><topic>X-ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Xinxiao</creatorcontrib><creatorcontrib>Zhou, Dayong</creatorcontrib><creatorcontrib>Kandavelu, Palani</creatorcontrib><creatorcontrib>Zhang, Hua</creatorcontrib><creatorcontrib>Yuan, Qipeng</creatorcontrib><creatorcontrib>Wang, Bi-Cheng</creatorcontrib><creatorcontrib>Rose, John</creatorcontrib><creatorcontrib>Yan, Yajun</creatorcontrib><creatorcontrib>Argonne National Laboratory (ANL), Argonne, IL (United States)</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Xinxiao</au><au>Zhou, Dayong</au><au>Kandavelu, Palani</au><au>Zhang, Hua</au><au>Yuan, Qipeng</au><au>Wang, Bi-Cheng</au><au>Rose, John</au><au>Yan, Yajun</au><aucorp>Argonne National Laboratory (ANL), Argonne, IL (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structural Insights into Substrate Specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-05-20</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>10355</spage><pages>10355-</pages><artnum>10355</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Coumarins belong to an important class of plant secondary metabolites. Feruloyl-CoA 6’-hydroxylase (F6’H), a 2-oxoglutarate dependent dioxygenase (2OGD), catalyzes a pivotal step in the biosynthesis of a simple coumarin scopoletin. In this study, we determined the 3-dimensional structure of the F6’H1 apo enzyme by X-ray crystallography. It is the first reported structure of a 2OGD enzyme involved in coumarin biosynthesis and closely resembles the structure of
Arabidopsis thaliana
anthocyanidin synthase. To better understand the mechanism of enzyme catalysis and substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C2’H) from sweet potato. By comparing these two structures, we targeted two amino acid residues and verified their roles in substrate binding and specificity by site-directed mutagenesis.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>25993561</pmid><doi>10.1038/srep10355</doi><oa>free_for_read</oa></addata></record> |
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| subjects | 631/45/603 631/535/1266 631/92/173 631/92/607 82 82/80 82/83 Amino acids Arabidopsis - enzymology Arabidopsis Proteins - chemistry Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism BASIC BIOLOGICAL SCIENCES Binding Sites Biocatalysis Biosynthesis Catalysis Coumarin Coumarins - chemistry Coumarins - metabolism Crystallography Crystallography, X-Ray Dioxygenase Dioxygenases - chemistry Dioxygenases - genetics Dioxygenases - metabolism enzyme mechanisms Enzymes Homology Humanities and Social Sciences Hydroxylase Ketoglutaric acid Metabolites Molecular Dynamics Simulation multidisciplinary Mutagenesis, Site-Directed Oxygenases - chemistry Oxygenases - metabolism Protein Structure, Tertiary Science Secondary metabolites Site-directed mutagenesis Substrate Specificity Substrates X-ray crystallography |
| title | Structural Insights into Substrate Specificity of Feruloyl-CoA 6’-Hydroxylase from Arabidopsis thaliana |
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