444 lines
59 KiB
XML
444 lines
59 KiB
XML
<document id="338017BF212821743614E43BE840B636" ID-DOI="10.1016/j.phytochem.2020.112626" ID-ISSN="1873-3700" ID-Zenodo-Dep="8291734" IM.bibliography_approvedBy="felipe" IM.illustrations_approvedBy="valdenar" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="felipe" IM.tables_approvedBy="valdenar" IM.taxonomicNames_approvedBy="valdenar" IM.treatments_approvedBy="valdenar" checkinTime="1693246558342" checkinUser="felipe" docAuthor="Miller, Justin C., Hollatz, Allison J. & Schuler, Mary A." docDate="2021" docId="8D608791DF611361FFCD2944FF78B2C5" docLanguage="en" docName="Phytochemistry.183.112626.pdf" docOrigin="Phytochemistry (112626) 183" docSource="http://dx.doi.org/10.1016/j.phytochem.2020.112626" docStyle="DocumentStyle:F36D69FC8B198FBE91029DF9C24697D3.5:Phytochemistry.2020-.journal_article" docStyleId="F36D69FC8B198FBE91029DF9C24697D3" docStyleName="Phytochemistry.2020-.journal_article" docStyleVersion="5" docTitle="Catharanthus" docType="treatment" docVersion="3" lastPageNumber="7" masterDocId="7159FFE9DF641366FFA92F64FFB3B679" masterDocTitle="P 450 variations bifurcate the early terpene indole alkaloid pathway in Catharanthus roseus and Camptotheca acuminata" masterLastPageNumber="13" masterPageNumber="1" pageNumber="6" updateTime="1693411865241" updateUser="valdenar">
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<mods:title id="F16D2224CDF05D2E1C7D9E1D987A8E28">P 450 variations bifurcate the early terpene indole alkaloid pathway in Catharanthus roseus and Camptotheca acuminata</mods:title>
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<mods:name id="503A4F5D8425BB26118FC703C1BD6BE1" type="personal">
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<mods:namePart id="8B1DCB58EA3231E889248874B080C3F9">Miller, Justin C.</mods:namePart>
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<mods:affiliation id="C66F24D09C902754916FE46F2EE8A91A">Department of Chemistry, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., 162 Edward R. Madigan Laboratory (ERML), Urbana, IL, 61801, USA</mods:affiliation>
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<mods:namePart id="E2894A2731A2887B1BF89A033F3AE017">Hollatz, Allison J.</mods:namePart>
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<mods:name id="0304A25D29EC4DE0325EF4D461395CC9" type="personal">
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<mods:roleTerm id="C79A1898720102FC5673D8A35D6477A0">Author</mods:roleTerm>
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<mods:namePart id="E192F5F77DAB25E1AF6CBA6AC96BA678">Schuler, Mary A.</mods:namePart>
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<mods:title id="18197D98F4C2F15D550F5153AB468DB6">Phytochemistry</mods:title>
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<mods:part id="644273C79A0FA9546C496DEA9EACEAFC">
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<mods:date id="D1EAD7080C46BAC0EFB6879D17BB4D20">2021</mods:date>
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<mods:title id="320E945C4C79BA283D255C495A76788B">112626</mods:title>
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<mods:number id="9CDF4E41DFD609E9F071B1790296DAA8">2021-03-31</mods:number>
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<mods:number id="0BA9AFCD44928C9E03FAF88D465EED5B">183</mods:number>
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<mods:url id="1A47CC339B43959603158BF1A8C8B42A">http://dx.doi.org/10.1016/j.phytochem.2020.112626</mods:url>
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<mods:classification id="DCAA1703BEA196F41F4B67DEDDA07184">journal article</mods:classification>
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<mods:identifier id="E970306ABFDBD0B345C1C0B658F87CDE" type="DOI">10.1016/j.phytochem.2020.112626</mods:identifier>
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<mods:identifier id="A458F23842EE2B8778253EB3744C9A49" type="ISSN">1873-3700</mods:identifier>
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<treatment id="8D608791DF611361FFCD2944FF78B2C5" LSID="urn:lsid:plazi:treatment:8D608791DF611361FFCD2944FF78B2C5" httpUri="http://treatment.plazi.org/id/8D608791DF611361FFCD2944FF78B2C5" lastPageId="7" lastPageNumber="7" pageId="5" pageNumber="6">
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<subSubSection id="4DD3650CDF611363FFCD2944FD0DB04A" box="[100,702,1568,1587]" pageId="5" pageNumber="6" type="nomenclature">
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<paragraph id="05763687DF611363FFCD2944FD0DB04A" blockId="5.[100,702,1568,1587]" box="[100,702,1568,1587]" pageId="5" pageNumber="6">
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<heading id="5E3E81EBDF611363FFCD2944FD0DB04A" bold="true" box="[100,702,1568,1587]" fontSize="36" level="1" pageId="5" pageNumber="6" reason="1">
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<emphasis id="37BDEA95DF611363FFCD2944FD0DB04A" bold="true" box="[100,702,1568,1587]" italics="true" pageId="5" pageNumber="6">
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2.8. Molecular modeling of
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<taxonomicName id="C2C94D04DF611363FECD2944FE6FB04A" ID-CoL="3JFJ" ID-ENA="4057" box="[356,476,1568,1587]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">Catharanthus</taxonomicName>
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and
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<taxonomicName id="C2C94D04DF611363FDA52944FD33B04A" box="[524,640,1568,1587]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">Camptotheca</taxonomicName>
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P450s
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</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection id="4DD3650CDF611361FF2D293CFF78B2C5" lastPageId="7" lastPageNumber="8" pageId="5" pageNumber="6" type="description">
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<paragraph id="05763687DF611363FF2D293CFCB1B013" blockId="5.[100,770,1623,1671]" box="[132,770,1623,1643]" pageId="5" pageNumber="6">
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Molecular models for
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<taxonomicName id="C2C94D04DF611363FEC42933FD93B012" authority="CYP" authorityName="CYP" box="[365,544,1623,1643]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">
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<emphasis id="37BDEA95DF611363FEC42933FE56B013" bold="true" box="[365,485,1623,1642]" italics="true" pageId="5" pageNumber="6">Catharanthus</emphasis>
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CYP
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</taxonomicName>
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72A1 and
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<taxonomicName id="C2C94D04DF611363FD272933FCB1B013" box="[654,770,1623,1642]" pageId="5" pageNumber="6">
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<emphasis id="37BDEA95DF611363FD272933FCB1B013" bold="true" box="[654,770,1623,1642]" italics="true" pageId="5" pageNumber="6">Camptotheca</emphasis>
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</taxonomicName>
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</paragraph>
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<paragraph id="05763687DF611363FFCD2910FA87B2A1" blockId="5.[100,770,1623,1671]" lastBlockId="5.[818,1488,1026,1659]" pageId="5" pageNumber="6">
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CYP72A564 and CYP72A565, constructed according to published procedures (
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<bibRefCitation id="61584B76DF611363FC032B66FB62B26C" author="Rupasinghe, S. & Schuler, M. A." box="[938,1233,1026,1045]" pageId="5" pageNumber="6" pagination="473 - 505" refId="ref15264" refString="Rupasinghe, S., Schuler, M. A., 2006. Homology modeling of plant cytochrome P 450 s. Phytochemistry Rev. 5, 473 - 505. https: // doi. org / 10.1007 / s 11101 - 006 - 9028 - y." type="journal article" year="2006">Rupasinghe and Schuler, 2006</bibRefCitation>
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), indicated that the backbones of these three proteins overlay well (RMSD less than 2.0 Å, green,
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<figureCitation id="9DF22A02DF611363FC9B2B5DFCC9B234" box="[818,890,1081,1101]" captionStart="Fig" captionStartId="6.[100,130,914,931]" captionTargetBox="[200,1386,149,884]" captionTargetId="figure-542@6.[199,1388,148,886]" captionTargetPageId="6" captionText="Fig. 7. Molecular models of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565. (A) Backbone overlays of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565 models are shown with the alpha-carbon RMSD amongst CYP72A1, CYP72A564 and CYP72A565 depicted from green (0.0 Å) to yellow (3.0 Å) to red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A564 (orange). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A565 (rose)." figureDoi="http://doi.org/10.5281/zenodo.8291748" httpUri="https://zenodo.org/record/8291748/files/figure.png" pageId="5" pageNumber="6">Fig. 7A</figureCitation>
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) except for the following regions: the C-terminus of the A
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<superScript id="F2BC9BCFDF611363FA1C2B52FA0AB23A" attach="left" box="[1461,1465,1078,1091]" fontSize="6" pageId="5" pageNumber="6">′</superScript>
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-A loop, β1-2, the N-terminus of the C helix, the D-E
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<superScript id="F2BC9BCFDF611363FB592B36FB47B226" attach="left" box="[1264,1268,1106,1119]" fontSize="6" pageId="5" pageNumber="6">′</superScript>
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loop, the N-terminus of the G-helix, the N-terminal half of the H–I loop, the middle of the loop between β1-3 and β1-4, and in a loop region immediately C-terminal of the PERF domain. None of these regions have RMSD values greater than 3.5 Å (orange), and all are outside the predicted SRSs.
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</paragraph>
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<paragraph id="05763687DF611363FCF82B85FC60B072" blockId="5.[818,1488,1026,1659]" pageId="5" pageNumber="6">
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Dockings of loganin in the
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<taxonomicName id="C2C94D04DF611363FBF82B85FB48B28D" authority="CYP" authorityName="CYP" box="[1105,1275,1249,1268]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">
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<emphasis id="37BDEA95DF611363FBF82B85FB7AB28D" bold="true" box="[1105,1225,1249,1268]" italics="true" pageId="5" pageNumber="6">Catharanthus</emphasis>
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CYP
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</taxonomicName>
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72A1 catalytic site and loganic acid in the
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<taxonomicName id="C2C94D04DF611363FC432B98FB23B369" authority="CYP" authorityName="CYP" box="[1002,1168,1276,1296]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">
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<emphasis id="37BDEA95DF611363FC432B98FBEDB376" bold="true" box="[1002,1118,1276,1295]" italics="true" pageId="5" pageNumber="6">Camptotheca</emphasis>
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CYP
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</taxonomicName>
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72A564 and CYP72A565 catalytic sites predicted that both substrates position C10 within 4.5 Å of the oxygen bound to the heme with comparable interaction energies (
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<tableCitation id="484B033CDF611363FC932A35FC32B31D" box="[826,897,1361,1380]" captionStart="Table 3" captionStartId="6.[100,150,1117,1133]" captionTargetPageId="6" captionText="Table 3 Docking parameters from homology models." pageId="5" pageNumber="6">Table 3</tableCitation>
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); as both proposed mechanisms for the C–C bond scission demand (
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<bibRefCitation id="61584B76DF611363FCD22A08FB74B3F9" author="Guengerich, F. P. & Yoshimoto, F. K." box="[891,1223,1388,1408]" pageId="5" pageNumber="6" pagination="6573 - 6655" refId="ref13988" refString="Guengerich, F. P., Yoshimoto, F. K., 2018. Formation and cleavage of C - C bonds by enzymatic oxidation - reduction reactions. Chem. Rev. 118, 6573 - 6655. https: // doi. org / 10.1021 / acs. chemrev. 8 b 00031." type="journal article" year="2018">Guengerich and Yoshimoto, 2018</bibRefCitation>
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;
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<bibRefCitation id="61584B76DF611363FB702A09FA72B3F9" author="Yamamoto, H. & Katano, N. & Ooi, A. & Inoue, K." box="[1241,1473,1388,1408]" pageId="5" pageNumber="6" pagination="7 - 12" refId="ref15716" refString="Yamamoto, H., Katano, N., Ooi, A., Inoue, K., 2000. Secologanin synthase which catalyzes the oxidative cleavage of loganin into secologanin is a cytochrome P 450. Phytochemistry 53, 7 - 12. https: // doi. org / 10.1016 / S 0031 - 9422 (99) 00471 - 9." type="journal article" year="2000">Yamamoto et al., 2000</bibRefCitation>
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), abstraction of a hydrogen from this carbon forms the radical needed to cleave the C–C bond in loganin. Even so, the orientations of these substrates were different with loganic acid oriented more vertically in the two
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<taxonomicName id="C2C94D04DF611363FCF42AB8FBB2B396" authority="CYP" authorityName="CYP" box="[861,1025,1500,1519]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">
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<emphasis id="37BDEA95DF611363FCF42AB8FC62B396" bold="true" box="[861,977,1500,1519]" italics="true" pageId="5" pageNumber="6">Camptotheca</emphasis>
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CYP
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</taxonomicName>
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72A proteins than loganin is in the
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<taxonomicName id="C2C94D04DF611363FAFE2AB8FCEDB072" authority="CYP" authorityName="CYP" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">
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<emphasis id="37BDEA95DF611363FAFE2AB8FA7CB396" bold="true" box="[1367,1487,1500,1519]" italics="true" pageId="5" pageNumber="6">Catharanthus</emphasis>
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CYP
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</taxonomicName>
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72A1 model.
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</paragraph>
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<paragraph id="05763687DF611360FCF82970FF51B0A3" blockId="5.[818,1488,1026,1659]" lastBlockId="6.[100,770,1512,1982]" lastPageId="6" lastPageNumber="7" pageId="5" pageNumber="6">
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Overlays of the predicted contact residues highlighting amino acids identical in each (
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<figureCitation id="9DF22A02DF611363FC762954FBD1B03A" box="[991,1122,1584,1603]" captionStart="Fig" captionStartId="6.[100,130,914,931]" captionTargetBox="[200,1386,149,884]" captionTargetId="figure-542@6.[199,1388,148,886]" captionTargetPageId="6" captionText="Fig. 7. Molecular models of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565. (A) Backbone overlays of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565 models are shown with the alpha-carbon RMSD amongst CYP72A1, CYP72A564 and CYP72A565 depicted from green (0.0 Å) to yellow (3.0 Å) to red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A564 (orange). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A565 (rose)." figureDoi="http://doi.org/10.5281/zenodo.8291748" httpUri="https://zenodo.org/record/8291748/files/figure.png" pageId="5" pageNumber="6">Fig. 7C and E</figureCitation>
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) and different in each (
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<figureCitation id="9DF22A02DF611363FAEC2954FA7AB03A" box="[1349,1481,1584,1603]" captionStart="Fig" captionStartId="6.[100,130,914,931]" captionTargetBox="[200,1386,149,884]" captionTargetId="figure-542@6.[199,1388,148,886]" captionTargetPageId="6" captionText="Fig. 7. Molecular models of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565. (A) Backbone overlays of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565 models are shown with the alpha-carbon RMSD amongst CYP72A1, CYP72A564 and CYP72A565 depicted from green (0.0 Å) to yellow (3.0 Å) to red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A564 (orange). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A565 (rose)." figureDoi="http://doi.org/10.5281/zenodo.8291748" httpUri="https://zenodo.org/record/8291748/files/figure.png" pageId="5" pageNumber="6">Fig. 7D and F</figureCitation>
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) show many identical residues within substrate contact distance and relatively few different residues in this area. Among the variant residues, several differences occur in SRS1 at positions 132, 133, 134, 135 and 138 (
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<figureCitation id="9DF22A02DF621360FF3C2960FF7BB06E" box="[149,200,1540,1559]" captionStart="Fig" captionStartId="2.[100,130,1939,1956]" captionTargetBox="[207,1380,1119,1909]" captionTargetId="figure-607@2.[206,1381,1117,1911]" captionTargetPageId="2" captionText="Fig. 2. CYP72A multiple sequence alignment. Signal anchor domain fusion of CYP72A565 into CYP72A564 is underlined; SRS regions are underlined in bold; predicted substrate contacts within 4.5 Å of loganic acid/loganin are gray-filled." figureDoi="http://doi.org/10.5281/zenodo.8291738" httpUri="https://zenodo.org/record/8291738/files/figure.png" pageId="6" pageNumber="7">Fig. 2</figureCitation>
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;
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<figureCitation id="9DF22A02DF621360FF7B2960FEE3B06E" box="[210,336,1540,1559]" captionStart="Fig" captionStartId="6.[100,130,914,931]" captionTargetBox="[200,1386,149,884]" captionTargetId="figure-542@6.[199,1388,148,886]" captionTargetPageId="6" captionText="Fig. 7. Molecular models of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565. (A) Backbone overlays of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565 models are shown with the alpha-carbon RMSD amongst CYP72A1, CYP72A564 and CYP72A565 depicted from green (0.0 Å) to yellow (3.0 Å) to red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A564 (orange). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A565 (rose)." figureDoi="http://doi.org/10.5281/zenodo.8291748" httpUri="https://zenodo.org/record/8291748/files/figure.png" pageId="6" pageNumber="7">Fig. 7B, C, 7E</figureCitation>
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). The
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<taxonomicName id="C2C94D04DF621360FE2E2967FE4CB06F" box="[391,511,1539,1558]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
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<emphasis id="37BDEA95DF621360FE2E2967FE4CB06F" bold="true" box="[391,511,1539,1558]" italics="true" pageId="6" pageNumber="7">Catharanthus</emphasis>
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</taxonomicName>
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protein differs from the two
|
||
<taxonomicName id="C2C94D04DF621360FFCD297BFF6BB04B" box="[100,216,1567,1586]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FFCD297BFF6BB04B" bold="true" box="[100,216,1567,1586]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
</taxonomicName>
|
||
proteins at all of these positions, and the two
|
||
<taxonomicName id="C2C94D04DF621360FD27297BFCB1B04B" box="[654,770,1567,1586]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FD27297BFCB1B04B" bold="true" box="[654,770,1567,1586]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
</taxonomicName>
|
||
proteins differ only at position 135 (Asn/Ser). One additional difference among these three proteins occurs in SRS3 at position 270 with all three proteins having different residues (Thr/Lys/Arg). Similar overlays of identical and different residues in these two
|
||
<taxonomicName id="C2C94D04DF621360FD9C29EBFD1AB0DB" box="[565,681,1679,1698]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FD9C29EBFD1AB0DB" bold="true" box="[565,681,1679,1698]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
</taxonomicName>
|
||
proteins (
|
||
<figureCitation id="9DF22A02DF621360FFC529CFFF76B0C7" box="[108,197,1707,1726]" captionStart="Fig" captionStartId="6.[100,130,914,931]" captionTargetBox="[200,1386,149,884]" captionTargetId="figure-542@6.[199,1388,148,886]" captionTargetPageId="6" captionText="Fig. 7. Molecular models of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565. (A) Backbone overlays of Catharanthus CYP72A1 and Camptotheca CYP72A564 and CYP72A565 models are shown with the alpha-carbon RMSD amongst CYP72A1, CYP72A564 and CYP72A565 depicted from green (0.0 Å) to yellow (3.0 Å) to red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A564 (orange). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in Catharanthus CYP72A1 (blue) and loganic acid (gray) docked in Camptotheca CYP72A565 (rose)." figureDoi="http://doi.org/10.5281/zenodo.8291748" httpUri="https://zenodo.org/record/8291748/files/figure.png" pageId="6" pageNumber="7">Fig. 7B–E</figureCitation>
|
||
) highlight their substantial identity in all SRSs comprising the catalytic site.
|
||
</paragraph>
|
||
<caption id="51B6660FDF611363FFCD29D6FDF2B0A4" pageId="5" pageNumber="6" startId="5.[100,150,1714,1730]" targetBox="[116,1471,1776,1917]" targetIsTable="true" targetPageId="5" targetType="table">
|
||
<paragraph id="05763687DF611363FFCD29D6FF14B0BA" blockId="5.[100,577,1714,1757]" box="[100,167,1714,1731]" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FFCD29D6FF14B0BA" bold="true" box="[100,167,1714,1731]" pageId="5" pageNumber="6">Table 2</emphasis>
|
||
</paragraph>
|
||
<paragraph id="05763687DF611363FFCD29A8FDF2B0A4" blockId="5.[100,577,1714,1757]" box="[100,577,1740,1757]" pageId="5" pageNumber="6">Kinetic parameters estimated from steady-state kinetics.</paragraph>
|
||
</caption>
|
||
<paragraph id="05763687DF611363FF2B2995FA05B104" pageId="5" pageNumber="6">
|
||
<table id="77C9C427DF61EC99FFDD2994FA0CB104" box="[116,1471,1776,1917]" gridcols="6" gridrows="6" pageId="5" pageNumber="6">
|
||
<tr id="BBF934C5DF61EC99FFDD2994FA0CB179" box="[116,1471,1776,1792]" gridrow="0" pageId="5" pageNumber="6">
|
||
<th id="F8285DB9DF61EC99FFDD2994FF03B179" box="[116,176,1776,1792]" gridcol="0" gridrow="0" pageId="5" pageNumber="6">CYP</th>
|
||
<th id="F8285DB9DF61EC99FEE42994FE1BB179" box="[333,424,1776,1792]" gridcol="1" gridrow="0" pageId="5" pageNumber="6">Substrate</th>
|
||
<th id="F8285DB9DF61EC99FDEC2994FD00B179" box="[581,691,1776,1792]" gridcol="2" gridrow="0" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FDD82995FDCFB086" bold="true" box="[625,636,1777,1791]" italics="true" pageId="5" pageNumber="6">K</emphasis>
|
||
M
|
||
</th>
|
||
<th id="F8285DB9DF61EC99FCF92994FC0DB179" box="[848,958,1776,1792]" gridcol="3" gridrow="0" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FCDF2995FC32B086" bold="true" box="[886,897,1777,1791]" italics="true" pageId="5" pageNumber="6">V</emphasis>
|
||
max
|
||
</th>
|
||
<th id="F8285DB9DF61EC99FBF22994FB0CB179" box="[1115,1215,1776,1792]" gridcol="4" gridrow="0" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FB292994FB3AB087" bold="true" box="[1152,1161,1776,1790]" italics="true" pageId="5" pageNumber="6">k</emphasis>
|
||
cat
|
||
</th>
|
||
<th id="F8285DB9DF61EC99FAF42994FA0CB179" box="[1373,1471,1776,1792]" gridcol="5" gridrow="0" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FADB2994FAC8B087" bold="true" box="[1394,1403,1776,1790]" italics="true" pageId="5" pageNumber="6">k</emphasis>
|
||
cat/
|
||
<emphasis id="37BDEA95DF611363FA3D2995FA2CB086" bold="true" box="[1428,1439,1777,1791]" italics="true" pageId="5" pageNumber="6">K</emphasis>
|
||
M
|
||
</th>
|
||
</tr>
|
||
<tr id="BBF934C5DF61EC99FFDD2874FA0CB15A" box="[116,1471,1808,1827]" gridrow="1" pageId="5" pageNumber="6" rowspan-0="1" rowspan-1="1">
|
||
<td id="F8285DB9DF61EC99FDEC2874FD00B15A" box="[581,691,1808,1827]" gridcol="2" gridrow="1" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FDC72870FD39B15B" bold="true" box="[622,650,1812,1826]" italics="true" pageId="5" pageNumber="6">mM</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF61EC99FCF92874FC0DB15A" box="[848,958,1808,1827]" gridcol="3" gridrow="1" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FCCA2877FCDFB15A" box="[867,876,1811,1827]" italics="true" pageId="5" pageNumber="6">μ</emphasis>
|
||
<emphasis id="37BDEA95DF611363FCC52870FC28B15B" bold="true" box="[876,923,1812,1826]" italics="true" pageId="5" pageNumber="6">M min</emphasis>
|
||
<emphasis id="37BDEA95DF611363FC0D2874FC18B160" bold="true" box="[932,939,1808,1817]" italics="true" pageId="5" pageNumber="6">1</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF61EC99FBF22874FB0CB15A" box="[1115,1215,1808,1827]" gridcol="4" gridrow="1" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FBDE2870FB21B15B" bold="true" box="[1143,1170,1812,1826]" italics="true" pageId="5" pageNumber="6">min</emphasis>
|
||
<emphasis id="37BDEA95DF611363FB352874FB10B160" bold="true" box="[1180,1187,1808,1817]" italics="true" pageId="5" pageNumber="6">1</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF61EC99FAF42874FA0CB15A" box="[1373,1471,1808,1827]" gridcol="5" gridrow="1" pageId="5" pageNumber="6">
|
||
<emphasis id="37BDEA95DF611363FAF42870FACBB15B" bold="true" box="[1373,1400,1812,1826]" italics="true" pageId="5" pageNumber="6">min</emphasis>
|
||
<emphasis id="37BDEA95DF611363FA282874FA3BB160" bold="true" box="[1409,1416,1808,1817]" italics="true" pageId="5" pageNumber="6">1</emphasis>
|
||
<emphasis id="37BDEA95DF611363FA242870FA1AB15B" bold="true" box="[1421,1449,1812,1826]" italics="true" pageId="5" pageNumber="6">mM</emphasis>
|
||
<emphasis id="37BDEA95DF611363FA112874FA0CB160" bold="true" box="[1464,1471,1808,1817]" italics="true" pageId="5" pageNumber="6">1</emphasis>
|
||
</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF61EC99FFDD284EFA0CB140" box="[116,1471,1834,1849]" gridrow="2" pageId="5" pageNumber="6">
|
||
<th id="F8285DB9DF61EC99FFDD284EFF03B140" box="[116,176,1834,1849]" gridcol="0" gridrow="2" pageId="5" pageNumber="6">72A564</th>
|
||
<td id="F8285DB9DF61EC99FEE4284EFE1BB140" box="[333,424,1834,1849]" gridcol="1" gridrow="2" pageId="5" pageNumber="6">loganic acid</td>
|
||
<td id="F8285DB9DF61EC99FDEC284EFD00B140" box="[581,691,1834,1849]" gridcol="2" gridrow="2" pageId="5" pageNumber="6">2.67 ± 0.80</td>
|
||
<td id="F8285DB9DF61EC99FCF9284EFC0DB140" box="[848,958,1834,1849]" gridcol="3" gridrow="2" pageId="5" pageNumber="6">3.49 ± 0.53</td>
|
||
<td id="F8285DB9DF61EC99FBF2284EFB0CB140" box="[1115,1215,1834,1849]" gridcol="4" gridrow="2" pageId="5" pageNumber="6">13.9 ± 2.1</td>
|
||
<td id="F8285DB9DF61EC99FAF4284EFA0CB140" box="[1373,1471,1834,1849]" gridcol="5" gridrow="2" pageId="5" pageNumber="6">5.2 ± 1.7</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF61EC99FFDD2825FA0CB129" box="[116,1471,1857,1872]" gridrow="3" pageId="5" pageNumber="6" rowspan-0="1">
|
||
<td id="F8285DB9DF61EC99FEE42825FE1BB129" box="[333,424,1857,1872]" gridcol="1" gridrow="3" pageId="5" pageNumber="6">loganin</td>
|
||
<td id="F8285DB9DF61EC99FDEC2825FD00B129" box="[581,691,1857,1872]" gridcol="2" gridrow="3" pageId="5" pageNumber="6">0.242 ± 0.023</td>
|
||
<td id="F8285DB9DF61EC99FCF92825FC0DB129" box="[848,958,1857,1872]" gridcol="3" gridrow="3" pageId="5" pageNumber="6">2.997 ± 0.075</td>
|
||
<td id="F8285DB9DF61EC99FBF22825FB0CB129" box="[1115,1215,1857,1872]" gridcol="4" gridrow="3" pageId="5" pageNumber="6">11.99 ± 0.30</td>
|
||
<td id="F8285DB9DF61EC99FAF42825FA0CB129" box="[1373,1471,1857,1872]" gridcol="5" gridrow="3" pageId="5" pageNumber="6">49.5 ± 4.8</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF61EC99FFDD283CFA0CB11E" box="[116,1471,1880,1895]" gridrow="4" pageId="5" pageNumber="6">
|
||
<th id="F8285DB9DF61EC99FFDD283CFF03B11E" box="[116,176,1880,1895]" gridcol="0" gridrow="4" pageId="5" pageNumber="6">72A565</th>
|
||
<td id="F8285DB9DF61EC99FEE4283CFE1BB11E" box="[333,424,1880,1895]" gridcol="1" gridrow="4" pageId="5" pageNumber="6">loganic acid</td>
|
||
<td id="F8285DB9DF61EC99FDEC283CFD00B11E" box="[581,691,1880,1895]" gridcol="2" gridrow="4" pageId="5" pageNumber="6">3.57 ± 0.42</td>
|
||
<td id="F8285DB9DF61EC99FCF9283CFC0DB11E" box="[848,958,1880,1895]" gridcol="3" gridrow="4" pageId="5" pageNumber="6">4.86 ± 0.32</td>
|
||
<td id="F8285DB9DF61EC99FBF2283CFB0CB11E" box="[1115,1215,1880,1895]" gridcol="4" gridrow="4" pageId="5" pageNumber="6">19.4 ± 1.3</td>
|
||
<td id="F8285DB9DF61EC99FAF4283CFA0CB11E" box="[1373,1471,1880,1895]" gridcol="5" gridrow="4" pageId="5" pageNumber="6">5.45 ± 0.74</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF61EC99FFDD280AFA0CB104" box="[116,1471,1902,1917]" gridrow="5" pageId="5" pageNumber="6" rowspan-0="1">
|
||
<td id="F8285DB9DF61EC99FEE4280AFE1BB104" box="[333,424,1902,1917]" gridcol="1" gridrow="5" pageId="5" pageNumber="6">loganin</td>
|
||
<td id="F8285DB9DF61EC99FDEC280AFD00B104" box="[581,691,1902,1917]" gridcol="2" gridrow="5" pageId="5" pageNumber="6">0.722 ± 0.068</td>
|
||
<td id="F8285DB9DF61EC99FCF9280AFC0DB104" box="[848,958,1902,1917]" gridcol="3" gridrow="5" pageId="5" pageNumber="6">1.92 ± 0.13</td>
|
||
<td id="F8285DB9DF61EC99FBF2280AFB0CB104" box="[1115,1215,1902,1917]" gridcol="4" gridrow="5" pageId="5" pageNumber="6">15.28 ± 0.52</td>
|
||
<td id="F8285DB9DF61EC99FAF4280AFA0CB104" box="[1373,1471,1902,1917]" gridcol="5" gridrow="5" pageId="5" pageNumber="6">21.2 ± 2.1</td>
|
||
</tr>
|
||
</table>
|
||
</paragraph>
|
||
<paragraph id="05763687DF611363FFCD28F7FEF7B1C4" blockId="5.[100,1487,1939,1981]" pageId="5" pageNumber="6">
|
||
Parameters ± S.E. estimated from a non-linear curve fit of corrected NADPH consumption rates against varying substrate concentrations (
|
||
<emphasis id="37BDEA95DF611363FAA328F7FAABB1DA" bold="true" box="[1290,1304,1939,1955]" italics="true" pageId="5" pageNumber="6">N</emphasis>
|
||
= 7) from combined technical triplicate assays.
|
||
</paragraph>
|
||
<caption id="51B6660FDF621360FFCD2CF6FEC4B25A" ID-DOI="http://doi.org/10.5281/zenodo.8291748" ID-Zenodo-Dep="8291748" httpUri="https://zenodo.org/record/8291748/files/figure.png" pageId="6" pageNumber="7" startId="6.[100,130,914,931]" targetBox="[200,1386,149,884]" targetPageId="6" targetType="figure">
|
||
<paragraph id="05763687DF621360FFCD2CF6FEC4B25A" blockId="6.[100,1487,914,1059]" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FFCD2CF6FF2FB5DB" bold="true" box="[100,156,914,931]" pageId="6" pageNumber="7">Fig. 7.</emphasis>
|
||
Molecular models of
|
||
<taxonomicName id="C2C94D04DF621360FEFC2CF6FE5EB5DA" authority="CYP" authorityName="CYP" box="[341,493,914,931]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FEFC2CF6FE72B5DA" bold="true" box="[341,449,914,931]" italics="true" pageId="6" pageNumber="7">Catharanthus</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A1 and
|
||
<taxonomicName id="C2C94D04DF621360FD972CF6FD63B5DA" authority="CYP" authorityName="CYP" box="[574,720,914,931]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FD972CF6FD15B5DA" bold="true" box="[574,678,914,931]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A564 and CYP72A565. (A) Backbone overlays of
|
||
<taxonomicName id="C2C94D04DF621360FBD72CF6FAA4B5DA" authority="CYP" authorityName="CYP" box="[1150,1303,914,931]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FBD72CF6FB59B5DA" bold="true" box="[1150,1258,914,931]" italics="true" pageId="6" pageNumber="7">Catharanthus</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A1 and
|
||
<taxonomicName id="C2C94D04DF621360FACE2CF6FF39B5C5" authority="CYP" authorityName="CYP" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FACE2CF6FA7CB5DA" bold="true" box="[1383,1487,914,931]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A564 and CYP72A565 models are shown with the alpha-carbon RMSD amongst CYP72A1, CYP72A564 and CYP72A565 depicted from green (0.0 Å) to yellow (3.0 Å) to red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in
|
||
<taxonomicName id="C2C94D04DF621360FDCC2CBAFD4CB589" authority="CYP" authorityName="CYP" box="[613,767,990,1008]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FDCC2CBAFD62B596" bold="true" box="[613,721,990,1007]" italics="true" pageId="6" pageNumber="7">Catharanthus</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A1 (blue) and loganic acid (gray) docked in
|
||
<taxonomicName id="C2C94D04DF621360FB202CBAFAAEB596" authority="CYP" authorityName="CYP" box="[1161,1309,990,1007]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FB202CBAFB42B596" bold="true" box="[1161,1265,990,1007]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A564 (orange). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganin (aqua) docked in
|
||
<taxonomicName id="C2C94D04DF621360FC1A2C9CFBFEB270" authority="CYP" authorityName="CYP" box="[947,1101,1016,1033]" class="Magnoliopsida" family="Apocynaceae" genus="Catharanthus" kingdom="Plantae" order="Gentianales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FC1A2C9CFBACB270" bold="true" box="[947,1055,1016,1033]" italics="true" pageId="6" pageNumber="7">Catharanthus</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A1 (blue) and loganic acid (gray) docked in
|
||
<taxonomicName id="C2C94D04DF621360FFCD2B75FF49B25B" authority="CYP" authorityName="CYP" box="[100,250,1041,1058]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FFCD2B75FF7FB25B" bold="true" box="[100,204,1041,1058]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A565 (rose).
|
||
</paragraph>
|
||
</caption>
|
||
<caption id="51B6660FDF621360FFCD2B39FE6CB2F1" pageId="6" pageNumber="7" startId="6.[100,150,1117,1133]" targetBox="[116,754,1180,1355]" targetIsTable="true" targetPageId="6" targetType="table">
|
||
<paragraph id="05763687DF621360FFCD2B39FF14B217" blockId="6.[100,479,1117,1160]" box="[100,167,1117,1134]" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FFCD2B39FF14B217" bold="true" box="[100,167,1117,1134]" pageId="6" pageNumber="7">Table 3</emphasis>
|
||
</paragraph>
|
||
<paragraph id="05763687DF621360FFCD2B13FE6CB2F1" blockId="6.[100,479,1117,1160]" box="[100,479,1143,1160]" pageId="6" pageNumber="7">Docking parameters from homology models.</paragraph>
|
||
</caption>
|
||
<paragraph id="05763687DF621360FE992BF8FD7EB332" pageId="6" pageNumber="7">
|
||
<table id="77C9C427DF62EC99FFDD2BF8FD41B332" box="[116,754,1180,1355]" gridcols="5" gridrows="7" pageId="6" pageNumber="7">
|
||
<tr id="BBF934C5DF62EC99FFDD2BF8FD41B2D3" box="[116,754,1180,1194]" gridrow="0" pageId="6" pageNumber="7" rowspan-0="1" rowspan-1="1" rowspan-3="1">
|
||
<th id="F8285DB9DF62EC99FE992BF8FE63B2D3" box="[304,464,1180,1194]" gridcol="2" gridrow="0" pageId="6" pageNumber="7">loganic acid</th>
|
||
<th id="F8285DB9DF62EC99FDCB2BF8FD41B2D3" box="[610,754,1180,1194]" gridcol="4" gridrow="0" pageId="6" pageNumber="7">loganin</th>
|
||
</tr>
|
||
<tr id="BBF934C5DF62EC99FFDD2BDFFD41B2B4" box="[116,754,1211,1229]" gridrow="1" pageId="6" pageNumber="7">
|
||
<th id="F8285DB9DF62EC99FFDD2BDFFF03B2B4" box="[116,176,1211,1229]" gridcol="0" gridrow="1" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FF2B2BDBFF11B2B4" bold="true" box="[130,162,1215,1229]" pageId="6" pageNumber="7">CYP</emphasis>
|
||
</th>
|
||
<td id="F8285DB9DF62EC99FF432BDFFE93B2B4" box="[234,288,1211,1229]" gridcol="1" gridrow="1" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FF542BDAFEA2B2B4" box="[253,273,1214,1229]" italics="true" pageId="6" pageNumber="7">
|
||
Δ
|
||
<emphasis id="37BDEA95DF621360FEA12BDBFEA2B2B4" bold="true" box="[264,273,1215,1229]" italics="true" pageId="6" pageNumber="7">E</emphasis>
|
||
</emphasis>
|
||
<emphasis id="37BDEA95DF621360FEB82BDFFEABB2BD" bold="true" box="[273,280,1211,1220]" italics="true" pageId="6" pageNumber="7">a</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF62EC99FE992BDFFE63B2B4" box="[304,464,1211,1229]" gridcol="2" gridrow="1" pageId="6" pageNumber="7">
|
||
C–O Distance
|
||
<emphasis id="37BDEA95DF621360FE632BDFFE63B2BC" bold="true" box="[458,464,1211,1221]" italics="true" pageId="6" pageNumber="7">b</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF62EC99FDA22BDFFDFFB2B4" box="[523,588,1211,1229]" gridcol="3" gridrow="1" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FDB72BDAFD81B2B4" box="[542,562,1214,1229]" italics="true" pageId="6" pageNumber="7">
|
||
Δ
|
||
<emphasis id="37BDEA95DF621360FD802BDBFD81B2B4" bold="true" box="[553,562,1215,1229]" italics="true" pageId="6" pageNumber="7">E</emphasis>
|
||
</emphasis>
|
||
<emphasis id="37BDEA95DF621360FD9B2BDFFD8AB2BD" bold="true" box="[562,569,1211,1220]" italics="true" pageId="6" pageNumber="7">a</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF62EC99FDCB2BDFFD41B2B4" box="[610,754,1211,1229]" gridcol="4" gridrow="1" pageId="6" pageNumber="7">
|
||
C–O Distance
|
||
<emphasis id="37BDEA95DF621360FD452BDFFD41B2BC" bold="true" box="[748,754,1211,1221]" italics="true" pageId="6" pageNumber="7">b</emphasis>
|
||
</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF62EC99FFDD2BBAFD41B289" box="[116,754,1246,1264]" gridrow="2" pageId="6" pageNumber="7" rowspan-0="1">
|
||
<td id="F8285DB9DF62EC99FF432BBAFE63B289" box="[234,464,1246,1264]" colspan="2" colspanRight="1" gridcol="1" gridrow="2" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FF432B86FEA9B289" bold="true" box="[234,282,1250,1264]" italics="true" pageId="6" pageNumber="7">kJ mol</emphasis>
|
||
<emphasis id="37BDEA95DF621360FE8D2BBAFE98B29E" bold="true" box="[292,299,1246,1255]" italics="true" pageId="6" pageNumber="7">1</emphasis>
|
||
<emphasis id="37BDEA95DF621360FE3C2BBAFE13B289" bold="true" box="[405,416,1246,1264]" italics="true" pageId="6" pageNumber="7">Å</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF62EC99FDA22BBAFDFFB289" box="[523,588,1246,1264]" gridcol="3" gridrow="2" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FDA22B86FD88B289" bold="true" box="[523,571,1250,1264]" italics="true" pageId="6" pageNumber="7">kJ mol</emphasis>
|
||
<emphasis id="37BDEA95DF621360FDEC2BBAFDFFB29E" bold="true" box="[581,588,1246,1255]" italics="true" pageId="6" pageNumber="7">1</emphasis>
|
||
</td>
|
||
<td id="F8285DB9DF62EC99FDCB2BBAFD41B289" box="[610,754,1246,1264]" gridcol="4" gridrow="2" pageId="6" pageNumber="7">
|
||
<emphasis id="37BDEA95DF621360FD1E2BBAFD71B289" bold="true" box="[695,706,1246,1264]" italics="true" pageId="6" pageNumber="7">Å</emphasis>
|
||
</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF62EC99FFDD2B9DFD41B37E" box="[116,754,1273,1287]" gridrow="3" pageId="6" pageNumber="7">
|
||
<th id="F8285DB9DF62EC99FFDD2B9DFF03B37E" box="[116,176,1273,1287]" gridcol="0" gridrow="3" pageId="6" pageNumber="7">72A1v3</th>
|
||
<td id="F8285DB9DF62EC99FF432B9DFE63B37E" box="[234,464,1273,1287]" colspan="2" colspanRight="1" gridcol="1" gridrow="3" pageId="6" pageNumber="7">140. 3.79</td>
|
||
<td id="F8285DB9DF62EC99FDA22B9DFDFFB37E" box="[523,588,1273,1287]" gridcol="3" gridrow="3" pageId="6" pageNumber="7">102</td>
|
||
<td id="F8285DB9DF62EC99FDCB2B9DFD41B37E" box="[610,754,1273,1287]" gridcol="4" gridrow="3" pageId="6" pageNumber="7">3.69</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF62EC99FFDD2A74FD41B367" box="[116,754,1296,1310]" gridrow="4" pageId="6" pageNumber="7">
|
||
<th id="F8285DB9DF62EC99FFDD2A74FF03B367" box="[116,176,1296,1310]" gridcol="0" gridrow="4" pageId="6" pageNumber="7">72A564</th>
|
||
<td id="F8285DB9DF62EC99FF432A74FE93B367" box="[234,288,1296,1310]" gridcol="1" gridrow="4" pageId="6" pageNumber="7">157</td>
|
||
<td id="F8285DB9DF62EC99FE992A74FE63B367" box="[304,464,1296,1310]" gridcol="2" gridrow="4" pageId="6" pageNumber="7">4.20</td>
|
||
<td id="F8285DB9DF62EC99FDA22A74FDFFB367" box="[523,588,1296,1310]" gridcol="3" gridrow="4" pageId="6" pageNumber="7">90.3</td>
|
||
<td id="F8285DB9DF62EC99FDCB2A74FD41B367" box="[610,754,1296,1310]" gridcol="4" gridrow="4" pageId="6" pageNumber="7">5.55</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF62EC99FFDD2A42FD41B34C" box="[116,754,1318,1333]" gridrow="5" pageId="6" pageNumber="7">
|
||
<th id="F8285DB9DF62EC99FFDD2A42FF03B34C" box="[116,176,1318,1333]" gridcol="0" gridrow="5" pageId="6" pageNumber="7">72A565</th>
|
||
<td id="F8285DB9DF62EC99FF432A42FE93B34C" box="[234,288,1318,1333]" gridcol="1" gridrow="5" pageId="6" pageNumber="7">183</td>
|
||
<td id="F8285DB9DF62EC99FE992A42FE63B34C" box="[304,464,1318,1333]" gridcol="2" gridrow="5" pageId="6" pageNumber="7">3.56</td>
|
||
<td id="F8285DB9DF62EC99FDA22A42FDFFB34C" box="[523,588,1318,1333]" gridcol="3" gridrow="5" pageId="6" pageNumber="7">100.</td>
|
||
<td id="F8285DB9DF62EC99FDCB2A42FD41B34C" box="[610,754,1318,1333]" gridcol="4" gridrow="5" pageId="6" pageNumber="7">4.32</td>
|
||
</tr>
|
||
<tr id="BBF934C5DF62EC99FFDD2A59FD41B332" box="[116,754,1341,1355]" gridrow="6" pageId="6" pageNumber="7">
|
||
<th id="F8285DB9DF62EC99FFDD2A59FF03B332" box="[116,176,1341,1355]" gridcol="0" gridrow="6" pageId="6" pageNumber="7">72A730</th>
|
||
<td id="F8285DB9DF62EC99FF432A59FE93B332" box="[234,288,1341,1355]" gridcol="1" gridrow="6" pageId="6" pageNumber="7">164</td>
|
||
<td id="F8285DB9DF62EC99FE992A59FE63B332" box="[304,464,1341,1355]" gridcol="2" gridrow="6" pageId="6" pageNumber="7">3.64</td>
|
||
<td id="F8285DB9DF62EC99FDA22A59FDFFB332" box="[523,588,1341,1355]" gridcol="3" gridrow="6" pageId="6" pageNumber="7">126</td>
|
||
<td id="F8285DB9DF62EC99FDCB2A59FD41B332" box="[610,754,1341,1355]" gridcol="4" gridrow="6" pageId="6" pageNumber="7">3.10</td>
|
||
</tr>
|
||
</table>
|
||
</paragraph>
|
||
<tableNote id="F82F3709DF621360FFCD2A05FDDCB3C6" pageId="6" pageNumber="7" targetBox="[116,754,1180,1355]" targetPageId="6">
|
||
<paragraph id="05763687DF621360FFCD2A05FDE2B3FB" blockId="6.[100,769,1377,1471]" pageId="6" pageNumber="7">
|
||
Results computed using MOE software of models docked with substrates and minimized to root mean squared ±0.01 kcal mol
|
||
<superScript id="F2BC9BCFDF621360FDA42A12FDA6B3FB" attach="right" box="[525,533,1398,1410]" fontSize="5" pageId="6" pageNumber="7">1</superScript>
|
||
(Å
|
||
<superScript id="F2BC9BCFDF621360FD862A12FD84B3FB" attach="left" box="[559,567,1398,1410]" fontSize="5" pageId="6" pageNumber="7">2</superScript>
|
||
)
|
||
<superScript id="F2BC9BCFDF621360FDE02A12FDE2B3FB" attach="left" box="[585,593,1398,1410]" fontSize="5" pageId="6" pageNumber="7">1</superScript>
|
||
</paragraph>
|
||
<paragraph id="05763687DF621360FFDA2AF4FD12B3DC" blockId="6.[100,769,1377,1471]" box="[115,673,1424,1445]" pageId="6" pageNumber="7">
|
||
<superScript id="F2BC9BCFDF621360FFDA2AF4FFC9B3E5" attach="left" box="[115,122,1424,1436]" fontSize="5" pageId="6" pageNumber="7">a</superScript>
|
||
Ligand-receptor interaction energy calculated in MOE software.
|
||
</paragraph>
|
||
<paragraph id="05763687DF621360FFDA2ACDFDDCB3C6" blockId="6.[100,769,1377,1471]" box="[115,623,1449,1471]" pageId="6" pageNumber="7">
|
||
<superScript id="F2BC9BCFDF621360FFDA2ACDFFC8B3CC" attach="left" box="[115,123,1449,1461]" fontSize="5" pageId="6" pageNumber="7">b</superScript>
|
||
Distance from C10 of substrate to oxygen ligand of heme.
|
||
</paragraph>
|
||
</tableNote>
|
||
<paragraph id="05763687DF621360FF2D2987FBEAB30F" blockId="6.[100,770,1512,1982]" lastBlockId="6.[818,1488,1099,1955]" pageId="6" pageNumber="7">
|
||
Molecular modeling and docking of
|
||
<taxonomicName id="C2C94D04DF621360FE4B2986FD3AB08F" authority="CYP" authorityName="CYP" box="[482,649,1762,1782]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FE4B2986FDE5B08C" bold="true" box="[482,598,1762,1781]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A730 with loganic acid, which it neither binds nor metabolizes, suggest that this non-substrate can be positioned within the catalytic site (
|
||
<figureCitation id="9DF22A02DF621360FD38287EFD7BB157" box="[657,712,1818,1838]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8</figureCitation>
|
||
). The loganic acid in the CYP72A730 model has a similar distance to the oxygen bound to the heme and interaction energy compared to the
|
||
<taxonomicName id="C2C94D04DF621360FFCD280AFEBBB1F8" authority="CYP" authorityName="CYP" box="[100,264,1902,1921]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FFCD280AFF6BB1F8" bold="true" box="[100,216,1902,1921]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
CYP
|
||
</taxonomicName>
|
||
72A564 and CYP72A565 models (
|
||
<tableCitation id="484B033CDF621360FDE9280AFD36B1F8" box="[576,645,1902,1921]" captionStart="Table 3" captionStartId="6.[100,150,1117,1133]" captionTargetPageId="6" captionText="Table 3 Docking parameters from homology models." pageId="6" pageNumber="7">Table 3</tableCitation>
|
||
). Overlays of the backbones in these three
|
||
<taxonomicName id="C2C94D04DF621360FE2928EEFE47B1E4" box="[384,500,1930,1949]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FE2928EEFE47B1E4" bold="true" box="[384,500,1930,1949]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
</taxonomicName>
|
||
models show the most substantial (
|
||
<emphasis id="37BDEA95DF621360FF1F28C2FF75B1C0" box="[182,198,1958,1977]" italics="true" pageId="6" pageNumber="7">></emphasis>
|
||
4.5 Å) RMSD variance extending from the F-helix through the G-helix (red in
|
||
<figureCitation id="9DF22A02DF621360FC142B2FFBB2B226" box="[957,1025,1099,1119]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8A</figureCitation>
|
||
) and little in most other regions (≤2.0 Å, green in
|
||
<figureCitation id="9DF22A02DF621360FC9B2B03FCC8B203" box="[818,891,1127,1146]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8A</figureCitation>
|
||
). Overlays of these three predicted catalytic sites highlighting amino acids identical in each (
|
||
<figureCitation id="9DF22A02DF621360FBCC2BE7FB43B2EF" box="[1125,1264,1155,1174]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8C and E</figureCitation>
|
||
) and different in each (
|
||
<figureCitation id="9DF22A02DF621360FC932BFBFC0DB2CB" box="[826,958,1183,1203]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8D and F</figureCitation>
|
||
) show multiple residues that differ within loganic acid contact distance and within the upper regions of its predicted catalytic site. Among the variant residues, several differences occur in SRS1: the
|
||
<emphasis id="37BDEA95DF621360FC9B2B96FC3BB37C" bold="true" box="[818,904,1266,1285]" italics="true" pageId="6" pageNumber="7">Camptoth</emphasis>
|
||
eca CYP72A730 protein differs from the CYP72A564 and CYP72A565 proteins at positions 132 and 133 (numbered according to CYP72A730) (
|
||
<figureCitation id="9DF22A02DF621360FC132A4FFC43B347" box="[954,1008,1323,1342]" captionStart="Fig" captionStartId="2.[100,130,1939,1956]" captionTargetBox="[207,1380,1119,1909]" captionTargetId="figure-607@2.[206,1381,1117,1911]" captionTargetPageId="2" captionText="Fig. 2. CYP72A multiple sequence alignment. Signal anchor domain fusion of CYP72A565 into CYP72A564 is underlined; SRS regions are underlined in bold; predicted substrate contacts within 4.5 Å of loganic acid/loganin are gray-filled." figureDoi="http://doi.org/10.5281/zenodo.8291738" httpUri="https://zenodo.org/record/8291738/files/figure.png" pageId="6" pageNumber="7">Fig. 2</figureCitation>
|
||
;
|
||
<figureCitation id="9DF22A02DF621360FC542A4FFBF0B347" box="[1021,1091,1323,1342]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8B</figureCitation>
|
||
). Differences between these three protein models also occur in SRS2 at position 234, SRS3 at position 268 and SRS4 at positions 323 and 327.
|
||
</paragraph>
|
||
<paragraph id="05763687DF621360FCF82A1AFB15B0BD" blockId="6.[818,1488,1099,1955]" pageId="6" pageNumber="7">
|
||
Other differences among these
|
||
<taxonomicName id="C2C94D04DF621360FB282A1AFB46B3E8" box="[1153,1269,1406,1425]" class="Magnoliopsida" family="Nyssaceae" genus="Camptotheca" kingdom="Plantae" order="Cornales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="37BDEA95DF621360FB282A1AFB46B3E8" bold="true" box="[1153,1269,1406,1425]" italics="true" pageId="6" pageNumber="7">Camptotheca</emphasis>
|
||
</taxonomicName>
|
||
proteins, while occurring in SRS regions (
|
||
<emphasis id="37BDEA95DF621360FC472AFEFBBAB3D4" bold="true" box="[1006,1033,1434,1453]" italics="true" pageId="6" pageNumber="7">i.e.</emphasis>
|
||
, SRS4 at position 325, SRS6 at positions 499 and 501) are more than 4.5 Å away from the docked substrate. Notable among the sequence variations within substrate contact distance are those in SRS2 at position 234 and SRS3 at 268 (numbering according to CYP72A730). Because of the substantial RMSD variance in the placement of the F-to G-helices shown in
|
||
<figureCitation id="9DF22A02DF621360FB292942FB76B040" box="[1152,1221,1574,1593]" captionStart="Fig" captionStartId="7.[100,130,979,996]" captionTargetBox="[197,1390,149,950]" captionTargetId="figure-547@7.[196,1392,148,952]" captionTargetPageId="7" captionText="Fig. 8. Molecular models of Camptotheca CYP72A564, CYP72A565 and CYP72A730. (A) Backbone overlays of Camptotheca CYP72A730, CYP72A564 and CYP72A565 models are shown with the RMSD variance of CYP72A564 and CYP72A565 from the CYP72A730 backbone depicted in green (0.0 Å), yellow (3.0 Å) and red (4.5 Å). (B) SRS regions in CYP72A proteins shown with predicted substrate contact residues (gray fill). (C) Identical versus (D) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A564 (orange) versus loganic acid (aqua) docked in CYP72A730 (magenta). (E) Identical versus (F) different side chain residues predicted within 4.5 Å of loganic acid (gray) docked in Camptotheca CYP72A565 (rose) versus loganic acid (aqua) docked in CYP72A730 (magenta)." figureDoi="http://doi.org/10.5281/zenodo.8291750" httpUri="https://zenodo.org/record/8291750/files/figure.png" pageId="6" pageNumber="7">Fig. 8A</figureCitation>
|
||
, the first of these differences (Ile
|
||
<quantity id="C2319B62DF621360FCF82926FC3FB02C" box="[849,908,1602,1621]" metricMagnitude="0" metricUnit="m" metricValue="5.9436" pageId="6" pageNumber="7" unit="in" value="234.0">234 in</quantity>
|
||
CYP72A730), is substantially closer to the docked loganic acid than Met
|
||
<quantity id="C2319B62DF621360FC242939FC7EB009" box="[909,973,1629,1648]" metricMagnitude="0" metricUnit="m" metricValue="5.9944" pageId="6" pageNumber="7" unit="in" value="236.0">236 in</quantity>
|
||
CYP72A564 and CYP72A565. The second of these (Gln
|
||
<quantity id="C2319B62DF621360FCF2291DFC2EB0F5" box="[859,925,1657,1676]" metricMagnitude="0" metricUnit="m" metricValue="6.8072" pageId="6" pageNumber="7" unit="in" value="268.0">268 in</quantity>
|
||
CYP72A730) is displaced so significantly compared to Arg
|
||
<quantity id="C2319B62DF621360FCFC29F1FC3DB0D1" box="[853,910,1685,1704]" metricMagnitude="0" metricUnit="m" metricValue="6.858" pageId="6" pageNumber="7" unit="in" value="270.0">270 in</quantity>
|
||
CYP72A564 and Lys
|
||
<quantity id="C2319B62DF621360FBF829F1FB3AB0D1" box="[1105,1161,1685,1704]" metricMagnitude="0" metricUnit="m" metricValue="6.858" pageId="6" pageNumber="7" unit="in" value="270.0">270 in</quantity>
|
||
CYP72A565 that it is not predicted to lie within substrate contact distance.
|
||
</paragraph>
|
||
<paragraph id="05763687DF621361FCF829A9FF78B2C5" blockId="6.[818,1488,1099,1955]" lastBlockId="7.[100,770,1165,1212]" lastPageId="7" lastPageNumber="8" pageId="6" pageNumber="7">The docking poses of their alternate substrate, 7-deoxyloganic acid, in the CYP72A564 and CYP72A565 homology models greatly resembled those of loganic acid in these models (Supplemental Fig. S12). Though considerable variability in the placement of the glucoside moiety is present, the iridoid cores of 7-deoxyloganic acid and loganic acid remain nestled between SRS1 and SRS4. Comparison of the contacts amongst the docked substrate-P450 pairs revealed that the residues predicted as essential for loganic acid docking (especially His132 hydrogen bonding to the carboxylic acid) are likewise predicted contacts for 7-deoxyloganic acid.</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |