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Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s

Jose A. Amaya Orcid Logo, David Lamb Orcid Logo, Steven Kelly, Patrick Caffrey Orcid Logo, Vidhi C. Murarka Orcid Logo, Thomas L. Poulos

Journal of Biological Chemistry, Volume: 298, Issue: 4, Start page: 101746

Swansea University Authors: David Lamb Orcid Logo, Steven Kelly

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DOI (Published version): 10.1016/j.jbc.2022.101746

Abstract

AmphL is a cytochrome P450 enzyme that catalyzes the C8 oxidation of 8-deoxyamphotericin B to the polyene macrolide antibiotic, amphotericin B. To understand this substrate selectivity, we solved the crystal structure of AmphL to a resolution of 2.0 Å in complex with amphotericin B and performed mol...

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Published in: Journal of Biological Chemistry
ISSN: 0021-9258
Published: Elsevier BV 2022
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URI: https://cronfa.swan.ac.uk/Record/cronfa59913
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spelling v2 59913 2022-04-27 Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s 1dc64e55c2c28d107ef7c3db984cccd2 0000-0001-5446-2997 David Lamb David Lamb true false b17cebaf09b4d737b9378a3581e3de93 Steven Kelly Steven Kelly true false 2022-04-27 MEDS AmphL is a cytochrome P450 enzyme that catalyzes the C8 oxidation of 8-deoxyamphotericin B to the polyene macrolide antibiotic, amphotericin B. To understand this substrate selectivity, we solved the crystal structure of AmphL to a resolution of 2.0 Å in complex with amphotericin B and performed molecular dynamics (MD) simulations. A detailed comparison with the closely related P450, PimD, which catalyzes the epoxidation of 4,5-desepoxypimaricin to the macrolide antibiotic, pimaricin, reveals key catalytic structural features responsible for stereo- and regio-selective oxidation. Both P450s have a similar access channel that runs parallel to the active site I helix over the surface of the heme. Molecular dynamics simulations of substrate binding reveal PimD can “pull” substrates further into the P450 access channel owing to additional electrostatic interactions between the protein and the carboxyl group attached to the hemiketal ring of 4,5-desepoxypimaricin. This substrate interaction is absent in AmphL although the additional substrate -OH groups in 8-deoxyamphotericin B help to correctly position the substrate for C8 oxidation. Simulations of the oxy-complex indicates that these -OH groups may also participate in a proton relay network required for O2 activation as has been suggested for two other macrolide P450s, PimD and P450eryF. These findings provide experimentally testable models that can potentially contribute to a new generation of novel macrolide antibiotics with enhanced antifungal and/or antiprotozoal efficacy. Journal Article Journal of Biological Chemistry 298 4 101746 Elsevier BV 0021-9258 cytochrome P450; crystal structure; antibiotics; molecular dynamics; substrate specificity 1 4 2022 2022-04-01 10.1016/j.jbc.2022.101746 COLLEGE NANME Medical School COLLEGE CODE MEDS Swansea University 2024-07-15T12:07:09.9459313 2022-04-27T16:46:59.0548149 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Jose A. Amaya 0000-0001-7826-0185 1 David Lamb 0000-0001-5446-2997 2 Steven Kelly 3 Patrick Caffrey 0000-0002-0132-2410 4 Vidhi C. Murarka 0000-0002-3471-9211 5 Thomas L. Poulos 6 59913__23976__07cac2a6fbaa47d099467c5df65d7147.pdf 59913.pdf 2022-05-04T10:52:45.4421216 Output 2032312 application/pdf Version of Record true © 2022 THE AUTHORS. This is an open access article under the CC BY-NC-ND license true eng http://creativecommons.org/licenses/by-nc-nd/4.0/
title Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
spellingShingle Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
David Lamb
Steven Kelly
title_short Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
title_full Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
title_fullStr Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
title_full_unstemmed Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
title_sort Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s
author_id_str_mv 1dc64e55c2c28d107ef7c3db984cccd2
b17cebaf09b4d737b9378a3581e3de93
author_id_fullname_str_mv 1dc64e55c2c28d107ef7c3db984cccd2_***_David Lamb
b17cebaf09b4d737b9378a3581e3de93_***_Steven Kelly
author David Lamb
Steven Kelly
author2 Jose A. Amaya
David Lamb
Steven Kelly
Patrick Caffrey
Vidhi C. Murarka
Thomas L. Poulos
format Journal article
container_title Journal of Biological Chemistry
container_volume 298
container_issue 4
container_start_page 101746
publishDate 2022
institution Swansea University
issn 0021-9258
doi_str_mv 10.1016/j.jbc.2022.101746
publisher Elsevier BV
college_str Faculty of Medicine, Health and Life Sciences
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hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
document_store_str 1
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description AmphL is a cytochrome P450 enzyme that catalyzes the C8 oxidation of 8-deoxyamphotericin B to the polyene macrolide antibiotic, amphotericin B. To understand this substrate selectivity, we solved the crystal structure of AmphL to a resolution of 2.0 Å in complex with amphotericin B and performed molecular dynamics (MD) simulations. A detailed comparison with the closely related P450, PimD, which catalyzes the epoxidation of 4,5-desepoxypimaricin to the macrolide antibiotic, pimaricin, reveals key catalytic structural features responsible for stereo- and regio-selective oxidation. Both P450s have a similar access channel that runs parallel to the active site I helix over the surface of the heme. Molecular dynamics simulations of substrate binding reveal PimD can “pull” substrates further into the P450 access channel owing to additional electrostatic interactions between the protein and the carboxyl group attached to the hemiketal ring of 4,5-desepoxypimaricin. This substrate interaction is absent in AmphL although the additional substrate -OH groups in 8-deoxyamphotericin B help to correctly position the substrate for C8 oxidation. Simulations of the oxy-complex indicates that these -OH groups may also participate in a proton relay network required for O2 activation as has been suggested for two other macrolide P450s, PimD and P450eryF. These findings provide experimentally testable models that can potentially contribute to a new generation of novel macrolide antibiotics with enhanced antifungal and/or antiprotozoal efficacy.
published_date 2022-04-01T12:07:08Z
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