7SHI

Crystal Structure of Cytochrome P450 AmphL from Streptomyces nodosus and the Structural Basis for Substrate Selectivity in Macrolide Metabolizing P450s

Summary for 7SHI

• Entry DOI: 10.2210/pdb7shi/pdb
• Descriptor: AmphL, PROTOPORPHYRIN IX CONTAINING FE, Amphotericin B, ... (5 entities in total)
• Functional Keywords: amphotericin b, hydroxylase, p450, cytochrome, oxidoreductase
• Biological source: Streptomyces nodosus
• Total number of polymer chains: 2
• Total formula weight: 89726.18

Authors

Amaya, J.A.,Poulos, T.L. (deposition date: 2021-10-08, release date: 2022-03-09, Last modification date: 2024-06-19)

Primary citation

Amaya, J.A.,Lamb, D.C.,Kelly, S.L.,Caffrey, P.,Murarka, V.C.,Poulos, T.L.
Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s.
J.Biol.Chem., 298:101746-101746, 2022

PubMed 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 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 O 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.

PubMed: 35189143
DOI: 10.1016/j.jbc.2022.101746

Experimental method

X-RAY DIFFRACTION (2 Å)