Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway [National Cryo-Electron Microscopy Facility]

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TitleMolecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway [National Cryo-Electron Microscopy Facility]
Publication TypeJournal Article
Year of Publication2019
AuthorsSathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR
JournalNature Communications
Volume10
Start Page4127
Date Published09, 2019
Type of ArticleArticle
KeywordsBacterial structural biology, Cryoelectron microscopy, Multienzyme complexes
Abstract

Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.