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Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.

Nitish SathyanarayananGiuseppe CannoneLokesh GakharNainesh KatagihallimathRamanathan SowdhaminiSubramanian RamaswamyVinothkumar Kutti R
Published in: Nature communications (2019)
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.
Keyphrases
  • high resolution
  • molecular dynamics simulations
  • fatty acid
  • crispr cas
  • gene expression
  • ionic liquid
  • heavy metals
  • climate change
  • dna methylation
  • case control
  • electron microscopy