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Structure paper

TitleMolecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 4127, Year 2019
Publish dateSep 11, 2019
AuthorsNitish Sathyanarayanan / Giuseppe Cannone / Lokesh Gakhar / Nainesh Katagihallimath / Ramanathan Sowdhamini / Subramanian Ramaswamy / Kutti R Vinothkumar /
PubMed AbstractSubstrate 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 ...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.
External linksNat Commun / PubMed:31511507 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.3 Å
Structure data

9873

6jql

EMDB-9873, PDB-6jql:
Structure of PaaZ, a bifunctional enzyme
Method: EM (single particle) / Resolution: 2.9 Å

9874

6jqm

EMDB-9874, PDB-6jqm:
Structure of PaaZ with NADPH
Method: EM (single particle) / Resolution: 3.3 Å

9875

6jqn

EMDB-9875, PDB-6jqn:
Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and OCoA
Method: EM (single particle) / Resolution: 3.1 Å

9876

6jqo

EMDB-9876, PDB-6jqo:
Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and CCoA
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-CO8:
OCTANOYL-COENZYME A

ChemComp-COO:
CROTONYL COENZYME A

Source
  • escherichia coli k-12 (bacteria)
KeywordsHYDROLASE / substrate channeling / bi-functional enzyme / dehydrogenase

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