6VP4

Ethylene forming enzyme (EFE) in complex with Fe(II), L-arginine, and 2OG

Summary for 6VP4

• Entry DOI: 10.2210/pdb6vp4/pdb
• Descriptor: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme, FE (III) ION, 2-OXOGLUTARIC ACID, ... (6 entities in total)
• Functional Keywords: oxidoreductase, 2-oxo-glutarate, iron, reactant complex
• Biological source: Pseudomonas savastanoi pv. phaseolicola
• Total number of polymer chains: 4
• Total formula weight: 159757.11

Authors

Davis, K.M.,Copeland, R.A.,Boal, A.K. (deposition date: 2020-02-01, release date: 2021-02-03, Last modification date: 2023-10-11)

Primary citation

Copeland, R.A.,Davis, K.M.,Shoda, T.K.C.,Blaesi, E.J.,Boal, A.K.,Krebs, C.,Bollinger Jr., J.M.
An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme.
J.Am.Chem.Soc., 143:2293-2303, 2021

PubMed Abstract: Ethylene-forming enzyme (EFE) is an ambifunctional iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase. In its major (EF) reaction, it converts carbons 1, 2, and 5 of 2OG to CO and carbons 3 and 4 to ethylene, a four-electron oxidation drastically different from the simpler decarboxylation of 2OG to succinate mediated by all other Fe/2OG enzymes. EFE also catalyzes a minor reaction, in which the normal decarboxylation is coupled to oxidation of l-arginine (a required activator for the EF pathway), resulting in its conversion to l-glutamate semialdehyde and guanidine. Here we show that, consistent with precedent, the l-Arg-oxidation (RO) pathway proceeds via an iron(IV)-oxo (ferryl) intermediate. Use of 5,5-[H]-l-Arg slows decay of the ferryl complex by >16-fold, implying that RO is initiated by hydrogen-atom transfer (HAT) from C5. That this large substrate deuterium kinetic isotope effect has no impact on the EF:RO partition ratio implies that the same ferryl intermediate cannot be on the EF pathway; the pathways must diverge earlier. Consistent with this conclusion, the variant enzyme bearing the Asp191Glu ligand substitution accumulates ∼4 times as much of the ferryl complex as the wild-type enzyme and exhibits a ∼40-fold diminished EF:RO partition ratio. The selective detriment of this nearly conservative substitution to the EF pathway implies that it has unusually stringent stereoelectronic requirements. An active-site, like-charge guanidinium pair, which involves the l-Arg substrate/activator and is unique to EFE among four crystallographically characterized l-Arg-modifying Fe/2OG oxygenases, may serve to selectively stabilize the transition state leading to the unique EF branch.

PubMed: 33522811
DOI: 10.1021/jacs.0c10923

Experimental method

X-RAY DIFFRACTION (1.83 Å)