title: Metal-dependent activity of Fe and Ni acireductone dioxygenases: how two electrons reroute the catalytic pathway.
abstract: Two virtually identical acireductone dioxygenases, ARD and ARD', catalyze completely different oxidation reactions of the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, depending exclusively on the nature of the bound metal. Fe(2+)-dependent ARD' produces the α-keto acid precursor of methionine and formate and allows for the recycling of methionine in cells. Ni(2+)-dependent ARD instead produces methylthiopropionate, CO, and formate, and exits the methionine salvage cycle. This mechanistic difference has not been understood to date but has been speculated to be due to the difference in coordination of the substrate to Fe(2+)versus Ni(2+): forming a five-membered ring versus a six-membered ring, respectively, thus exposing different carbon atoms for the attack by O2. Here, using mixed quantum-classical molecular dynamics simulations followed by the density functional theory mechanistic investigation, we show that, contrary to the old hypothesis, both metals preferentially bind the substrate as a six-membered ring, exposing the exact same sites to the attack by O2. It is the electronic properties of the metals that are then responsible for the system following different reaction paths, to yield the respective products. We fully explain the puzzling metal-induced difference in functionality between ARD and ARD' and, in particular, propose a new mechanism for ARD'. All results are in agreement with available isotopic substitution and other experimental data.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, USA.
authors.forename: Manuel
authors.initials: M
authors.lastname: Sparta
authors.forename: Crystal E
authors.initials: CE
authors.lastname: Valdez
authors.forename: Anastassia N
authors.initials: AN
authors.lastname: Alexandrova
mesh_terms: D002413:Cations, Divalent / Q000737:chemistry / Q000378:metabolism*; D003067:Coenzymes / Q000737:chemistry / Q000378:metabolism*; D049308:Dioxygenases / Q000737:chemistry / Q000378:metabolism*; D007501:Iron / Q000737:chemistry / Q000378:metabolism*; D007709:Klebsiella / Q000201:enzymology; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009532:Nickel / Q000737:chemistry / Q000378:metabolism*; D010100:Oxygen / Q000378:metabolism
chemical_list: D002413:Cations, Divalent; D003067:Coenzymes; D009532:Nickel; D007501:Iron; D049308:Dioxygenases; C083734:aci-reductone oxidase (CO-forming); D010100:Oxygen
keywords: ARD; DFT; NPA; PDB; Protein Data Bank; QM/DMD; acireductone dioxygenase; density functional theory; metalloenzyme; methionine salvage pathway; natural population analysis