Binding of isotopically labeled substrates, inhibitors, and cyanide by protocatechuate 3,4-dioxygenase

Binding of ligands to the active site Fe³⁺ of protocatechuate 3,4-dioxygenase is investigated using EPR-detected transferred hyperfine coupling from isotopically labeled substrates, inhibitors, and cyanide. Broadening is observed in EPR resonances from the anaerobic enzyme complex with homoprotocatechuate (3,4-dihydroxyphenylacetate), a slow substrate, enriched with ¹⁷O (I = 5/2) in either the 3-OH or the 4-OH group. This shows that this substrate binds directly to the Fe³⁺ and strongly suggests that an iron chelate can be formed. Cyanide is known to bind to the enzyme in at least two steps, forming first a high spin and then a low spin complex (Whittaker, J.W., and Lipscomb, J.D. (1984) J. Biol. Chem. 259, 4487-4495). Hyperfine broadening from [¹³C]cyanide (I = 1/2 ) is observed in the EPR spectra of both complexes, showing that cyanide is an Fe³⁺ ligand in each case. Cyanide binding is also at least biphasic in the presence of protocatechuate (PCA). The initial high spin enzyme-PCA-cyanide complex forms rapidly and exhibits a unique EPR spectrum. Broadening from PCA enriched with ¹⁷O in either the 3-OH or the 4-OH group is detected showing that PCA binds to the iron, probably as a chelate complex. In contrast, no broadening from [¹³C]cyanide is detected for this complex suggesting that cyanide binds at a site away from the Fe³⁺. Steady state kinetic measurements of cyanide inhibition of PCA turnover are consistent with two rapidly exchanging cyanide binding sites that inhibit PCA binding and which can be simultaneously occupied. Formation of the nearly irreversible, low spin enzyme-PCA-cyanide complex is competitively inhibited by PCA. Transient kinetics of the formation of this complex are second order in cyanide implying that two cyanides bind. Broadening in the EPR spectrum of this complex is detected from [¹³C]cyanide, but not from [¹⁷O]PCA, suggesting that PCA is displaced. This study provides the first direct evidence for chelation of the active site Fe³⁺ by substrates and for a small molecule binding site away from the iron in intradiol dioxygenases.