Theoretical Study on the Mechanism of the Oxygen Activation Process in Cysteine Dioxygenase Enzymes

Abstract

Cysteine dioxygenase (CDO) is a vital enzyme for human health involved in the biodegradation of toxic cysteine and thereby regulation of the cysteine concentration in the body. The enzyme belongs to the group of nonheme iron dioxygenases and utilizes molecular oxygen to transfer two oxygen atoms to cysteinate to form cysteine sulfinic acid products. The mechanism for this reaction is currently disputed, with crystallographic studies implicating a persulfenate intermediate in the catalytic cycle. To resolve the dispute we have performed quantum mechanics/molecular mechanics (QM/MM) calculations on substrate activation by CDO enzymes using an enzyme monomer and a large QM active region. We find a stepwise mechanism, whereby the distal oxygen atom of the iron(II)-superoxo complex attacks the sulfur atom of cysteinate to form a ring structure, followed by dioxygen bond breaking and the formation of a sulfoxide bound to an iron(IV)-oxo complex. A sulfoxide rotation precedes the second oxygen atom transfer to the substrate to give cysteine sulfinic acid products. The reaction takes place on several low-lying spin-state surfaces via multistate reactivity patterns. It starts in the singlet ground state of the iron(II)-superoxo reactant and then proceeds mainly on the quintet and triplet surfaces. The initial and rate-determining attack of the superoxo group on the cysteinate sulfur atom involves a spin-state crossing from singlet to quintet. We have also investigated an alternative mechanism via a persulfenate intermediate, with a realignment of hydrogen bonding interactions in the substrate binding pocket. However, this alternative mechanism of proximal oxygen atom attack on the sulfur atom of cysteinate is computed to be a high-energy pathway, and therefore, the persulfenate intermediate is unlikely to participate in the catalytic cycle of CDO enzymes.

Mono- and binuclear non-heme iron chemistry from a theoretical perspective

“…The O2 activation reactivity at certain NHFe centers may be less amenable to classification into some Studies on cysteine dioxygenase [111] and on its model complex [112] clarified the full O2 activation mechanism; clues as to the role of the thiolate ligand [113] and to the differences in pertinent O2 activation pathways explaining why the enzyme cannot oxidize selenocysteine were also obtained. [114,115] O2 activation [116,117] and the preceding required water dissociation [118] was also investigated in the tetrahydrobiopterin-iron amino acid hydroxylases.…”

Transition Metal Complexes and the Activation of Dioxygen

“…Related pathways are implicated for non-heme iron enzymes that are supported by three histidine ligands instead of the 2-His-1-carboxylate triad [174], such as cysteine dioxygenase [175][176][177] and β-diketone dioxygenase [178]. Also notable is the chemistry of a low-spin Fe(III)-OOH species identified in the anticancer drug bleomycin, which may perform hydrogen atom abstraction from deoxyribonucleic acid directly or via prior O-O bond scission pathways [179,180].…”

The Role of Nonheme Transition Metal-Oxo, -Peroxo, and -Superoxo Intermediates in Enzyme Catalysis and Reactions of Bioinspired Complexes

“…The results were further validated with various experimental methods such as chemical quenching and freeze-quench, and thus giving the same outcomes of dioxygenation reactions for anaerobic cysteine-bound CDO. 82 In addition, computational modeling using density functional theory on model complexes as well as quantum mechanics/molecular mechanics studies on the full enzyme, calculated high reaction barriers for formation of the iron(III)-superoxo and the iron(III)-bicyclic ring species, and, therefore, these calculations predicted a finite lifetime of the two complexes B and C. 35,37 On the other hand, formation of the iron-cysteine sulfoxide and iron-cysteine sulfinic acid products is calculated to be strongly exothermic with small barriers of formation and decay. Consequently, the lifetime of these intermediates is expected to be rather short.…”