Charge Maintenance during Catalysis in Nonheme Iron Oxygenases

Abstract

Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme–substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme–substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.

Mechanistic Investigation on C–C Bond Cleavage of Anthraquinone Catalyzed by an Atypical Nonheme Iron-Dependent Dioxygenase BTG13

“…These electronic structures are further confirmed by the analysis of spin natural orbitals (SNO) (Figure b). The electronic structures of the activated species in 7 (E·S·O 2 ) I and 5 (E·S·O 2 ) I are thus demonstrated to be the Fe III –O 2 •– species, which is consistent with the previous studies on other nonheme iron-dependent dioxygenases. − , As previous studies on the iron-peroxo indicate that the side-on iron-dioxygen complex conformation at the septet ground state is a potential favorable starting point of the reactant complex, ,− the side-on binding pattern was also investigated. However, by using QC calculations, the side-on structure could be obtained only at the septet state.…”

“…Note that it is interesting that previous studies proposed that the charge maintenance is an important factor that affects the activity of the nonheme iron oxygenases. ,,− In our calculations, with the coordination of Kcx, the overall charge of the iron center of BTG13 maintains a +1 charge throughout the catalysis. As shown in Table S16, from the reactant complex ( 7 (E·S·O 2 ) I and 5 (E·S·O 2 ) I ) to IM1 I , the spin distribution in the Kcx ligand coordination complex is similar to that of the carboxylate (mimics of Asp or Glu residue) ligand.…”

Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O–O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations

“…The pyridine ring is a dominant constituent of heterocyclic aromatic compounds, widely existing in natural plant alkaloids, coenzymes, and pyridine derivatives. − The hydrophilic pyridine-based chemicals can be easily released into the groundwater, causing pollution to the natural environment. , 2,5-dihydroxypyridine (DHP) is one of the key intermediates in the microbial transformation of nicotine and nicotinic acid (see Scheme ), . ,− which can be a potential carcinogen and cause DNA stand scission. , As nicotine dependence can cause a high risk of lung cancer for lifelong smokers, − an effective degradation of nicotine is highly required. Biodegradation of nicotine and its derivatives has attracted considerable attentions, − and particularly, the enzymatic degradation provides one of the most effective ways for the ring cleavage of aromatic compounds. − , As shown in Scheme , the 2,5-dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 can catalyze the conversion of DHP into N -formylmaleamic acid (NFM). − …”

“…Biodegradation of nicotine and its derivatives has attracted considerable attentions, 16−23 and particularly, the enzymatic degradation provides one of the most effective ways for the ring cleavage of aromatic compounds. [24][25][26][27][28][29][30][31][32][33]112 As shown in Scheme 1, the 2,5-dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 can catalyze the conversion of DHP into N-formylmaleamic acid (NFM). 34−36 Most recently, Xu and coworkers reported the X-ray crystal structures of NicX and the NicX−DHP−NFM complex.…”

Enzyme‐Catalyzed Oxidative Degradation of Ergothioneine

“…Since these mutations also reduce catalytic activity (Table 1, entries 4, 9 and 10), it is possible that Tyr149 and His147 have a similar stabilizing effect on Fe II −O 2 species in the catalytic cycle. Equivalent Tyr residues in TDOs and their involvement in O 2 activation is well documented [36,37] . The idea that the active site His also interacts with the metal‐coordinated oxygen species directly has received less attention [36a,38] …”