Unravelling the Molecular Origin of the Regiospecificity in Extradiol Catechol Dioxygenases

Proton Transfer via Arginine with Suppressed pKa Mediates Catalysis by Gentisate and Salicylate Dioxygenase

Gentisate and salicylate 1,2-dioxygenases (GDO and SDO) facilitate aerobic degradation of aromatic rings by inserting both atoms of dioxygen into their substrates, thereby participating in global carbon cycling. The role of acid-base catalysts in the reaction cycles of these enzymes is debatable. We present evidence of the participation of a proton shuffler during catalysis by GDO and SDO. The pH dependence of Michaelis-Menten parameters demonstrates that a single proton transfer is mandatory for the catalysis. Measurements at variable temperatures and pHs were used to determine the standard enthalpy of ionization (ΔHion°) of 51 kJ/mol for the proton transfer event. Although the observed apparent pKa in the range of 6.0-7.0 for substrates of both enzymes is highly suggestive of a histidine residue, ΔHion° establishes an arginine residue as the likely proton source, providing phylogenetic relevance for this strictly conserved residue in the GDO family. We propose that the atypical 3-histidine ferrous binding scaffold of GDOs contributes to the suppression of arginine pKa and provides support for this argument by employing a 2-histidine-1-carboxylate variant of the enzyme that exhibits elevated pKa. A reaction mechanism considering the role of the proton source in stabilizing key reaction intermediates is proposed.

QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase

The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.

Homoprotocatechuate dioxygenase active site: Imitating the secondary sphere base via computational design

Oxidative ring cleavage reactions have attracted great interest and various studies on the catechol ring-cleaving enzyme homoprotocatechuate dioxygenase (HPCD) have been reported in the literature. The available data on how the proton transfer takes place led us to design a potential HPCD model structure. A secondary sphere effect of utmost importance, the assistance of His200, which is critical for the catechol proton to migrate to dioxygen, was cautiously included on the first coordination shell. This was done mainly by modifying the axial ligands in the first coordination shell of HPCD such that the dual basic/acidic role in the proton transfer pathway of His200 was reproduced. Model systems with mono-, bi-, and tridentate ligands are reported. Energetically feasible reaction channels on synthetically promising ligand structures are identified. Key structural and electronic principles for obtaining viable proton transfer paths are outlined.

Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage

The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.

Polyhedral Dicobaltadithiaboranes and Dicobaltdiselenaboranes as Examples of Bimetallic Nido Structures without Bridging Hydrogens

The geometries and energetics of the n-vertex polyhedral dicobaltadithiaboranes and dicobaltadiselenaboranes Cp2Co2E2Bn−4Hn−4 (E = S, Se; n = 8 to 12) have been investigated via the density functional theory. Most of the lowest-energy structures in these systems are generated from the (n + 1)-vertex most spherical closo deltahedra by removal of a single vertex, leading to a tetragonal, pentagonal, or hexagonal face depending on the degree of the vertex removed. In all of these low-energy structures, the chalcogen atoms are located at the vertices of the non-triangular face. Alternatively, the central polyhedron in most of the 12-vertex structures can be derived from a Co2E2B8 icosahedron with adjacent chalcogen (E) vertices by breaking the E–E edge and 1 or more E–B edges to create a hexagonal face. Examples of the arachno polyhedra with two tetragonal and/or pentagonal faces derived from the removal of two vertices from isocloso deltahedra were found among the set of lowest-energy Cp2Co2E2Bn−4Hn−4 (E = S, Se; n = 8 and 12) structures.

Aromaticity in P8 allotropes and (CH)8 analogues: significance of their 40 valence electrons?

The currently unknown phosphorus allotrope P₈ is of interest since its 40 total valence electrons is a "magic number" corresponding to a filled 1S²1P⁶1D¹⁰1S²1F¹⁴2P⁶ shell such as found in the relatively stable main group element clusters Al₁₃^- and Ge₉^4-. However, P₈ still remains as an elusive structure not realized experimentally. The lowest energy P₈ structure by a margin of ∼9 kcal mol^-1 is shown by density functional theory to be a cuneane analogue with no PP double bonds and two each of P₅, P₄, and P₃ rings. Higher energy P₈ structures are polycyclic systems having at most a single PP double bond. These P₈ systems are not "carbon copies" of the corresponding (CH)₈ hydrocarbons with exactly one hydrogen atom bonded to each carbon atom. Thus the lowest energy (CH)₈ structure is cyclooctatetraene with four CC bonds followed by benzocyclobutene with three CC bonds. The cuneane (CH)₈ structure is a relatively high energy isomer lying ∼36 kcal mol^-1 above cyclooctatetraene. The cubane P₈ and (CH)₈ structures are even higher energy structures, lying ∼37 and ∼74 kcal mol^-1 in energy above the corresponding global minima. Our results demonstrate differences in medium sized aggregates of elemental phosphorus and isolobal hydrocarbon species.

A theoretical study on the on-off phosphorescence of novel Pt(ii)/Pt(iv)-bisphenylpyridinylmethane complexes

An in-depth theoretical study on the Pt(ii)/Pt(iv)-bisphenylpyridinylmethane complexes was carried out, which focused on the geometric/electronic structures, excitation procedures, on-off phosphorescence mechanisms, and structure-optical performance relationships. The key roles of the linkages (LK) connected in the middle of phenylpyridines were carefully investigated using multiple wavefunction analysis methods, such as non-covalent interaction (NCI) visualizations and natural bond orbital (NBO) studies. The phosphorescence-off phenomenon was considered by hole-electron analysis and visualizations, spin-orbit coupling (SOC) studies, and NBO analysis. Through these investigations, the relationship of the substituents in LK and the optical performances were revealed, as well as the fundamental principles of the phosphorescence-quenching mechanism in Pt(iv) complexes, which pave the way for further performance/structural renovation works. In addition, an intuitive visualization method was developed using a heatmap to quantitatively express the SOC matrix elementary (SOCME), which is helpful for big data simplification for phosphorescence analysis.

Charge Maintenance during Catalysis in Nonheme Iron Oxygenases

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 Insights into Pyridine Ring Degradation Catalyzed by 2,5-Dihydroxypyridine Dioxygenase NicX

2,5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 is a mononuclear non-heme iron oxygenase that can catalyze the oxidative pyridine ring cleavage. Recently, the reported crystal structure of NicX has lent support to an apical dioxygen catalytic mechanism, while the mechanistic details remain unclear. In this work, we constructed a Fe(II)-O2-substrate complex model and performed a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations to illuminate the catalysis of NicX. Our results reveal that although the substrate does not directly coordinate with the central iron ion, there is an electron transfer from the substrate to the Fe-coordinated dioxygen, and the active form of the reactant complex can be described as DHP•+-Fe(II)-O2•-, which is different from other similar mononuclear non-heme iron. The NicX-catalyzed pyridine ring degradation contains three parts, including the attack of Fe(II)-superoxo on the activated pyridine ring, the dissociation of the Op-Od bond, and the ring-opening of the seven-membered-ring lactone. Owing to the radical characteristic of the pyridine ring, the first attack of Fe(II)-superoxo on the C6 of the pyridine ring was calculated to be quite easy. In the second step of the reaction, the dissociation of the Op-Od bond leads to the incorporation of the first oxygen atom into the substrate, which is the rate-limiting step of the overall reaction with an energy barrier of 18.0 kcal/mol. The resultant intermediate then undergoes an arrangement by the intramolecular attack of Od• on the carbonyl C5, forming the seven-membered-ring lactone. Finally, the Fe(III)-oxo attacks the carbonyl C5 of lactone, accompanied by the ring-opening to generate N-formylmaleamic acid. His105 can promote reactivity by donating a proton to Fe(III)-oxo, but it is not a necessary residue. In addition to the ligated residues of iron, other pocket residues such as Glu177, His189, and His105 mainly play roles in anchoring the substrate.

N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement

The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the Fe^II-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent Fe^IV═O species. In the catalytic reaction pathway, the O₂ binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the C^ε-N^ω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.

Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX

Biodegradation of aromatic and heterocyclic compounds requires an oxidative ring cleavage enzymatic step. Extensive biochemical research has yielded mechanistic insights about catabolism of aromatic substrates; yet much less is known about the reaction mechanisms underlying the cleavage of heterocyclic compounds such as pyridine-ring-containing ones like 2,5-hydroxy-pyridine (DHP). 2,5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 uses a mononuclear nonheme Fe(II) to catalyze the oxidative pyridine ring cleavage reaction by transforming DHP into N-formylmaleamic acid (NFM). Herein, we report a crystal structure for the resting form of NicX, as well as a complex structure wherein DHP and NFM are trapped in different subunits. The resting state structure displays an octahedral coordination for Fe(II) with two histidine residues (His²⁶⁵ and His³¹⁸), a serine residue (Ser³⁰²), a carboxylate ligand (Asp³²⁰), and two water molecules. DHP does not bind as a ligand to Fe(II), yet its interactions with Leu¹⁰⁴ and His¹⁰⁵ function to guide and stabilize the substrate to the appropriate position to initiate the reaction. Additionally, combined structural and computational analyses lend support to an apical dioxygen catalytic mechanism. Our study thus deepens understanding of non-heme Fe(II) dioxygenases.

A novel concept for the biodegradation mechanism of dianionic catechol with homoprotocatechuate 2,3-dioxygenase: A non-proton-assisted process

The theory of "proton-assisted process" can well explain the catalytic mechanism of homoprotocatechuate 2,3-dioxygenase (2,3-HPCD) with a monoanionic substrate (homoprotocatechuate, HPCA). Here a "non-proton-assisted process" is presented to interpret catalytic mechanism of 2,3-HPCD with a dianionic substrate (4-nitrocatechol, 4NC). The ONIOM calculation is performed to investigate the reaction pathway of a wild-type 2,3-HPCD with 4NC (H200H-4NC system). The catalytic reaction is comprised of four steps: (1) A dioxygen attacks the aromatic ring to produce an alkylperoxo species. (2) O-O bond cleavage and the formation of an epoxide species occur. (3) A seven-membered O-heterocyclic compound is generated by the extinction of the epoxy structure. (4) The seven-membered ring undergoes ring opening to form the final product (C2-C3 cleavage product). The effective free energy barrier of the catalytic reaction of the H200H-4NC system is 26.2 kcal mol^-1, which is much higher than that of the H200H-HPCA system. Furthermore, two calculated electronic configurations (Fe(III)-O₂^•- and Fe(III)-SQ^•) have a high similarity to previously detected ones, which demonstrates that the Asn200 variant (H200N-4NC variant system) employs a C4 (para-carbon) pathway to produce a C4-C5 cleavage product. Our findings provide an in-depth understanding of the catalytic mechanisms of dianionic catechol and its derivatives.

The role of halogen substituents and substrate pKa in defining the substrate specificity of 2,6-dichlorohydroquinone 1,2-dioxygenase (PcpA)

2,6-Dichlorohydroquinone 1,2-dioxygenase (PcpA) is a non-heme Fe(II) enzyme that is specific for ortho-dihalohydroquinones. Here we deconvolute the role of halogen polarizability vs. substrate pK_a in defining this specificity, and show how substrate binding compares to the structurally homologous catechol extradiol dioxygenases. The substrates 2,6-dichloro- and 2,6-dibromohydroquinone (polarizable halogens, pK_a1 = 7.3), 2,6-difluorohydroquinone (nonpolarizable halogens, pK_a1 = 7.5), and 2-chloro-6-methylhydroquinone (polarizable halogen, pK_a1 = 9.0) were examined through spectrophotometric titrations and steady-state kinetics. The results show that binding of the substrates to the enzyme decreased [Formula: see text] by about 0.5, except for 2,6-difluorohydroquinone, which showed no change. Additionally, the K_d values of 2,6-dichloro- and 2,6-dibromohydroquinone are about equal to their respective [Formula: see text]. For comparison, with catechol 2,3-dioxygenase (XylE), the substrates 4-methyl- and 3-bromocatechol are bound to the enzyme exclusively in the monoanion form over a wide pH range, indicating a [Formula: see text] of at least - 2.9 and - 1.2, respectively. The steady-state kinetic studies showed that 2,6-difluorohydroquinone is a poor substrate, with [Formula: see text] approximately 40-fold lower and [Formula: see text] 20-fold higher than 2,6-dichlorohydroquinone, despite its similar pK_a1. Likewise, the pH dependence of [Formula: see text] for 2-chloro-6-methylhydroquinone is nearly identical to that of 2,6-dichlorohydroquinone, despite its very different pK_a1. These results show that (1) it is clearly the halogen polarizability and not the lower substrate pK_a that determines the substrate specificity of PcpA, and (2) that PcpA, unlike the catechol extradiol dioxygenases, lacks an active site base that assists with substrate deprotonation, highlighting a key functional difference in what are otherwise similar active sites that defines their different reactivity.

Mechanistic Insights into a Stibene Cleavage Oxygenase NOV1 from Quantum Mechanical/Molecular Mechanical Calculations

NOV1, a stilbene cleavage oxygenase, catalyzes the cleavage of the central double bond of stilbenes to two phenolic aldehydes, using a 4-His Fe(II) center and dioxygen. Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the reaction mechanism of the central double bond cleavage of phytoalexin resveratrol by NOV1. Our results showed that the oxygen molecule prefers to bind to the iron center in a side-on fashion, as suggested from the experiment. The quintet Fe-O2 complex with the side-on superoxo antiferromagnetic coupled to the resveratrol radical is identified as the reactive oxygen species. The QM/MM results support the dioxygenase mechanism involving a dioxetane intermediate with a rate-limiting barrier of 10.0 kcal mol-1. The alternative pathway through an epoxide intermediate is ruled out due to a larger rate-limiting barrier (26.8 kcal mol-1). These findings provide important insight into the catalytic mechanism of carotenoid cleavage oxygenases and also the dioxygen activation of non-heme enzymes.

Mechanistic insights into ring cleavage of hydroquinone by PnpCD from quantum mechanical/molecular mechanical calculations

QM/MM calculations for ring cleavage of hydroquinone by PnpCD show that Asn258 loses coordination to the iron when the reaction begins. The first-sphere Glu262 can act as an acid–base catalyst to lower the rate-limiting barrier.

Reversible complexation of ammonia by breaking a manganese–manganese bond in a manganese carbonyl ethylenedithiolate complex: a theoretical study of an unusual type of Lewis acid

The addition of bases such as ammonia and trimethylphosphine to H₂C₂S₂Mn₂(CO)₆ to give yellow 1 : 1 adducts is shown to break the metal–metal bond rather than displace the coordinated double bond.

Computational Understanding of the Selectivities in Metalloenzymes

Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.

Deviations from the Most Spherical Deltahedra in Rhenatricarbaboranes Having 2n + 2 Wadean Skeletal Electrons

Density functional theory studies on the rhenatricarbaboranes C₃B_n-4H_n-1Re(CO)₃ (n = 7-12) show that the lowest energy polyhedra for n-vertex metallaboranes having 2n + 2 skeletal electrons and sufficiently dissimilar vertex atoms can deviate from the most spherical closo deltahedra predicted by application of the Wade-Mingos rules. Furthermore, the lowest energy structures of these rhenatricarbaboranes are found to avoid C-C edges and have carbon atoms located at degree 4 rather than degree 5 vertices. The lowest energy structures for the 7-vertex C₃B₃H₆Re(CO)₃ system all have a central C₃B₃Re closo deltahedron, namely the pentagonal bipyramid with the rhenium atom at a degree 5 axial vertex and all three carbon atoms at degree 4 equatorial vertices. However, the lowest energy structure for the 8-vertex C₃B₄H₇Re(CO)₃ is not the most spherical closo 8-vertex deltahedron, namely the bisdisphenoid, but instead a central C₃B₄Re hexagonal bipyramid with mutually nonadjacent degree 4 vertices for the carbon atoms. Similarly, the lowest energy 10-vertex C₃B₆H₉Re(CO)₃ structures are derived from isocloso deltahedra having three degree 4 vertices for all three carbon atoms rather than from the most spherical 10-vertex closo deltahedron, namely the bicapped square antiprism with only two degree 4 vertices. However, for the 9-vertex C₃B₅H₈Re(CO)₃ system, the most spherical closo deltahedron, namely the tricapped trigonal prism, has three mutually nonadjacent degree 4 vertices, which is ideal for the three carbon atoms and thus is the preferred deltahedron. The preferred deltahedron for the 11-vertex C₃B₇H₁₀Re(CO)₃ remains the most spherical closo deltahedron despite having only two degree 4 vertices for the carbon atoms. Furthermore, the six lowest energy 12-vertex C₃B₈H₁₁Re(CO)₃ structures are all based on the regular icosahedron generally favored in polyhedral borane chemistry despite its complete lack of degree 4 vertices for the carbon atoms.

C-H Activation from Iron(II)-Nitroxido Complexes

The reaction of nitroxyl radicals TEMPO (2,2',6,6'-tetramethylpiperidinyloxyl) and AZADO (2-azaadamantane-N-oxyl) with an iron(I) synthon affords iron(II)-nitroxido complexes (Ar L)Fe(κ1 -TEMPO) and (Ar L)Fe(κ2 -N,O-AZADO) (Ar L=1,9-(2,4,6-Ph3 C6 H2 )2 -5-mesityldipyrromethene). Both high-spin iron(II)-nitroxido species are stable in the absence of weak C-H bonds, but decay via N-O bond homolysis to ferrous or ferric iron hydroxides in the presence of 1,4-cyclohexadiene. Whereas (Ar L)Fe(κ1 -TEMPO) reacts to give a diferrous hydroxide [(Ar L)Fe]2 (μ-OH)2 , the reaction of four-coordinate (Ar L)Fe(κ2 -N,O-AZADO) with hydrogen atom donors yields ferric hydroxide (Ar L)Fe(OH)(AZAD). Mechanistic experiments reveal saturation behavior in C-H substrate and are consistent with rate-determining hydrogen atom transfer.

Theoretical Study of the Mechanism of the Nonheme Iron Enzyme EgtB

EgtB is a nonheme iron enzyme catalyzing the C-S bond formation between γ-glutamyl cysteine (γGC) and N-α-trimethyl histidine (TMH) in the ergothioneine biosynthesis. Density functional calculations were performed to elucidate and delineate the reaction mechanism of this enzyme. Two different mechanisms were considered, depending on whether the sulfoxidation or the S-C bond formation takes place first. The calculations suggest that the S-O bond formation occurs first between the thiolate and the ferric superoxide, followed by homolytic O-O bond cleavage, very similar to the case of cysteine dioxygenase. Subsequently, proton transfer from a second-shell residue Tyr377 to the newly generated iron-oxo moiety takes place, which is followed by proton transfer from the TMH imidazole to Tyr377, facilitated by two crystallographically observed water molecules. Next, the S-C bond is formed between γGC and TMH, followed by proton transfer from the imidazole CH moiety to Tyr377, which was calculated to be the rate-limiting step for the whole reaction, with a barrier of 17.9 kcal/mol in the quintet state. The calculated barrier for the rate-limiting step agrees quite well with experimental kinetic data. Finally, this proton is transferred back to the imidazole nitrogen to form the product. The alternative thiyl radical attack mechanism has a very high barrier, being 25.8 kcal/mol, ruling out this possibility.

Theoretical investigation on proton transfer mechanism of extradiol dioxygenase

The formation mechanism of alkyl(hydro)peroxo species is performed via two parallel pathways.