Mechanism and energy diagram for O-O bond formation in the oxygen-evolving complex in photosystem II

The recent finding of a transition state with a significantly lower barrier than previously found, has made the mechanism for O-O bond formation in photosystem II much clearer. The full mechanism can be described in the following way. Electrons and protons are ejected from the oxygen-evolving complex (OEC) in an alternating fashion, avoiding unnecessary build-up of charge. The S0-S1 and S1-S2 transitions are quite exergonic, while the S2-S3 transition is only weakly exergonic. The strong endergonic S3-S4 transition is a key step in the mechanism in which an oxygen radical is produced, held by the dangling manganese outside the Mn3Ca cube. The O-O bond formation in the S4-state occurs by an attack of the oxygen radical on a bridging oxo ligand in the cube. The mechanism explains the presence of both a cube with bridging oxo ligands and a dangling manganese. Optimal orbital overlap puts further constraints on the structure of the OEC. An alternating spin alignment is necessary for a low barrier. The computed rate-limiting barrier of 14.7 kcal mol(-1) is in good agreement with experiments.     

Important roles of tyrosines in photosystem II and cytochrome oxidase

Theoretical studies (B3LYP) on models of the active sites in Photosystem II (PSII) and cytochrome oxidase are discussed. The role of a tyrosyl radical in the O-O bond formation in PSII is investigated, as well as the tyrosyl radical formation. In cytochrome oxidase, mechanisms for O-O bond cleavage involving tyrosyl radical formation are investigated, together with possible roles for the tyrosine in the proton translocation.     

O-O bond cleavage and alkane hydroxylation in methane monooxygenase

Several new aspects of the O-O bond cleavage and alkane hydroxylation mechanisms have been studied by hybrid density functional theory in this reinvestigation of methane monooxygenase. As concerning key intermediates in these reactions, a new important low-lying state is found, described either as Fe2(III,V) or as Fe2(III,IV)O. A fully optimized transition state for O-O bond cleavage has been determined. It is suggested that the large difference in optimal size (as determined in gas phase) of the complex, before and after the O-O bond cleavage, leads to an additional driving force for the reaction, not considered previously. The strain of the enzyme is estimated to lead to a driving force in the forward direction of about 5 kcal/mol, which could explain some of the pH dependence found in recent experiments. For the hydroxylation reaction, a clean hydrogen abstraction transition state leading to a substrate radical is again found, in contrast to interpretations of radical clock experiments. An explanation, based on new results, is suggested that could account for both the experimental and theoretical results.     

Water oxidation chemistry of photosystem II

The O(2)-evolving complex of photosystem II catalyses the light-driven four-electron oxidation of water to dioxygen in photosynthesis. In this article, the steps leading to photosynthetic O(2) evolution are discussed. Emphasis is given to the proton-coupled electron-transfer steps involved in oxidation of the manganese cluster by oxidized tyrosine Z (Y(*)(Z)), the function of Ca(2+) and the mechanism by which water is activated for formation of an O-O bond. Based on a consideration of the biophysical studies of photosystem II and inorganic manganese model chemistry, a mechanism for photosynthetic O(2) evolution is presented in which the O-O bond-forming step occurs via nucleophilic attack on an electron-deficient Mn(V)=O species by a calcium-bound water molecule. The proposed mechanism includes specific roles for the tetranuclear manganese cluster, calcium, chloride, Y(Z) and His190 of the D1 polypeptide. Recent studies of the ion selectivity of the calcium site in the O(2)-evolving complex and of a functional inorganic manganese model system that test key aspects of this mechanism are also discussed.     

The mechanism for isopenicillin N synthase from density-functional modeling highlights the similarities with other enzymes in the 2-His-1-carboxylate family

Isopenicillin N synthase (IPNS) catalyzes a key step in the biosynthesis of the important beta-lactam antibiotics penicillins and cephalosporins. Density-functional calculations with the B3LYP functional are used to propose a detailed mechanism for this reaction. The results support the general scheme outlined from experimental observations, with formation of a four-membered beta-lactam ring followed by formation of a five-membered thiazolidine ring. However, an alternative mechanism for the heterolytic O-O bond cleavage and beta-lactam ring formation steps is proposed. The former part involves protonation of the distal oxygen by an iron-bound water ligand. This mechanism highlights the strong similarities that exist between IPNS and other enzymes of the 2-histidine-1-carboxylate family, especially pterin-dependent amino acid hydroxylases and alpha-keto acid-dependent dioxygenases. Both activation of the cysteine beta-C-H bond by an iron-bound superoxo radical and activation of the valine beta-C-H bond by a ferryl-oxo species show reaction barriers close to the experimentally measured one. These results are in agreement with kinetic isotope experiments that suggest both C-H bond activation steps to be partially rate limiting. The ring formation sequence is determined by the relative strengths of the two C-H bonds. Only the ferryl-oxo intermediate is capable of activating the stronger valine beta-C-H bond.     

Cytochrome P-450-catalyzed rearrangement of a peroxyquinol derived from butylated hydroxytoluene. Involvement of radical and cationic intermediates

The p-peroxyquinol derived from butylated hydroxytoluene, 2,6-di-t-butyl-4-hydroperoxy-4-methyl-2,5-cyclohexadienone, was degraded by the ferric form of rat liver cytochrome P-450, and the resulting products and their mechanisms of formation were investigated. Quinoxy radical BO. from homolysis of the O-O bond reacted by competing pathways; beta-scission yielded 2,6-di-t-butyl-p-benzoquinone, and rearrangement with ring-expansion produced an oxacycloheptadienone free radical (X(.)). This rearranged radical was stabilized by the captodative effect that facilitated competitive interactions with the P-450 iron-oxo complexes formed during O-O bond scission. Approximately 15% of X(.) was captured by oxygen rebound with a hydroxyl radical from the P-450 complex (FeOH)3+ to form a hemiketal, that led to the ring-contracted product 2,5-di-t-butyl-5-(2'-oxopropyl)-4-oxa-2-cyclopentenone by spontaneous rearrangement. The major fraction of X(.), however, underwent electron transfer oxidation to form the corresponding cation. Hydration of this cation produced the ring-contracted product, and proton elimination (or, alternatively, direct H(.) removal from X(.) led to the product 2,7-di-t-butyl-4-methylene-5-oxacyclohepta-2,6-dienone. The findings indicate that cytochrome P-450 intermediate complexes are mainly responsible for oxidation of X(.). The results complement our previous study with 2,6-di-t-butyl-4-hydroperoxy-4-methyl-2,5-cyclohexadienone (Thompson, J. A., and Wand, M. D. (1985) J. Biol. Chem. 260, 10637-10644), demonstrating competitive heterolytic and homolytic mechanisms of O-O bond cleavage, and competitive rebound and oxidation processes when a substrate-derived radical interacts with P-450 complexes.     

The tetranuclear manganese complex of Photosystem II

A polynuclear manganese complex functions in Photosystem II both to accumulate oxidizing equivalents and to bind water and catalyze its four-electron oxidation. Recent electron paramagnetic resonance (EPR) spectroscopic studies of the manganese complex show that four manganese ions are required to account for its magnetic properties. The exchange couplings between manganese ions in the S₂ state are characteristic of a Mn₄O₄ cubane-like structure. Based on this structure for the manganese complex in the S₂ state, as well as a consideration of the known properties of the manganese complex in Photosystem II and the coordination chemistry of manganese, structures are proposed for the five intermediate oxidation states of the manganese complex. A molecular mechanism for the formation of an O-O bond and the displacement of O₂ from the S₄ state is suggested.     

Oxoferryl-porphyrin radical catalytic intermediate in cytochrome bd oxidases protects cells from formation of reactive oxygen species

The quinol-linked cytochrome bd oxidases are terminal oxidases in respiration. These oxidases harbor a low spin heme b(558) that donates electrons to a binuclear heme b(595)/heme d center. The reaction with O(2) and subsequent catalytic steps of the Escherichia coli cytochrome bd-I oxidase were investigated by means of ultra-fast freeze-quench trapping followed by EPR and UV-visible spectroscopy. After the initial binding of O(2), the O-O bond is heterolytically cleaved to yield a kinetically competent heme d oxoferryl porphyrin π-cation radical intermediate (compound I) magnetically interacting with heme b(595). Compound I accumulates to 0.75-0.85 per enzyme in agreement with its much higher rate of formation (~20,000 s(-1)) compared with its rate of decay (~1,900 s(-1)). Compound I is next converted to a short lived heme d oxoferryl intermediate (compound II) in a phase kinetically matched to the oxidation of heme b(558) before completion of the reaction. The results indicate that cytochrome bd oxidases like the heme-copper oxidases break the O-O bond in a single four-electron transfer without a peroxide intermediate. However, in cytochrome bd oxidases, the fourth electron is donated by the porphyrin moiety rather than by a nearby amino acid. The production of reactive oxygen species by the cytochrome bd oxidase was below the detection level of 1 per 1000 turnovers. We propose that the two classes of terminal oxidases have mechanistically converged to enzymes in which the O-O bond is broken in a single four-electron transfer reaction to safeguard the cell from the formation of reactive oxygen species.     

Does the non-heme monooxygenase sMMO share a unified oxidation mechanism with the heme monooxygenase cytochrome P-450?

 Until recently, the majority of experts would have replied "yes" to the question in the title of this commentary. In fact, the answer is not so evident. Recent investigations have permitted us to gain insight into the similarities and the differences between the mechanisms of these two remarkable monooxygenases. In the generally accepted mechanism of cytochrome P-450, reductive activation of dioxygen and the presence of an external electrophile leads to heterolytic O-O bond cleavage to yield water and a highly electron-deficient terminally bound iron oxenoid species that is capable of attacking unactivated hydrocarbons by an electrophilic mechanism. The recently suggested "bridge mechanism" for sMMO involves homolytic O-O bond cleavage of a diferric "side-on" peroxide intermediate to yield a bridged intermediate bis-μ-oxo-diiron(IV) species, in which both oxygen atoms are derived from the dioxygen molecule. In contrast to terminal oxenoid species, this bridged diiron(IV) intermediate has stronger steric selectivity for substrates; this explains the unusual selectivity observed in sMMO alkane oxidation. Received: 7 October 1997 / Accepted: 4 February 1998     

A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese

Homoprotocatechuate (HPCA) dioxygenases are enzymes that take part in the catabolism of aromatic compounds in the environment. They use molecular oxygen to perform the ring cleavage of ortho-dihydroxylated aromatic compounds. A theoretical investigation of the catalytic cycle for HPCA 2,3-dioxygenase isolated from Brevibacterium fuscum (Bf 2,3-HPCD) was performed using hybrid DFT with the B3LYP functional, and a reaction mechanism is suggested. Models of different sizes were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the enzyme follows a reaction pathway similar to that for other non-heme iron dioxygenases, and for the manganese-dependent analog MndD, although with different energetics. The computational results suggest that the rate-limiting step for the whole reaction of Bf 2,3-HPCD is the protonation of the activated oxygen, with an energy barrier of 17.4 kcal/mol, in good agreement with the experimental value of 16 kcal/mol obtained from the overall rate of the reaction. Surprisingly, a very low barrier was found for the O-O bond cleavage step, 11.3 kcal/mol, as compared to 21.8 kcal/mol for MndD (sextet spin state). This result motivated additional studies of the manganese-dependent enzyme. Different spin coupling between the unpaired electrons on the metal and on the evolving substrate radical was observed for the two enzymes, and therefore the quartet spin state potential energy surface of the MndD reaction was studied. The calculations show a crossing between the sextet and the quartet surfaces, and it was concluded that a spin transition occurs and determines a barrier of 14.4 kcal/mol for the O-O bond cleavage, which is found to be the rate-limiting step in MndD. Thus the two 83% identical enzymes, using different metal ions as co-factors, were found to have similar activation energies (in agreement with experiment), but different rate-limiting steps.     

Oxygen activation by cytochrome P450 monooxygenase

Unlike photosystem II (PSII) that catalyzes formation of the O-O bond, the cytochromes P450 (P450), members of a superfamily of hemoproteins, catalyze the scission of the O-O bond of dioxygen molecules and insert a single oxygen atom into unactivated hydrocarbons through a hydrogen abstraction-oxygen rebound mechanism. Hydroxylation of the unactivated hydrocarbons at physiological temperatures is vital for many cellar processes such as the biosynthesis of many endogenous compounds and the detoxification of xenobiotics in humans and plants. Even though it carries out the opposite of the water splitting reaction, P450 may share similarities to PSII in proton delivery networks, oxygen and water access channels, and consecutive electron transfer processes. In this article, we review recent advances in understanding the molecular mechanisms by which P450 activates dioxygen.     

Substrate water binding and oxidation in photosystem II

This mini review presents a general introduction to photosystem II with an emphasis on the oxygen evolving complex. An attempt is made to summarise what is currently known about substrate interaction in the oxygen evolving complex of photosystem II in terms of the nature of the substrate, the timing and the location of its binding. As the nature of substrate water binding has a direct bearing on the mechanism of O-O bond formation in PSII, a discussion of O-O bond formation follows the summary of current opinion in substrate interaction.     

The role of the D- and K-pathways of proton transfer in the function of the haem-copper oxidases

The X-ray structures of several haem-copper oxidases now at hand have given important constraints on how these enzymes function. Yet, dynamic data are required to elucidate the mechanisms of electron and proton transfer, the activation of O(2) and its reduction to water, as well as the still enigmatic mechanism by which these enzymes couple the redox reaction to proton translocation. Here, some recent observations will be briefly reviewed with special emphasis on the functioning of the so-called D- and K-pathways of proton transfer. It turns out that only one of the eight protons taken up by the enzyme during its catalytic cycle is transferred via the K-pathway. The D-pathway is probably responsible for the transfer of all other protons, including the four that are pumped across the membrane. The unique K-pathway proton may be specifically required to aid O-O bond scission by the haem-copper oxidases.     

Superoxide dismutases—a review of the metal-associated mechanistic variations

Superoxide dismutases are enzymes that function to catalytically convert superoxide radical to oxygen and hydrogen peroxide. These enzymes carry out catalysis at near diffusion controlled rate constants via a general mechanism that involves the sequential reduction and oxidation of the metal center, with the concomitant oxidation and reduction of superoxide radicals. That the catalytically active metal can be copper, iron, manganese or, recently, nickel is one of the fascinating features of this class of enzymes. In this review, we describe these enzymes in terms of the details of their catalytic properties, with an emphasis on the mechanistic differences between the enzymes. The focus here will be concentrated mainly on two of these enzymes, copper, zinc superoxide dismutase and manganese superoxide dismutase, and some relatively subtle variations in the mechanisms by which they function.     

The mechanism for dioxygen formation in PSII studied by quantum chemical methods.

The availability of an X-ray structure for PSII including the water-oxidizing cluster, where the metal atoms and the amino acids are assigned, has opened up new possibilities to study the mechanism for dioxygen formation. In the present paper the main results of an ongoing hybrid DFT study are presented. The model used follows the structure suggested by the X-ray analysis as closely as possible. After nearly one thousand optimizations of different structures, each one with about 70 atoms, the main features of a water oxidizing mechanism start to emerge. The key intermediate is an oxyl radical state in S(3), stabilized by a weak trans effect to a bridging oxo in the cube. To reach this radical state a structural rearrangement appears necessary, in which one additional bridging oxo is formed between the dangling manganese and a manganese in the cube. The calculated energetics is reasonable but still not fully consistent with a correct mechanism. It is suggested that some part of the structure is not correct, probably the presence of the bicarbonate.     

The enzymology of sulfur activation during thiamin and biotin biosynthesis.

The thiamin and biotin biosynthetic pathways utilize elaborate strategies for the transfer of sulfur from cysteine to cofactor precursors. For thiamin, the sulfur atom of cysteine is transferred to a 66-amino-acid peptide (ThiS) to form a carboxy-terminal thiocarboxylate group. This sulfur transfer requires three enzymes and proceeds via a ThiS-acyladenylate intermediate. The biotin synthase Fe-S cluster functions as the immediate sulfur donor for biotin formation. C-S bond formation proceeds via radical intermediates that are generated by hydrogen atom transfer from dethiobiotin to the adenosyl radical. This radical is formed by the reductive cleavage of S-adenosylmethionine by the reduced Fe-S cluster of biotin synthase.     

4-Hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism

Density functional calculations using the B3LYP functional has been used to study the reaction mechanism of 4-hydroxyphenylpyruvate dioxygenase. The first part of the catalytic reaction, dioxygen activation, is found to have the same mechanism as in alpha-ketoglutarate-dependent enzymes; the ternary enzyme-substrate-dioxygen complex is first decarboxylated to the iron(II)-peracid intermediate, followed by heterolytic cleavage of the O-O bond yielding an iron(IV)-oxo species. This highly reactive intermediate attacks the aromatic ring at the C1 position and forms a radical sigma complex, which can either form an arene oxide or undergo a C1-C2 side-chain migration. The arene oxide is found to have no catalytic relevance. The side-chain migration is a two-step process; the carbon-carbon bond cleavage first affords a biradical intermediate, followed by a decay of this species forming the new C-C bond. The ketone intermediate formed by a 1,2 shift of an acetic acid group rearomatizes either at the active site of the enzyme or in solution. The hypothetical oxidation of the aromatic ring at the C2 position was also studied to shed light on the 4-HPPD product specificity. In addition, the benzylic hydroxylation reaction, catalyzed by 4-hydroxymandelate synthase, was also studied. The results are in good agreement with the experimental findings.     

The mechanism of cumene hydroperoxide-dependent lipid peroxidation: the function of cytochrome P-450

The addition of limiting amounts of cumene hydroperoxide to rat liver microsomes resulted in the rapid uptake of molecular oxygen, the formation of thiobarbituric acid reactive products, and the loss of hydroperoxide. The stoichiometry of lipid peroxidation and the yields of 2-phenyl-2-propanol (a major product of the reaction) and acetophenone (a minor product) observed with liver microsomes prepared from untreated rats is greater than that seen with liver microsomes from ciprofibrate-treated rats which, in turn, is greater than that observed with liver microsomes from phenobarbital-treated rats. The Km's and Vmax's of oxygen uptake varied with the type of rat liver microsomes used. Cytochrome P-450 substrates and inhibitors decreased the extents and initial rates of oxygen uptake and thiobarbituric acid reactive product formation. A mechanism is proposed involving the cytochrome P-450-catalyzed homolytic cleavage of the cumene hydroperoxide O-O bond to give the cumyloxyl radical. It is proposed that this oxygen-centered radical abstracts a hydrogen atom from an unsaturated fatty acid associated with a lipid (initiating lipid peroxidation) to give 2-phenyl-2-propanol or that the radical undergoes beta-scission to produce acetophenone and a methyl radical.     

A ligand field chemistry of oxygen generation by the oxygen-evolving complex and synthetic active sites

Oxygen-oxygen bond formation and O2 generation occur from the S4 state of the oxygen-evolving complex (OEC). Several mechanistic possibilities have been proposed for water oxidation, depending on the formal oxidation state of the Mn atoms. All fall under two general classifications: the AB mechanism in which nucleophilic oxygen (base, B) attacks electrophilic oxygen (acid, A) of the Mn4Ca cluster or the RC mechanism in which radical-like oxygen species couple within OEC. The critical intermediate in either mechanism involves a metal oxo, though the nature of this oxo for AB and RC mechanisms is disparate. In the case of the AB mechanism, assembly of an even-electron count, high-valent metal-oxo proximate to a hydroxide is needed whereas, in an RC mechanism, two odd-electron count, high-valent metal oxos are required. Thus the two mechanisms give rise to very different design criteria for functional models of the OEC active site. This discussion presents the electron counts and ligand geometries that support metal oxos for AB and RC O-O bond-forming reactions. The construction of architectures that bring two oxygen functionalities together under the purview of the AB and RC scenarios are described.     

O-O bond splitting mechanism in cytochrome oxidase

Hybrid density functional theory (DFT) calculations have been used to investigate different mechanisms for O–O bond splitting in cytochrome oxidase. It is shown that the requirement for a low activation barrier for the O–O bond splitting is that two protons, apart from the tyrosine hydroxyl proton, are available at the binuclear center. A mechanism is suggested for the transformation from a species with a molecularly coordinated O₂, to an O–O cleaved species with an oxo-ferryl group. The mechanism has a calculated activation barrier in reasonable agreement with experimental estimates, and the overall reaction is close to thermoneutral, in line with the requirement that the energy wasted as heat should be minimized. The rate limiting step in the mechanism occurs at the initial Fe–O₂ intermediate, consistent with experimental observations that the decay of the oxy intermediate parallels the increase of the oxo product. The formation of a radical at the cross-linked tyrosine–histidine structure is a possible source for one of the electrons required in the bond cleavage process. Possible sources for the two protons are discussed, including a suggested key role for the hydroxyl group on the farnesyl side chain of heme a₃.