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.     

Does the structure of the water-oxidizing photosystem II-manganese complex at room temperature differ from its low-temperature structure? A comparative X-ray absorption study

Detailed information on room-temperature structure and oxidation state of the Photosystem II (PS II) manganese complex is needed to put mechanistic considerations on solid grounds. Because previously this information had not been available, the tetranuclear manganese complex was investigated by X-ray absorption spectroscopy (XAS) on PS II membrane particles at 290 K. Due to methodical progress (collection of XAS spectra within 10 s or less), significant X-ray radiation damage can be avoided; room-temperature XAS investigations on the PS II in its native membrane environment become feasible. Thus, the ambiguity with respect to the mechanistic relevance of low-temperature XAS results is avoidable. At 290 K as well as at 18 K, the manganese complex in its dark-stable state (S(1)-state) seemingly is a Mn(III)(2)Mn(IV)(2) complex comprising two di-mu(2)-oxo bridged binuclear manganese units characterized by the same Mn-Mn distance of 2.71-2.72 A at both temperatures. Most likely, manganese oxidation states and the protonation state of the bridging oxides are fully temperature independent. Remarkably, at room-temperature manganese-ligand distances of 3.10 and 3.65 A are clearly discernible in the EXAFS spectra. The type of bridging assumed to result in Mn-Mn or Mn-Ca distances around 3.1 A is, possibly, temperature-dependent as suggested by distance lengthening upon cooling by 0.13 A. However, mechanistic proposals on photosynthetic water oxidation, which involve the dimer-of-dimers model [Yachandra, V. K., et al. (1993) Science 260, 675-679] are not invalidated by the presented results.     

The lack of a solvent accessible hydroxide or water ligand to iron at the 3Fe center of Azotobacter vinelandii ferredoxin I

The X-ray crystal structure of Azotobacter vinelandii ferredoxin I (FdI) describes a planar 3Fe-3S center in which one of the iron atoms is ligated to a solvent accessible oxo ligand, presumably from water or hydroxide (Ghosh et al., (1982) J. Mol. Biol. 158, 73-109). Efforts to displace the proposed oxo ligand with cyanide were unsuccessful, even in 80% dimethylsulfoxide. In addition, comparison of the electron spin echo envelopes for H2O- and D2O-equilibrated samples of FdI showed only a slight deuterium modulation, far less than would be expected were water to be bound as an iron ligand. These results do not support the presence of a solvent accessible oxo ligand to the 3Fe center as described in the X-ray crystal structure.     

A new approach to the problem of oxygen formation in photosynthesis

A detailed quantum-mechanical analysis of the model of water oxidizing complex, based on recent X-ray data on the structure of PSII, was made. A mechanism of water oxidation was suggested and explained for the first time. The role of three manganese atoms that are not involved directly in water oxidation, the role of the cubic structure of the complex, and the necessity of the presence of calcium and chlorine atoms during water oxidation are discussed. Theoretical computations of the energies of the complex in each S-state were made.     

Structure of the high-valent FeIIIFeIV state in ribonucleotide reductase (RNR) of Chlamydia trachomatis--combined EPR, 57Fe-, 1H-ENDOR and X-ray studies

A recently discovered subgroup of class I ribonucleotide reductase (RNR) found in the infectious bacterium Chlamydia trachomatis (C. trachomatis) was shown to exhibit a high-valent Fe(III)Fe(IV) center instead of the tyrosyl radical observed normally in all class I RNRs. The X-ray structure showed that C. trachomatis WT RNR has a phenylalanine at the position of the active tyrosine in Escherichia coli RNR. In this paper the X-ray structure of variant F127Y is presented, where the tyrosine is restored. Using (1)H- and (57)Fe-ENDOR spectroscopy it is shown, that in WT and variants F127Y and Y129F of C. trachomatis RNR, the Fe(III)Fe(IV) center is virtually identical with the short-lived intermediate X observed during the iron oxygen reconstitution reaction in class I RNR from E. coli. The experimental data are consistent with a recent theoretical model for X, proposing two bridging oxo ligands and one terminal water ligand. A surprising extension of the lifetime of the Fe(III)Fe(IV) state in C. trachomatis from a few seconds to several hours at room temperature was observed under catalytic conditions in the presence of substrate. These findings suggest a possible new role for the Fe(III)Fe(IV) state also in other class I RNR, during the catalytic radical transfer reaction, by which the substrate turnover is started.     

Quantum chemical studies of manganese centers in biology

During the past five years, hybrid density functional theory has been used to study mechanisms for redox-active enzymes containing complexes with a variety of different transition metals. In this paper, suggested mechanisms of some manganese enzymes are described. For photosystem II, a mechanism is proposed leading to an oxyl radical in the S(3)-state, which is the precursor for the O-O bond formation. For manganese catalase, the suggested mechanism instead leads to the formation of a hydroxyl radical after the O-O bond of hydrogen peroxide is cleaved. This radical is immediately quenched by a manganese center. Parallels between these enzymes are highlighted. Jahn-Teller and trans effects are emphasized.     

Arginase-boronic acid complex highlights a physiological role in erectile function.

The crystal structure of the complex between the binuclear manganese metalloenzyme arginase and the boronic acid analog of L-arginine, 2(S)-amino-6-boronohexanoic acid (ABH), has been determined at 1.7 A resolution from a crystal perfectly twinned by hemihedry. ABH binds as the tetrahedral boronate anion, with one hydroxyl oxygen symmetrically bridging the binuclear manganese cluster and a second hydroxyl oxygen coordinating to Mn2+A. This binding mode mimics the transition state of a metal-activated hydroxide mechanism. This transition state structure differs from that occurring in NO biosynthesis, thereby explaining why ABH does not inhibit NO synthase. We also show that arginase activity is present in the penis. Accordingly, the tight binding and specificity of ABH allows us to probe the physiological role of arginase in modulating the NO-dependent smooth muscle relaxation required for erection. Strikingly, ABH causes significant enhancement of nonadrenergic, noncholinergic nerve-mediated relaxation of penile corpus cavernosum smooth muscle, suggesting that arginase inhibition sustains L-arginine concentrations for NO synthase activity. Therefore, human penile arginase is a potential target for therapeutic intervention in the treatment of erectile dysfunction.     

Extended X-ray absorption fine structure studies on the iron-containing subunit of ribonucleotide reductase from Escherichia coli

Iron K-edge X-ray absorption spectra were obtained on the protein B2, the small subunit of ribonucleotide reductase from Escherichia coli. Protein B2 contains a binuclear iron center with many properties in common with the iron center of oxidized hemerythrins. The extended X-ray absorption fine structure (EXAFS) measurements on protein B2 were analyzed and compared with published data for oxyhemerythrin. In protein B2 there are, in the first coordination shell around each Fe atom, five or six oxygen or nitrogen atoms that are directly coordinated ligands. In oxyhemerythrin there are six ligands to each iron. As in oxyhemerythrin, one of the ligands in the first shell of protein B2 is at a short distance, about 1.78 A, confirming the existence of a mu-oxo bridge. The other atoms of the first shell are at an average distance of 2.04 A, which is about 0.1 A shorter than in oxyhemerythrin. In protein B2 the Fe-Fe distance is in the range 3.26-3.48 A, and the bridging angle falls between 130 and 150 degrees. On the basis of these data, there is no direct evidence for any histidine ligands in protein B2, but the noise level leaves way for the possibility of a maximum of about three histidines for each Fe pair. The X-ray absorption spectrum of a hydroxyurea-treated sample was not significantly different from that of the native protein B2, which implies that no significant alteration in the structure of the iron site occurs upon destruction of the tyrosine radical.     

The S0 state of photosystem II induced by hydroxylamine: differences between the structure of the manganese complex in the S0 and S1 states determined by X-ray absorption spectroscopy

Hydroxylamine at low concentrations causes a two-flash delay in the first maximum flash yield of oxygen evolved from spinach photosystem II (PSII) subchloroplast membranes that have been excited by a series of saturating flashes of light. Untreated PSII membrane preparations exhibit a multiline EPR signal assigned to a manganese cluster and associated with the S2 state when illuminated at 195 K, or at 273 K in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). We used the extent of suppression of the multiline EPR signal observed in samples illuminated at 195 K to determine the fraction of PSII reaction centers set back to a hydroxylamine-induced S0-like state, which we designate S0*. The manganese K-edge X-ray absorption edges for dark-adapted PSII preparations with or without hydroxylamine are virtually identical. This indicates that, despite its high binding affinity to the oxygen-evolving complex (OEC) in the dark, hydroxylamine does not reduce chemically the manganese cluster within the OEC in the dark. After a single turnover of PSII, a shift to lower energy is observed in the inflection of the Mn K-edge of the manganese cluster. We conclude that, in the presence of hydroxylamine, illumination causes a reduction of the OEC, resulting in a state resembling S0. This lower Mn K-edge energy of S0*, relative to the edge of S1, implies the storage and stabilization of an oxidative equivalent within the manganese cluster during the S0----S1 state transition. An analysis of the extended X-ray absorption fine structure (EXAFS) of the S0* state indicates that a significant structural rearrangement occurs between the S0* and S1 states. The X-ray absorption edge position and the structure of the manganese cluster in the S0* state are indicative of a heterogeneous mixture of formal valences of manganese including one Mn(II) which is not present in the S1 state.     

Rapid loss of structural motifs in the manganese complex of oxygenic photosynthesis by X-ray irradiation at 10-300 K

Structural changes upon photoreduction caused by x-ray irradiation of the water-oxidizing tetramanganese complex of photosystem II were investigated by x-ray absorption spectroscopy at the manganese K-edge. Photoreduction was directly proportional to the x-ray dose. It was faster in the higher oxidized S2 state than in S1; seemingly the oxidizing potential of the metal site governs the rate. X-ray irradiation of the S1 state at 15 K initially caused single-electron reduction to S0* accompanied by the conversion of one di-mu-oxo bridge between manganese atoms, previously separated by approximately 2.7 A, to a mono-mu-oxo motif. Thereafter, manganese photoreduction was 100 times slower, and the biphasic increase in its rate between 10 and 300 K with a breakpoint at approximately 200 K suggests that protein dynamics is rate-limiting the radical chemistry. For photoreduction at similar x-ray doses as applied in protein crystallography, halfway to the final Mn(II)4 state the complete loss of inter-manganese distances <3 A was observed, even at 10 K, because of the destruction of mu-oxo bridges between manganese ions. These results put into question some structural attributions from recent protein crystallography data on photosystem II. It is proposed to employ controlled x-ray photoreduction in metalloprotein research for: (i) population of distinct reduced states, (ii) estimating the redox potential of buried metal centers, and (iii) research on protein dynamics.     

Regioselectivity of substrate hydroxylation versus halogenation by a nonheme iron(IV)–oxo complex: possibility of rearrangement pathways

Several nonheme iron enzymes and biomimetic model complexes catalyze a substrate halogenation reaction. Recent computational studies (Borowski et al. J Am Chem Soc 132:12887-12898, 2010) on α-ketoglutarate dependent halogenase proposed an initial isomerization reaction that is important to give halogenated products. We present here a series of density functional theory calculations on a biomimetic model complex-[Fe(IV)(O)(TPA)Cl](+), where TPA is tris(2-pyridylmethyl)amine-and investigate the mechanisms of substrate halogenation versus hydroxylation using the reactant and its isomer where the oxo and chloro groups have changed positions. We show here that the reactions occur on a dominant quintet spin state surface, although the reactants are in a triplet state. Despite the fact that the reactants can exist in two stable isomers with the oxo group either trans or cis to the axial ligand, they react differently with substrates, where one gives dominant hydroxylation and the other gives dominant chlorination of substrates. The ligand in the cis position of the oxo group is found to be active in the reaction mechanism and donated to the substrate during the reaction. A detailed thermochemical analysis of possible reaction mechanisms reveals that the strengths of the Fe-OH and Fe-Cl bonds in the radical intermediates are the key reasons for this regioselectivity switch of hydroxylation over halogenation. This study highlights the differences between enzymatic and biomimetic halogenases, where the former only react after an essential isomerization step, which is not necessary in model complexes.     

The tetra-manganese complex of photosystem II during its redox cycle - X-ray absorption results and mechanistic implications

Using X-ray absorption spectroscopy (XAS), relevant information on structure and oxidation state of the water-oxidizing Mn complex of photosystem II has been obtained for all four semi-stable intermediate states of its catalytic cycle. We summarize our recent XAS results and discuss their mechanistic implications. The following aspects are covered: (a) information content of X-ray spectra (pre-edge feature, edge position, extended X-ray absorption fine-structure (EXAFS), dichroism in the EXAFS of partially oriented samples); (b) S(1)-state structure; (c) X-ray edge results on oxidation state changes; (d) EXAFS results on structural changes during the S-state cycle; (e) a structural model for the Mn complex in its S(3)-state; (f) XAS-based working model for the S(2)-S(3) transition; (g) XAS-based working model for the S(0)-S(1) transition; (h) potential role of hydrogen atom abstraction by the Mn complex. Finally, we present a specific hypothesis on the mechanism of dioxygen formation during the S(3)-(S(4))-S(0) transition. According to this hypothesis, water oxidation is facilitated by manganese reduction that is coupled to proton transfer from a substrate water to bridging oxides.     

AdoMet radical proteins--from structure to evolution--alignment of divergent protein sequences reveals strong secondary structure element conservation

Eighteen subclasses of S-adenosyl-l-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple sequence alignment correctly predicted all but one of the core helices in HemN, and correctly predicted the residues in the enzyme active site. This alignment further suggests that the AdoMet radical proteins may have evolved from half-barrel structures (alphabeta)4 to three-quarter-barrel structures (alphabeta)6 to full-barrel structures (alphabeta)8. It predicts that anaerobic ribonucleotide reductase (RNR) activase, an ancient enzyme that, it has been suggested, serves as a link between the RNA and DNA worlds, will have a half-barrel structure, whereas the three-quarter barrel, exemplified by HemN, will be the most common architecture for AdoMet radical enzymes, and fewer members of the superfamily will join BioB in using a complete (alphabeta)8 TIM-barrel fold to perform radical chemistry. These differences in barrel architecture also explain how AdoMet radical enzymes can act on substrates that range in size from 10 atoms to 608 residue proteins.     

Manganese in the shell of Centropyxis (Rhizopodea: Protozoa)

Summary The proteinaceous shells of Centropyxis hirsuta contain a relatively high concentration of manganese in an amorphous state. The concentrations of manganese fill the alveoli which are characteristic of the shell structure. Observations based on cultured animals and subsequently examined by X-ray diffraction, a solid state energy dispersive X-ray analyser, and an analytical electron microscope, lead to the conclusions that manganese is selectively absorbed by Centropyxis hirsuta and deposited in the shell.     

High-valent corrole metal complexes

This commentary concentrates on corrole complexes with the three metal ions that are most relevant to oxidation catalysis: chromium, manganese, and iron. Particular emphasis is devoted to the only recently introduced meso-triarylcorroles and a comparison with the traditionally investigated beta-pyrrole-substituted corroles. Based on a combination of spectroscopic methods, electrochemistry, and X-ray crystallography, it is concluded that in most high-valent metallocorroles the corrole is not oxidized. Both experimental (for (oxo)chromium(V) corrole) and computational (for (oxo)manganese(V) corrole) evidence indicate that the stabilization of high-valent metal ions by corroles originates from a combination of short metal-nitrogen bonds and large metal out-of-plane displacements in the corrole, which lead to quite unexpected interactions of the oxo-metal pi* orbitals with the in-plane orbitals of the corrole.     

Structure of the Mn<Subscript>4</Subscript>–Ca cluster as derived from X-ray diffraction

The catalytic centre for light-induced water oxidation in photosystem II (PSII) is a multinuclear metal cluster containing four manganese and one calcium cations. Knowing the structure of this biological catalyst is of utmost importance for unravelling the mechanism of water oxidation in photosynthesis. In this review we describe the current state of the X-ray structure determination at 3.0 A resolution of the water oxidation complex (WOC) of PSII. The arrangement of metal cations in the cluster, their coordination and protein surroundings are discussed with regard to spectroscopic and mutagenesis studies. Limitations of the presently available structural data are pointed out and possible perspectives for the future are outlined, including the combination of X-ray diffraction and X-ray spectroscopy on single crystals.     

Outer sphere mutagenesis of Lactobacillus plantarum manganese catalase disrupts the cluster core. Mechanistic implications.

X-ray crystallography of the nonheme manganese catalase from Lactobacillus plantarum (LPC) [Barynin, V.V., Whittaker, M.M., Antonyuk, S.V., Lamzin, V.S., Harrison, P.M., Artymiuk, P.J. & Whittaker, J.W. (2001) Structure9, 725-738] has revealed the structure of the dimanganese redox cluster together with its protein environment. The oxidized [Mn(III)Mn(III)] cluster is bridged by two solvent molecules (oxo and hydroxo, respectively) together with a micro 1,3 bridging glutamate carboxylate and is embedded in a web of hydrogen bonds involving an outer sphere tyrosine residue (Tyr42). A novel homologous expression system has been developed for production of active recombinant LPC and Tyr42 has been replaced by phenylalanine using site-directed mutagenesis. Spectroscopic and structural studies indicate that disruption of the hydrogen-bonded web significantly perturbs the active site in Y42F LPC, breaking one of the solvent bridges and generating an 'open' form of the dimanganese cluster. Two of the metal ligands adopt alternate conformations in the crystal structure, both conformers having a broken solvent bridge in the dimanganese core. The oxidized Y42F LPC exhibits strong optical absorption characteristic of high spin Mn(III) in low symmetry and lower coordination number. MCD and EPR measurements provide complementary information defining a ferromagnetically coupled electronic ground state for a cluster containing a single solvent bridge, in contrast to the diamagnetic ground state found for the native cluster containing a pair of solvent bridges. Y42F LPC has less than 5% of the catalase activity and much higher Km for H2O2 ( approximately 1.4 m) at neutral pH than WT LPC, although the activity is slightly restored at high pH where the cluster is converted to a diamagnetic form. These studies provide new insight into the contribution of the outer sphere tyrosine to the stability of the dimanganese cluster and the role of the solvent bridges in catalysis by dimanganese catalases.     

Synthesis, characterization, electrochemical and magnetic studies on manganese(III) complexes involving bridging carboxylates

A series of carboxylate-bridged manganese(III) complexes derived from Schiff bases obtained by the condensation of salicylaldehyde or 5-bromo-salicylaldehyde and different types of diamine have been synthesized and characterized and, in the case of [Mn₂(L1)₂(μ-ClCH₂COO)](ClO₄) (1), the structure has been obtained by X-ray crystallography. The structure of 1 consists of two manganese atoms separated by 5.487(3) Å and bridged by a carboxylate anion. This dinuclear structural unit is linked by bridging phenoxy oxygens to adjacent dinuclear units to produce a one-dimensional chain. Cyclic voltammograms of all the compounds exhibit grossly similar features consisting of a reversible or quasi-reversible Mn^III/Mn^II reduction and a Mn^III/Mn^IV oxidation. It has been observed that bromo-substitution stabilizes the lower oxidation state in the Mn^III/Mn^II couple and destabilizes the higher oxidation state in the Mn^III/Mn^IV couple. Variable temperature magnetic susceptibility measurements of 1 show a weak antiferromagnetic interaction. The magnetic behavior is satisfactorily modeled by inclusion of zero-field splitting and an intermolecular interaction component.     

An analysis of structural similarity in the iron and manganese superoxide dismutases based on known structures and sequences

There are two types of homologous enzymes catalysing the dismutationof the superoxide radical – Cu–Zn superoxide dismutases, and manganese oriron superoxide dismutases. In the latter two forms there is a highpercentage of identity in the primary structures, and the tertiarystructures are very similar particu-larly in the areas of the activesite and in the residues responsible for the formation of the dimer.The quaternary structure of the dimer is also highly conserved.However, it has been found that despite this conservation thereis strong metal ion specificity and many enzymes in the familywill only be active if the correct metal ion is present. The purposeof this study has been to analyse solved X-ray structures forinter-actions common in both the manganese and iron forms andthose that are specific to each, which may indi-cate reasonsfor the metal ion specificity. Initial analysis points to theprobability that it is a combination of a number of residues,and not necessarily the same ones in every instance, which conferthe specificity. In addition we have identified some anomalies inthe currently available Fe/MnSOD structures which may require furtherremodelling and refinement. © Rapid Science 1998     

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.