Internal electron transfer and structural dynamics of cd1 nitrite reductase revealed by laser CO photodissociation

Ligand coordination and spin crossover in a nickel porphyrin anchored to mesoporous TiO2 thin films

The coordination and spin equilibrium of a Ni(II) meso-tetra(4-carboxyphenyl)porphyrin compound, NiP, was quantified both in fluid solution and when anchored to mesoporous, nanocrystalline TiO2 thin films. This comparison provides insights into the relative rate constants for excited-state injection and ligand field population. In the presence of pyridine, the spectroscopic data were consistent with the presence of equilibrium concentrations of a 4-coordinate low-spin S = 0 ((1)A1g) Ni(II) compound and a high-spin S = 1 ((3)B1g) 6-coordinate compound. Temperature-dependent equilibrium constants were consistently smaller for the surface-anchored NiP/TiO2, as were the absolute values of ΔH and ΔS. In the presence of diethylamine (DEA), the ground-state 6-coordinate compound was absent, but evidence for it was present after pulsed light excitation of NiP. Arrhenius analysis of data, measured from -40 to -10 °C, revealed activation energies for ligand dissociation that were the same for the compound in fluid solution and anchored to TiO2, Ea = 6.6 kcal/mol, within experimental error. At higher temperatures, a significantly smaller activation energy of 3.5 kcal/mol was found for NiP(DEA)2/TiO2. A model is proposed wherein the TiO2 surface sterically hinders ligand coordination to NiP. The lack of excited-state electron transfer from Ni(II)P*/TiO2 indicates that internal conversion to ligand field states was at least 10 times greater than that of excited-state injection into TiO2.

Nitric oxide, substrate of Euphorbia characias peroxidase, switches off the CN(-) inhibitory effect

The oxidation of nitric oxide (NO) by Euphorbia characias latex peroxidase (ELP-Fe^III), in the presence or in the absence of added calcium, has been investigated. The addition of hydrogen peroxide to the native enzyme leads to the formation of Compound I and serves to catalyse the NO oxidation. The addition of NO to Compound I leads to the formation of Compound II and, afterwards, to the native enzyme spectrum. Under anaerobic conditions, the incubation of the native enzyme (ELP-Fe^III)with NO leads to the formation of the stable complex, showing a characteristic absorption spectrum (ELP-Fe^II–NO⁺). The rate of the formation of this complex is slower in the presence of calcium than in its absence, and the same applies to the rate of the formation of Compound II from Compound I, using NO as substrate. Finally, we demonstrate that NO protects ELP from the inactivation caused by CN⁻via a mechanism presumably requiring the formation of an enzyme-nitrosyl cyanide complex.

Dynamic hydrogen-bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase

cd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme cofactor, found only in this class of enzymes, where the substrate, nitrite, binds and is converted to NO. For a long time, it was believed that NO must be released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of ferrous-nitroso complex, which was considered as a dead-end product. However, recently an enhanced rate of NO dissociation from the ferrous form, not observed in standard b-type hemes, has been reported and attributed to the unique d(1)-heme structure (Rinaldo, S.; Arcovito, A.; Brunori, M.; Cutruzzolà, F. J. Biol. Chem. 2007, 282, 14761-14767). Here, we report on a detailed study of the spatial and electronic structure of the ferrous d(1)-heme NO complex from Pseudomonas aeruginosa cd(1) NIR and two mutants Y10F and H369A/H327A in solution, searching for the unique properties that are responsible for the relatively fast release. There are three residues at the "distal" side of the heme (Tyr(10), His(327), and His(369)), and in this work we focus on the identification and characterization of possible H-bonds they can form with the NO, thereby affecting the stability of the complex. For this purpose, we have used high field pulse electron-nuclear double resonance (ENDOR) combined with density functional theory (DFT) calculations. The DFT calculations were essential for assigning and interpreting the ENDOR spectra in terms of geometric structure. We have shown that the NO in the nitrosyl d(1)-heme complex of cd(1) NIR forms H-bonds with Tyr(10) and His(369), whereas the second conserved histidine, His(327), appears to be less involved in NO H-bonding. This is in contrast to the crystal structure that shows that Tyr(10) is removed from the NO. We have also observed a larger solvent accessibility to the distal pocket in the mutants as compared to the wild-type. Moreover, it was shown that the H-bonding network within the active site is dynamic and that a change in the protonation state of one of the residues does affect the strength and position of the H-bonds formed by the others. In the Y10F mutant, His(369) is closer to the NO, whereas mutation of both distal histidines displaces Tyr(10), removing its H-bond. The implications of the H-bonding network found in terms of the complex stability and catalysis are discussed.

Is the redox state of the ci heme of the cytochrome b6f complex dependent on the occupation and structure of the Qi site and vice versa?

Oxidoreductases of the cytochrome bc(1)/b(6)f family transfer electrons from a liposoluble quinol to a soluble acceptor protein and contribute to the formation of a transmembrane electrochemical potential. The crystal structure of cyt b(6)f has revealed the presence in the Q(i) site of an atypical c-type heme, heme c(i). Surprisingly, the protein does not provide any axial ligand to the iron of this heme, and its surrounding structure suggests it can be accessed by exogenous ligand. In this work we describe a mutagenesis approach aimed at characterizing the c(i) heme and its interaction with the Q(i) site environment. We engineered a mutant of Chlamydomonas reinhardtii in which Phe(40) from subunit IV was substituted by a tyrosine. This results in a dramatic slowing down of the reoxidation of the b hemes under single flash excitation, suggesting hindered accessibility of the heme to its quinone substrate. This modified accessibility likely originates from the ligation of the heme iron by the phenol(ate) side chain introduced by the mutation. Indeed, it also results in a marked downshift of the c(i) heme midpoint potential (from +100 mV to -200 mV at pH 7). Yet the overall turnover rate of the mutant cytochrome b(6)f complex under continuous illumination was found similar to the wild type one, both in vitro and in vivo. We propose that, in the mutant, a change in the ligation state of the heme upon its reduction could act as a redox switch that would control the accessibility of the substrate to the heme and trigger the catalysis.

Fast Dissociation of Nitric Oxide from Ferrous Pseudomonas aeruginosa cd1 Nitrite Reductase

The heme-containing periplasmic nitrite reductase (cd(1) NIR) is responsible for the production of nitric oxide (NO) in denitrifying bacterial species, among which are several animal and plant pathogens. Heme NIRs are homodimers, each subunit containing one covalently bound c-heme and one d(1)-heme. The reduction of nitrite to NO involves binding of nitrite to the reduced protein at the level of d(1)-heme, followed by dehydration of nitrite to yield NO and release of the latter. The crucial rate-limiting step in the catalytic mechanism is thought to be the release of NO from the d(1)-heme, which has been proposed, but never demonstrated experimentally, to occur when the iron is in the ferric form, given that the reduced NO-bound derivative was presumed to be very stable, as in other hemeproteins. We have measured for the first time the kinetics of NO binding and release from fully reduced cd(1) NIR, using the enzyme from Pseudomonas aeruginosa and its site-directed mutant H369A. Quite unexpectedly, we found that NO dissociation from the reduced d(1)-heme is very rapid, several orders of magnitude faster than that measured for b-type heme containing reduced hemeproteins. Because the rate of NO dissociation from reduced cd(1) NIR, measured in the present report, is faster than or comparable with the turnover number, contrary to expectations this event may well be on the catalytic cycle and not necessarily rate-limiting. This finding also provides a rationale for the presence in cd(1) NIR of the peculiar d(1)-heme cofactor, which has probably evolved to ensure fast product dissociation.

Critical role of His369 in the reactivity of Pseudomonas aeruginosa cytochrome cd1nitrite reductase with oxygen

In the denitrification pathway, Pseudomonas aeruginosa cytochrome cd1 nitrite reductase catalyzes the reduction of nitrite to nitric oxide; in vitro, this enzyme is also competent in the reduction of O2 to 2H2O. In this article, we present a comparative kinetic study of the O2 reaction in the wild-type nitrite reductase and in three site-directed mutants (Tyr10-->Phe, His369-->Ala and His327-->Ala/His369-->Ala) of the amino acid residues close to the d1 heme on the distal side. The results clearly indicate that His369 is the key residue in the control of reactivity, as its substitution with Ala, previously shown to affect the reduction of nitrite, also impairs the reaction with O2, affecting both the properties and lifespan of the intermediate species. Our findings allow the presentation of an overall picture for the reactivity of cytochrome cd1 nitrite reductase and extend our previous conclusion that the conserved distal histidines are essential for the binding to reduced d1 heme of different anions, whether a substrate such as nitrite, a ligand such as cyanide, or an intermediate in the O2 reduction. Moreover, we propose that His369 also exerts a protective role against degradation of the d1 heme, by preventing the formation and adverse effects of the reactive O2 species (never present in significant amounts in wild-type cytochrome cd1 nitrite reductase), a finding with clear physiological implications.

Fast coordination changes in cytochrome c do not necessarily imply folding

Folding of globular proteins occurs with rates that range from microseconds to minutes; consequently, it has been necessary to develop new strategies to follow the faster processes that exceed stopped-flow capabilities. Rapid photochemical methods have been employed to study the rate of folding of reduced cytochrome c. In this protein, the iron of the covalently bound heme binds a His and a Met, proximal and distal. Unfolding by guanidine or urea weakens the Fe-Met bond, and the reduced unfolded cytochrome c easily binds CO and other heme ligands, which would react slowly or not at all with the native protein. Therefore in the presence of CO, reduced cytochrome c unfolds at lower denaturant concentrations than in the absence of this ligand, and rapid photochemical removal of CO from unfolded cytochrome c, is expected to trigger at least an incomplete refolding. This approach is complicated by the breakage of the proximal His-Fe bond that may occur as a consequence of CO photodissociation in the unfolded cytochrome c because of the so-called base elimination mechanism. Rebinding of CO to the four-coordinate heme yields kinetic intermediates unrelated to folding. Our hypothesis is supported by parallel observations carried out with protoheme and microperoxidase.

Domain swing upon His to Ala mutation in nitrite reductase of Pseudomonas aeruginosa

The nitrite reductase (NIR) from Pseudomonas aeruginosa (NIR-Pa) is a soluble enzyme catalysing the reduction of nitrite (NO2(-)) to nitric oxide (NO). The enzyme is a 120 kDa homodimer, in which the monomers carry a c-heme domain and a d(1)-heme domain. The structures of the enzyme in both the oxidised and reduced state were solved previously and indicate His327 and His369 as putative catalytic residues. The kinetic characterisation of site-directed mutants has shown that the substitution of either one of these two His with Ala dramatically reduces the physiologically relevant reactivity towards nitrite, leaving the reactivity towards oxygen unaffected. The three-dimensional structures of P. aeruginosa NIR mutant H327A, and H369A in complex with NO have been solved by multiple wavelength anomalous dispersion (MAD), using the iron anomalous signal, and molecular replacement techniques. In both refined crystal structures the c-heme domain, whilst preserving its classical c-type cytochrome fold, has undergone a 60 degrees rigid-body rotation around an axis parallel with the pseudo 8-fold axis of the beta-propeller, and passing through residue Gln115. Even though the distance between the Fe ions of the c and d(1)-heme remains 21 A, the edge-to-edge distance between the two hemes has increased by 5 A. Furthermore the distal side of the d(1)-heme pocket appears to have undergone structural re-arrangement and Tyr10 has moved out of the active site. In the H369A-NO complex, the position and orientation of NO is significantly different from that of the NO bound to the reduced wild-type structure. Our results provide insight into the flexibility of the enzyme and the distinction between nitrite and oxidase reduction mechanisms. Moreover they demonstrate that the two histidine residues play a crucial role in the physiological activity of nitrite reduction, ligand binding and in the structural organisation of nitrite reductase from P. aeruginosa.

Photochemically induced electron transfer

Biochemical reactions involving electron transfer between substrates or enzyme cofactors are both common and physiologically important; they have been studied by means of a variety of techniques. In this paper we review the application of photochemical methods to the study of intramolecular electron transfer in hemoproteins, thus selecting a small, well-defined sector of this otherwise enormous field. Photoexcitation of the heme populates short-lived excited states which decay by thermal conversion and do not usually transfer electrons, even when a suitable electron acceptor is readily available, e.g., in the form of a second oxidized heme group in the same protein; because of this, the experimental setup demands some manipulation of the hemoprotein. In this paper we review three approaches that have been studied in detail: (i) the covalent conjugation to the protein moiety of an organic ruthenium complex, which serves as the photoexcitable electron donor (in this case the heme acts as the electron acceptor); (ii) the replacement of the heme group with a phosphorescent metal-substituted porphyrin, which on photoexcitation populates long-lived excited states, capable of acting as electron donors (clearly the protein must contain some other cofactor acting as the electron acceptor, most often a second heme group in the oxidized state); (iii) the combination of the reduced heme with CO (the photochemical breakdown of the iron-CO bond yields transiently the ground-state reduced heme which is able to transfer one electron (or a fraction of it) to an oxidized electron acceptor in the protein; this method uses a "mixed-valence hybrid" state of the redox active hemoprotein and has the great advantage of populating on photoexcitation an electron donor at physiological redox potential).

Kinetics of CO binding and CO photodissociation in Pseudomonas stutzeri cd(1) nitrite reductase: probing the role of extended N-termini in fast structural relaxation upon CO photodissociation

cd(1) nitrite reductase from Pseudomonas stutzeri is a di-haem- containing enzyme, comprising a c-type haem and a d-type haem. Studies with the highly related cd(1) nitrite reductase of Pseudomonas aeruginosa have established that this enzyme undergoes fast (microsecond) and global structural relaxation upon CO photodissociation from the reduced enzyme. A key difference between the Ps. aeruginosa and Ps. stutzeri enzyme is the absence of a flexible N-terminal extension in the Ps. stutzeri enzyme. In Ps. aeruginosa cd(1) nitrite reductase the N-terminal extension wraps around the second subunit of the homodimer and with Tyr(10) stabilizing a water molecule co-ordinated to the d(1)-haem. Given the intimate association of the N-terminal extension with the d(1)-haem, we hypothesized that the presence of the N-terminal extension likely contributes to the fast structural reorganization seen during photodissociation of CO from the reduced enzyme. In the present study we have investigated the kinetics of CO association and CO photodissociation of Ps. stutzeri cd(1) nitrite reductase (which lacks the N-terminal arm seen in the Ps. aeruginosa enzyme) to probe the role and influence of the N-terminal arm in the fast global structural reorganization seen with Ps. aeruginosa. Surprisingly, we find that Ps. stutzeri cd(1) nitrite reductase also undergoes fast structural reorganization during CO photodissociation. We also show, in stopped-flow experiments, that the kinetics of CO binding and dissociation with reduced Ps. stutzeri cd(1) nitrite reductase are similar to those observed with Ps. aeruginosa enzyme, thus ruling out a major role for the N-terminal flexible arm found in Ps. aeruginosa in the kinetics of these processes. Our data indicate that global structural reorganization following CO photodissociation is an intrinsic property of the haem domains in cd(1) nitrite reductases. The absence of an N-terminal extension, as in the Ps. stutzeri cd(1) nitrite reductase, does not lead to loss of global structural reorganization following CO photodissociation.

The nitrite reductase from Pseudomonas aeruginosa: essential role of two active-site histidines in the catalytic and structural properties

Cd(1) nitrite reductase catalyzes the conversion of nitrite to NO in denitrifying bacteria. Reduction of the substrate occurs at the d(1)-heme site, which faces on the distal side some residues thought to be essential for substrate binding and catalysis. We report the results obtained by mutating to Ala the two invariant active site histidines, His-327 and His-369, of the enzyme from Pseudomonas aeruginosa. Both mutants have lost nitrite reductase activity but maintain the ability to reduce O(2) to water. Nitrite reductase activity is impaired because of the accumulation of a catalytically inactive form, possibly because the productive displacement of NO from the ferric d(1)-heme iron is impaired. Moreover, the two distal His play different roles in catalysis; His-369 is absolutely essential for the stability of the Michaelis complex. The structures of both mutants show (i) the new side chain in the active site, (ii) a loss of density of Tyr-10, which slipped away with the N-terminal arm, and (iii) a large topological change in the whole c-heme domain, which is displaced 20 A from the position occupied in the wild-type enzyme. We conclude that the two invariant His play a crucial role in the activity and the structural organization of cd(1) nitrite reductase from P. aeruginosa.