Superoxide reductase from Desulfoarculus baarsii: identification of protonation steps in the enzymatic mechanism.

International audienceSuperoxide reductase (SOR) is a metalloenzyme that catalyzes the reduction of O2*- to H2O2 and provides an antioxidant mechanism in some anaerobic and microaerophilic bacteria. Its active site contains an unusual mononuclear ferrous center (center II). Protonation processes are essential for the reaction catalyzed by SOR, since two protons are required for the formation of H2O2. We have investigated the acido-basic and pH dependence of the redox properties of the active site of SOR from Desulfoarculus baarsii, both in the absence and in the presence of O2*-. In the absence of O2*-, the reduction potential and the absorption spectrum of the iron center II exhibit a pH transition. This is consistent with the presence of a base (BH) in close proximity to the iron center which modulates its reduction properties. Studies of mutants of the closest charged residues to the iron center II (E47A and K48I) show that neither of these residues are the base responsible for the pH transitions. However, they both interact with this base and modulate its pKa value. By pulse radiolysis, we confirm that the reaction of SOR with O2*- involves two reaction intermediates that were characterized by their absorption spectra. The precise step of the catalytic cycle in which one protonation takes place was identified. The formation of the first reaction intermediate, from a bimolecular reaction of SOR with O2*-, does not involve proton transfer as a rate-limiting step, since the rate constant k1 does not vary between pH 5 and pH 9.5. On the other hand, the rate constant k2 for the formation of the second reaction intermediate is proportional to the H+ concentration in solution, suggesting that the proton arises directly from the solvent. In fact, BH, E47, and K48 have no role in this step. This is consistent with the first intermediate being an iron(III)-peroxo species and the second one being an iron(III)-hydroperoxo species. We propose that BH may be involved in the second protonation process corresponding to the release of H2O2 from the iron(III)-hydroperoxo species

Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis

Funding Information: This work was financially supported by Fundação para a Ciência e Tecnologia (FCT, Portugal) through fellowship SFRH/BD/116515/2016, COVID/BD/151766/2021, grant PTDC/BII-BBF/2050/2020, R&D units MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020) and UCIBIO (UIDP/04378/2020 and UIDB/04378/2020), and associated laboratories LS4FUTURE (LA/P/0087/2020) and i4HB (LA/P/0140/2020). European Union’s Horizon 2020 research and innovation program (grant agreement no. 810856) is also acknowledged. This work was also funded by the French national research agency (ANR─MOLYERE project, grant number 16-CE-29-0010-01) and supported by the computing facilities of the CRCMM, “Centre Régional de Compétences en Modélisation Moléculaire de Marseille”. The authors are grateful to the EPR facilities at the French EPR network RENARD (IR CNRS 3443, now INFRANALYTICS, FR2054) and the Aix-Marseille University EPR center. Publisher Copyright: © 2022 American Chemical Society. All rights reserved.Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO2reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Desulfovibrio vulgaris Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S]1+clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S]1+centers range between -250 and -530 mV. Two distinct WVsignals were detected, WDVand WFV, which differ in only the g2-value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of WVI/Vwas determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate WVstate of FdhAB.publishersversionpublishe

Toward the Mechanistic Understanding of Enzymatic CO2 Reduction

SFRH/BD/116515/2014 PTDC/BBB-EBB/2723/2014 UID/Multi/04378/2019 grant agreement number 810856Reducing CO2 is a challenging chemical transformation that biology solves easily, with high efficiency and specificity. In particular, formate dehydrogenases are of great interest since they reduce CO2 to formate, a valuable chemical fuel and hydrogen storage compound. The metal-dependent formate dehydrogenases of prokaryotes can show high activity for CO2 reduction. Here, we report an expression system to produce recombinant W/Sec-FdhAB from Desulfovibrio vulgaris Hildenborough fully loaded with cofactors, its catalytic characterization and crystal structures in oxidized and reduced states. The enzyme has very high activity for CO2 reduction and displays remarkable oxygen stability. The crystal structure of the formate-reduced enzyme shows Sec still coordinating the tungsten, supporting a mechanism of stable metal coordination during catalysis. Comparison of the oxidized and reduced structures shows significant changes close to the active site. The DvFdhAB is an excellent model for studying catalytic CO2 reduction and probing the mechanism of this conversion.publishersversionpublishe

Etude des proprietes magnetiques et structurales des centres a 3 fer des proteines fer-soufre par spectrometrie R.P.E

SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Le complexe nitrate réductase A chez Escherichia coli (étude fonctionnelle par spectroscopie RPE et mutagenèse dirigée)

AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

Functional study of the [Ni-Fe] hydrogenase (approach by EPR spectroscopy and photochemistry)

Les hydrogénases sont les métalloenzymes, issues de micro-organismes anaérobies, qui catalysent l'oxydation réversible de l'hydrogène moléculaire, suivant la réaction : H2 2H+ +2e-. Notre objectif est de progresser dans la compréhension du mécanisme réactionnel de ces enzymes, à savoir : le processus d'activation de H2 au niveau du centre catalytique à Ni-Fe et les voies de transfert des électrons et des protons issus de l'oxydation de H2. Nous utilisons une approche combinant la spectroscopie RPE et la photochimie pour étudier à températures cryogéniques, les propriétés de photosensibilité d'un intermédiaire clé du mécanisme catalytique, l'état Ni-C. Nous étudions en détail le profil énergétique de la photoconversion, la cinétique des processus de recombinaison, et l'influence de différents facteurs comme la température, les effets isotopiques H/D et la fixation d'inhibiteur (CO), dans le cas de plusieurs hydrogénases à [Ni-Fe-] et à [Ni-Fe-Se] de bactéries sulfato-réductrices ou d'organismes hyperthermophiles (A. aeolicus). L'analyse des interactions magnétiques entre le centre actif à Ni-Fe et le centre [4Fe-4S]1+ proximal par la simulation numérique des spectres RPE multifréquences est également utilisée pour sonder les changements structuraux induits par l'irradiation. Nos résultats mettent en évidence un transfert de protons photo-induits au niveau des cystéines terminales de l'ion nickel, et permettent d'identifier le résidu Glutamate impliqué dans la première étape de transfert de protons, comme le confirment nos études de mutagénèse dirigée vers ce résidu.AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

Etude fonctionnelle de la nitrate réductase périplasmique de Rhodobacter sphaeroides par spectroscopie RPE et électrochimie directe

AIX-MARSEILLE1-BU Sci.St Charles (130552104) / SudocSudocFranceF

Etude des transitions structurales dans les protéines flexibles par marquage de spin suivi par spectroscopie de Résonance Paramagnétique Electronique (RPE)

L étude des transitions structurales dans les protéines est d un intérêt crucial car ces transformations sont impliquées dans de nombreux processus biologiques essentiels. De tels phénomènes structuraux peuvent être à l origine de propriétés remarquables dans les protéines flexibles ou désordonnées, propriétés difficilement accessibles par les techniques structurales usuelles. Le marquage de spin couplé à la spectroscopie de résonance paramagnétique électronique (RPE) est une technique bien adaptée pour l étude de ces transitions structurales. L insertion d un radical nitroxyde sur une cystéine, naturelle ou introduite par mutagenèse dirigée, située à un endroit clé de la protéine permet d obtenir des informations locales sur les changements structuraux éventuels provoqués par l ajout d un partenaire.Cette technique a été appliquée à deux systèmes biologiques comportant un degré de flexibilité différent. La flexibilité de la protéine chaperon NarJ, intervenant dans la biogenèse du complexe Nitrate Réductase de la bactérie Escherichia coli, a été étudiée en présence de son peptide partenaire. Ces études ont permis d une part de déterminer le site d interaction et d autre part, de montrer que l association des deux partenaires entraîne un verrouillage dans une conformation préférentielle de NarJ. Le deuxième sujet d étude est la protéine CP12 de Chlamydomonas reinhardtii, intervenant dans la régulation d un complexe supramoléculaire du cycle de Calvin. La CP12 s apparente à une protéine intrinsèquement désordonnée, ayant la particularité de posséder des cystéines naturelles et fonctionnelles. Le marquage classique a permis de mettre en évidence un nouveau rôle de son partenaire et de montrer que la CP12 garde un caractère désordonné dans le complexe. Par ailleurs, cette protéine a servi de système d étude pour développer une nouvelle stratégie de marquage sur Tyrosine et démontrer sa faisabilité.The study of structural transitions in proteins is of crucial interest because these transformations are involved in many biological processes. Such structural phenomena can be the source of remarkable properties in flexible or disordered proteins, properties hardly accessible by conventional structural techniques. Site-directed spin labeling combined with electron paramagnetic resonance spectroscopy (EPR) is a technique well suited for the study of these structural transitions. The insertion of a nitroxide reagent on a cysteine, natural or introduced by site-directed mutagenesis, located in a key position of a protein provides local information on possible structural changes induced by the addition of a partner. This technique was applied on two biological systems with a different degree of flexibility. The flexibility of NarJ, a chaperon protein involved in the biogenesis of the complex nitrate reductase of Escherichia coli was studied in the presence of its peptide partner. These studies enabled us to determine the interaction site and to show that the association of the two partners induced a locked conformation of NarJ. The second system is the CP12 protein of Chlamydomonas reinhardtii, involved in the regulation of a supramolecular complex of the Calvin cycle. CP12 shares some similarities with the intrinsically disordered protein but having natural and functional cysteines. The conventional labeling allowed us to highlight a new role of its partner and to demonstrate that CP12 remains disordered in the complex. Moreover, this protein was used as a model system to develop a new labeling strategy on tyrosine and to demonstrate its feasibility.AIX-MARSEILLE1-Bib.electronique (130559902) / SudocSudocFranceF

Electron paramagnetic resonance studies of molybdenum enzymes

International audienceElectron Paramagnetic Resonance (EPR) is certainly the first and the most widely used spectroscopic technique for studying structure and function of Mo and W enzymes. Although only Mo(v) and W(v) states can be detected, a considerable wealth of data was provided since the seminal EPR works performed on xanthine oxidase and nitrate reductase more than 55 years ago. In this chapter, we give a comprehensive overview of the various applications of EPR on the ubiquitous Mo-enzymes, which exhibit such an extraordinary diversity of substrates and catalyzed reactions. Elucidating the nature of Mo(v) intermediates is a considerable challenge to progress in understanding these processes. The g-tensor analyses are helpful in that aim. But it is essentially thanks to the advances in pulsed EPR methods like ENDOR, ESEEM and HYSCORE, combined with efficient isotopic enrichment strategies, that the measurements of hyperfine couplings of Mo-cofactor with neighbouring magnetic nuclei have brought the most interesting data. Thus, we illustrate how the analysis of hyperfine parameters associated with computational chemistry methods is becoming a powerful way to provide high-resolution structural data on Mo(v) species and enzyme mechanisms. In addition, EPR study of spin–spin couplings between Mo-cofactor and other paramagnetic centres appears as a promising way to gain long-range structural data in these systems

Electron Flow in Multicenter Enzymes: Theory, Applications, and Consequences on the Natural Design of Redox Chains

International audienceIn protein film voltammetry, a redox enzyme is directly connected to an electrode; in the presence of substrate and when the driving force provided by the electrode is appropriate, a current flow reveals the steady-state turnover. We show that, in the case of a multicenter enzyme, this signal reports on the energetics and kinetics of electron transfer (ET) along the redox chain that wires the active site to the electrode, and this provides a new strategy for studying intramolecular ET. We propose a model which takes into account all the enzyme’s redox microstates, and we prove it useful to interpret data for various enzymes. Several general ideas emerge from this analysis. Considering the reversibility of ET is a requirement: the usual picture, where ET is depicted as a series of irreversible steps, is oversimplified and lacks the important features that we emphasize. We give justification to the concept of apparent reduction potential on the time scale of turnover and we explain how the value of this potential relates to the thermodynamic and kinetic properties of the system. When intramolecular ET does not limit turnover, the redox chain merely mediates the driving force provided by the electrode or the soluble redox partner, whereas when intramolecular ET is slow, the enzyme behaves as if its active active site had apparent redox properties which depend on the reduction potentials of the relays. This suggests an alternative to the idea that redox chains are optimized in terms of speed: evolutionary pressure may have resulted in slowing down intramolecular ET in order to tune the enzyme’s “operating potential”