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1.
J Am Chem Soc ; 145(28): 15230-15250, 2023 07 19.
Artículo en Inglés | MEDLINE | ID: mdl-37414058

RESUMEN

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.


Asunto(s)
Dioxigenasas , Dioxigenasas/química , Compuestos Férricos , Catecoles/química , Análisis Espectral , Compuestos Ferrosos
2.
Proc Natl Acad Sci U S A ; 117(23): 12624-12635, 2020 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-32434915

RESUMEN

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.


Asunto(s)
Fotosíntesis , Complejo de Proteína del Fotosistema II/metabolismo , Hidrógeno/metabolismo , Magnesio/metabolismo , Oxidación-Reducción , Oxígeno/metabolismo , Fotones , Complejo de Proteína del Fotosistema II/química , Quinonas/metabolismo , Agua/metabolismo
3.
Proc Natl Acad Sci U S A ; 117(1): 300-307, 2020 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-31852825

RESUMEN

A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs - Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.


Asunto(s)
Ficobilinas/metabolismo , Ficocianina/metabolismo , Fitocromo/química , Fitocromo/efectos de la radiación , Adenilil Ciclasas/química , Adenilil Ciclasas/metabolismo , Cristalografía , Cristalografía por Rayos X , Cianobacterias/química , GMP Cíclico , Luz , Modelos Moleculares , Hidrolasas Diéster Fosfóricas/química , Hidrolasas Diéster Fosfóricas/metabolismo , Células Fotorreceptoras/metabolismo , Ficobilinas/química , Ficocianina/química , Conformación Proteica , Dominios Proteicos , Thermosynechococcus , Transactivadores/química
4.
J Am Chem Soc ; 142(44): 18886-18896, 2020 11 04.
Artículo en Inglés | MEDLINE | ID: mdl-33103886

RESUMEN

The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV═O complexes in two different substrate orientations (one more along [σ channel] and another more perpendicular [π channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the π channel by the significantly larger oxyl character present in the pπ orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.


Asunto(s)
Hidrógeno/química , Hierro/química , Oxígeno/química , Catálisis , Teoría Funcional de la Densidad , Dioxigenasas/química , Dioxigenasas/metabolismo , Hidrógeno/metabolismo , Ácidos Cetoglutáricos/química , Espectroscopía de Resonancia Magnética
5.
J Am Chem Soc ; 142(33): 14249-14266, 2020 08 19.
Artículo en Inglés | MEDLINE | ID: mdl-32683863

RESUMEN

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. This study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.


Asunto(s)
Oxigenasas/química , Temperatura , Methylosinus trichosporium/enzimología , Modelos Moleculares , Oxidación-Reducción , Oxigenasas/metabolismo , Solubilidad , Rayos X
6.
Inorg Chem ; 59(9): 6000-6009, 2020 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-32309932

RESUMEN

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.


Asunto(s)
Dioxigenasas/química , Proteínas de Hierro no Heme/química , Sitios de Unión , Dioxigenasas/metabolismo , Compuestos Férricos/química , Compuestos Férricos/metabolismo , Ligandos , Conformación Molecular , Proteínas de Hierro no Heme/metabolismo
7.
J Am Chem Soc ; 140(16): 5544-5559, 2018 04 25.
Artículo en Inglés | MEDLINE | ID: mdl-29618204

RESUMEN

The Rieske dioxygenases are a major subclass of mononuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin FeIII-(hydro)peroxy intermediate (BZDOp) has been trapped in the peroxide shunt reaction of benzoate 1,2-dioxygenase. Defining the structure of this intermediate is essential to understanding the reactivity of these enzymes. Nuclear resonance vibrational spectroscopy (NRVS) is a recently developed synchrotron technique that is ideal for obtaining vibrational, and thus structural, information on Fe sites, as it gives complete information on all vibrational normal modes containing Fe displacement. In this study, we present NRVS data on BZDOp and assign its structure using these data coupled to experimentally calibrated density functional theory calculations. From this NRVS structure, we define the mechanism for the peroxide shunt reaction. The relevance of the peroxide shunt to the native FeII/O2 reaction is evaluated. For the native FeII/O2 reaction, an FeIII-superoxo intermediate is found to react directly with substrate. This process, while uphill thermodynamically, is found to be driven by the highly favorable thermodynamics of proton-coupled electron transfer with an electron provided by the Rieske [2Fe-2S] center at a later step in the reaction. These results offer important insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo species in nonheme Fe biochemistry.


Asunto(s)
Comamonas/enzimología , Dioxigenasas/metabolismo , Hierro/metabolismo , Peróxidos/metabolismo , Comamonas/química , Comamonas/metabolismo , Dioxigenasas/química , Hierro/química , Modelos Moleculares , Peróxidos/química , Análisis Espectral , Termodinámica
8.
J Am Chem Soc ; 140(48): 16495-16513, 2018 12 05.
Artículo en Inglés | MEDLINE | ID: mdl-30418018

RESUMEN

The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O2. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O2-4NC species and a Fe-O2-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as FeIII-superoxo-catecholate and FeIII-peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on FeIII-superoxo-catecholate and an end-on FeIII-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a FeIII-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.


Asunto(s)
Proteínas Bacterianas/química , Catecoles/química , Complejos de Coordinación/química , Dioxigenasas/química , Oxígeno/química , Proteínas Bacterianas/genética , Brevibacterium/enzimología , Cristalografía por Rayos X , Teoría Funcional de la Densidad , Dioxigenasas/genética , Histidina/química , Hierro/química , Modelos Químicos , Estructura Molecular , Mutación , Análisis Espectral/métodos , Vibración
9.
J Am Chem Soc ; 139(26): 8800-8803, 2017 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-28628312

RESUMEN

Mononuclear nonheme iron(V)-oxo complexes have been reported previously. Herein, we report the first example of a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [(TAML)FeV(NTs)]- (1). The spectroscopic characterization of 1 revealed an S = 1/2 Fe(V) oxidation state, an Fe-N bond length of 1.65(4) Å, and an Fe-N vibration at 817 cm-1. The reactivity of 1 was demonstrated in C-H bond functionalization and nitrene transfer reactions.


Asunto(s)
Complejos de Coordinación/química , Imidas/química , Hierro/química , Aminación , Hemo/química , Ligandos , Compuestos Macrocíclicos/química , Estructura Molecular
10.
Biochemistry ; 55(46): 6363-6374, 2016 Nov 22.
Artículo en Inglés | MEDLINE | ID: mdl-27792301

RESUMEN

The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O2 activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods that provide significant insight into the correlation of structure with function have now been developed. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O2 activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O2 activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin FeIII-OOH non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin FeIV═O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Finally, for several subclasses of non-heme Fe enzymes, binding of the substrate to the FeII site leads to the one-electron reductive activation of O2 to an FeIII-superoxide capable of H atom abstraction and electrophilic attack.


Asunto(s)
Dioxigenasas/química , Enzimas/química , Proteínas de Hierro no Heme/química , Oxígeno/química , Dominio Catalítico , Dicroismo Circular/métodos , Dioxigenasas/metabolismo , Enzimas/metabolismo , Enlace de Hidrógeno , Cinética , Modelos Químicos , Modelos Moleculares , Proteínas de Hierro no Heme/metabolismo , Oxidación-Reducción , Oxígeno/metabolismo , Unión Proteica , Especificidad por Sustrato , Termodinámica
11.
J Am Chem Soc ; 138(43): 14294-14302, 2016 11 02.
Artículo en Inglés | MEDLINE | ID: mdl-27726349

RESUMEN

FeIII-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on FeIII-peroxy and end-on FeIII-hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of FeIII-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.


Asunto(s)
Hierro/química , Compuestos Organometálicos/química , Vibración , Teoría Cuántica , Análisis Espectral
12.
Inorg Chem ; 55(23): 12391-12399, 2016 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-27934432

RESUMEN

The reactivity of mononuclear metal-hydroperoxo adducts has fascinated researchers in many areas due to their diverse biological and catalytic processes. In this study, a mononuclear cobalt(III)-peroxo complex bearing a tetradentate macrocyclic ligand, [CoIII(Me3-TPADP)(O2)]+ (Me3-TPADP = 3,6,9-trimethyl-3,6,9-triaza-1(2,6)-pyridinacyclodecaphane), was prepared by reacting [CoII(Me3-TPADP)(CH3CN)2]2+ with H2O2 in the presence of triethylamine. Upon protonation, the cobalt(III)-peroxo intermediate was converted into a cobalt(III)-hydroperoxo complex, [CoIII(Me3-TPADP)(O2H)(CH3CN)]2+. The mononuclear cobalt(III)-peroxo and -hydroperoxo intermediates were characterized by a variety of physicochemical methods. Results of electrospray ionization mass spectrometry clearly show the transformation of the intermediates: the peak at m/z 339.2 assignable to the cobalt(III)-peroxo species disappears with concomitant growth of the peak at m/z 190.7 corresponding to the cobalt(III)-hydroperoxo complex (with bound CH3CN). Isotope labeling experiments further support the existence of the cobalt(III)-peroxo and -hydroperoxo complexes. In particular, the O-O bond stretching frequency of the cobalt(III)-hydroperoxo complex was determined to be 851 cm-1 for 16O2H samples (803 cm-1 for 18O2H samples), and its Co-O vibrational energy was observed at 571 cm-1 for 16O2H samples (551 cm-1 for 18O2H samples; 568 cm-1 for 16O22H samples) by resonance Raman spectroscopy. Reactivity studies performed with the cobalt(III)-peroxo and -hydroperoxo complexes in organic functionalizations reveal that the latter is capable of conducting oxygen atom transfer with an electrophilic character, whereas the former exhibits no oxygen atom transfer reactivity under the same reaction conditions. Alternatively, the cobalt(III)-hydroperoxo complex does not perform hydrogen atom transfer reactions, while analogous low-spin Fe(III)-hydroperoxo complexes are capable of this reactivity. Density functional theory calculations indicate that this lack of reactivity is due to the high free energy cost of O-O bond homolysis that would be required to produce the hypothetical Co(IV)-oxo product.

13.
J Am Chem Soc ; 135(38): 14024-7, 2013 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-24040838

RESUMEN

We present the synthesis and spectroscopic characterization of [Fe(NO)(N3PyS)]BF4 (3), the first structural and electronic model of NO-bound cysteine dioxygenase. The nearly isostructural all-N-donor analogue [Fe(NO)(N4Py)](BF4)2 (4) was also prepared, and comparisons of 3 and 4 provide insight regarding the influence of S vs N ligation in {FeNO}(7) species. One key difference occurs upon photoirradiation, which causes the fully reversible release of NO from 3, but not from 4.


Asunto(s)
Complejos de Coordinación/química , Cisteína-Dioxigenasa/química , Donantes de Óxido Nítrico/química , Óxido Nítrico/química , Compuestos de Azufre/química , Complejos de Coordinación/síntesis química , Complejos de Coordinación/efectos de la radiación , Luz , Estructura Molecular , Donantes de Óxido Nítrico/síntesis química , Donantes de Óxido Nítrico/efectos de la radiación
14.
Science ; 382(6666): 109-113, 2023 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-37797025

RESUMEN

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.


Asunto(s)
Proteínas Bacterianas , Entomoplasmataceae , Ribonucleótido Reductasas , Transporte de Electrón , Protones , Ribonucleótido Reductasas/química , Cristalografía por Rayos X/métodos , Entomoplasmataceae/enzimología , Dominio Catalítico , Proteínas Bacterianas/química
15.
Elife ; 112022 09 09.
Artículo en Inglés | MEDLINE | ID: mdl-36083619

RESUMEN

Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b-NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b-NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b-NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.


Asunto(s)
Ribonucleótido Reductasas , Cristalografía por Rayos X , Flavinas/metabolismo , Oxidación-Reducción , Ribonucleótido Reductasas/química , Superóxidos
16.
Nat Commun ; 12(1): 6531, 2021 11 11.
Artículo en Inglés | MEDLINE | ID: mdl-34764256

RESUMEN

Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.


Asunto(s)
Complejo de Proteína del Fotosistema II/metabolismo , Enlace de Hidrógeno , Complejo de Proteína del Fotosistema II/genética , Protones , Agua
17.
Sci Rep ; 11(1): 21787, 2021 11 08.
Artículo en Inglés | MEDLINE | ID: mdl-34750381

RESUMEN

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.


Asunto(s)
Complejo de Proteína del Fotosistema I/química , Vitamina K 1/química , Cristalografía por Rayos X , Fotosíntesis , Estructura Terciaria de Proteína , Temperatura , Thermosynechococcus
18.
Sci Adv ; 7(34)2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-34417180

RESUMEN

Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.


Asunto(s)
Electrones , Oxidorreductasas , Catálisis , Dominio Catalítico , Cristalografía por Rayos X , Compuestos Férricos , Humanos , Rayos Láser , Oxidorreductasas/química , Oxígeno/química , Penicilinas/química , Penicilinas/metabolismo , Especificidad por Sustrato
19.
Chem Sci ; 9(34): 6952-6960, 2018 Sep 14.
Artículo en Inglés | MEDLINE | ID: mdl-30210769

RESUMEN

While the synthesis and characterization of {FeNO}7,8,9 complexes have been well documented in heme and nonheme iron models, {FeNO}6 complexes have been less clearly understood. Herein, we report the synthesis and structural and spectroscopic characterization of mononuclear nonheme {FeNO}6 and iron(iii)-nitrito complexes bearing a tetraamido macrocyclic ligand (TAML), such as [(TAML)FeIII(NO)]- and [(TAML)FeIII(NO2)]2-, respectively. First, direct addition of NO(g) to [FeIII(TAML)]- results in the formation of [(TAML)FeIII(NO)]-, which is sensitive to moisture and air. The spectroscopic data of [(TAML)FeIII(NO)]-, such as 1H nuclear magnetic resonance and X-ray absorption spectroscopies, combined with computational study suggest the neutral nature of nitric oxide with a diamagnetic Fe center (S = 0). We also provide alternative pathways for the generation of [(TAML)FeIII(NO)]-, such as the iron-nitrite reduction triggered by protonation in the presence of ferrocene, which acts as an electron donor, and the photochemical iron-nitrite reduction. To the best of our knowledge, the present study reports the first photochemical nitrite reduction in nonheme iron models.

20.
Nat Commun ; 5: 5440, 2014 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-25510711

RESUMEN

Mononuclear non-haem iron(III)-superoxo species (Fe(III)-O2(-·)) have been implicated as key intermediates in the catalytic cycles of dioxygen activation by non-haem iron enzymes. Although non-haem iron(III)-superoxo species have been trapped and characterized spectroscopically in enzymatic and biomimetic reactions, no structural information has yet been obtained. Here we report the isolation, spectroscopic characterization and crystal structure of a mononuclear side-on (η(2)) iron(III)-superoxo complex with a tetraamido macrocyclic ligand. The non-haem iron(III)-superoxo species undergoes both electrophilic and nucleophilic oxidation reactions, as well as O2-transfer between metal complexes. In the O2-transfer reaction, the iron(III)-superoxo complex transfers the bound O2 unit to a manganese(III) analogue, resulting in the formation of a manganese(IV)-peroxo complex, which is characterized structurally and spectroscopically as a mononuclear side-on (η(2)) manganese(IV)-peroxo complex. The difference in the redox distribution between the metal ions and O2 in iron(III)-superoxo and manganese(IV)-peroxo complexes is rationalized using density functional theory calculations.


Asunto(s)
Complejos de Coordinación/química , Compuestos Férricos/química , Compuestos Macrocíclicos/química , Oxígeno/química , Superóxidos/química , Cristalografía por Rayos X , Espectroscopía de Resonancia por Spin del Electrón , Enlace de Hidrógeno , Ligandos , Compuestos de Manganeso/química , Oxidación-Reducción , Teoría Cuántica , Termodinámica
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