Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

18O kinetic isotope effects in non-heme iron enzymes: probing the nature of Fe/O2 intermediates.

ABSTRACT: Contrasted here are the competitive 18O/16O kinetic isotope effects (18O KIEs) on kcat/Km(O2) for three non-heme iron enzymes that activate O2 at an iron center coordinated by a 2-His-1-carboxylate facial triad: taurine dioxygenase (TauD), (S)-(2)-hydroxypropylphosphonic acid epoxidase (HppE), and 1-aminocyclopropyl-1-carboxylic acid oxidase (ACCO). Measured 18O KIEs of 1.0102 +/- 0.0002 (TauD), 1.0120 +/- 0.0002 (HppE), and 1.0215 +/- 0.0005 (ACCO) suggest the formation in the rate-limiting step of O2 activation of an FeIII-peroxohemiketal, FeIII-OOH, and FeIV O species, respectively. The comparison of the measured 18O KIEs with calculated or experimental 18O equilibrium isotope effects (18O EIEs) provides new insights into the O2 activation through an inner-sphere mechanism at a non-heme iron center.

SUBMITTER: Mirica LM

PROVIDER: S-EPMC2788235 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

18O kinetic isotope effects in non-heme iron enzymes: probing the nature of Fe/O2 intermediates.

Mirica Liviu M LM McCusker Kevin P KP Munos Jeffrey W JW Liu Hung-wen HW Klinman Judith P JP

Journal of the American Chemical Society 20080607 26

Contrasted here are the competitive 18O/16O kinetic isotope effects (18O KIEs) on kcat/Km(O2) for three non-heme iron enzymes that activate O2 at an iron center coordinated by a 2-His-1-carboxylate facial triad: taurine dioxygenase (TauD), (S)-(2)-hydroxypropylphosphonic acid epoxidase (HppE), and 1-aminocyclopropyl-1-carboxylic acid oxidase (ACCO). Measured 18O KIEs of 1.0102 +/- 0.0002 (TauD), 1.0120 +/- 0.0002 (HppE), and 1.0215 +/- 0.0005 (ACCO) suggest the formation in the rate-limiting ste ...[more]

PMID: 18540575

Similar Datasets

Finding intermediates in the O2 activation pathways of non-heme iron oxygenases.

Project description:Intermediates in the reaction cycle of an oxygenase are usually very informative with respect to the chemical mechanism of O 2 activation and insertion. However, detection of these intermediates is often complicated by their short lifetime and the regulatory mechanism of the enzyme designed to ensure specificity. Here, the methods used to detect the intermediates in an extradiol dioxygenase, a Rieske cis-dihydrodiol dioxygenase, and soluble methane monooxygenase are discussed. The methods include the use of alternative, chromophoric substrates, mutagenesis of active site catalytic residues, forced changes in substrate binding order, control of reaction rates using regulatory proteins, and initialization of catalysis in crystallo.

| S-EPMC2720168 | biostudies-literature

Probing reversible chemistry in coenzyme B12 -dependent ethanolamine ammonia lyase with kinetic isotope effects.

Project description:Coenzyme B12 -dependent enzymes such as ethanolamine ammonia lyase have remarkable catalytic power and some unique properties that enable detailed analysis of the reaction chemistry and associated dynamics. By selectively deuterating the substrate (ethanolamine) and/or the ?-carbon of the 5'-deoxyadenosyl moiety of the intrinsic coenzyme B12 , it was possible to experimentally probe both the forward and reverse hydrogen atom transfers between the 5'-deoxyadenosyl radical and substrate during single-turnover stopped-flow measurements. These data are interpreted within the context of a kinetic model where the 5'-deoxyadenosyl radical intermediate may be quasi-stable and rearrangement of the substrate radical is essentially irreversible. Global fitting of these data allows estimation of the intrinsic rate constants associated with Co?C homolysis and initial H-abstraction steps. In contrast to previous stopped-flow studies, the apparent kinetic isotope effects are found to be relatively small.

| S-EPMC4497352 | biostudies-literature

First- and second-sphere contributions to Fe(II) site activation by cosubstrate binding in non-heme Fe enzymes.

Project description:Non-heme Fe(II) enzymes exhibit a general mechanistic strategy where binding all cosubstrates opens a coordination site on the Fe(II) for O2 activation. This study shows that strong-donor ligands, steric interactions with the substrate and second-sphere H-bonding to the facial triad carboxylate allow for five-coordinate site formation in this enzyme superfamily.

| S-EPMC3976902 | biostudies-other

Proton-coupled electron transfer reactivities of electronically divergent heme superoxide intermediates: a kinetic, thermodynamic, and theoretical study.

Project description:Heme superoxides are one of the most versatile metallo-intermediates in biology, and they mediate a vast variety of oxidation and oxygenation reactions involving O2(g). Overall proton-coupled electron transfer (PCET) processes they facilitate may proceed via several different mechanistic pathways, attributes of which are not yet fully understood. Herein we present a detailed investigation into concerted PCET events of a series of geometrically similar, but electronically disparate synthetic heme superoxide mimics, where unprecedented, PCET feasibility-determining electronic effects of the heme center have been identified. These electronic factors firmly modulate both thermodynamic and kinetic parameters that are central to PCET, as supported by our experimental and theoretical observations. Consistently, the most electron-deficient superoxide adduct shows the strongest driving force for PCET, whereas the most electron-rich system remains unreactive. The pivotal role of these findings in understanding significant heme systems in biology, as well as in alternative energy applications is also discussed.

| S-EPMC8246096 | biostudies-literature

Sideroflexin 4 affects Fe-S cluster biogenesis, iron metabolism, mitochondrial respiration and heme biosynthetic enzymes.

Project description:Sideroflexin4 (SFXN4) is a member of a family of nuclear-encoded mitochondrial proteins. Rare germline mutations in SFXN4 lead to phenotypic characteristics of mitochondrial disease including impaired mitochondrial respiration and hematopoetic abnormalities. We sought to explore the function of this protein. We show that knockout of SFXN4 has profound effects on Fe-S cluster formation. This in turn diminishes mitochondrial respiratory chain complexes and mitochondrial respiration and causes a shift to glycolytic metabolism. SFXN4 knockdown reduces the stability and activity of cellular Fe-S proteins, affects iron metabolism by influencing the cytosolic aconitase-IRP1 switch, redistributes iron from the cytosol to mitochondria, and impacts heme synthesis by reducing levels of ferrochelatase and inhibiting translation of ALAS2. We conclude that SFXN4 is essential for normal functioning of mitochondria, is necessary for Fe-S cluster biogenesis and iron homeostasis, and plays a critical role in mitochondrial respiration and synthesis of heme.

| S-EPMC6928202 | biostudies-literature

Investigating human geographic origins using dual-isotope (87Sr/86Sr, ?18O) assignment approaches.

Project description:Substantial progress in the application of multiple isotope analyses has greatly improved the ability to identify nonlocal individuals amongst archaeological populations over the past decades. More recently the development of large scale models of spatial isotopic variation (isoscapes) has contributed to improved geographic assignments of human and animal origins. Persistent challenges remain, however, in the accurate identification of individual geographic origins from skeletal isotope data in studies of human (and animal) migration and provenance. In an attempt to develop and test more standardized and quantitative approaches to geographic assignment of individual origins using isotopic data two methods, combining 87Sr/86Sr and ?18O isoscapes, are examined for the Circum-Caribbean region: 1) an Interval approach using a defined range of fixed isotopic variation per location; and 2) a Likelihood assignment approach using univariate and bivariate probability density functions. These two methods are tested with enamel isotope data from a modern sample of known origin from Caracas, Venezuela and further explored with two archaeological samples of unknown origin recovered from Cuba and Trinidad. The results emphasize both the potential and limitation of the different approaches. Validation tests on the known origin sample exclude most areas of the Circum-Caribbean region and correctly highlight Caracas as a possible place of origin with both approaches. The positive validation results clearly demonstrate the overall efficacy of a dual-isotope approach to geoprovenance. The accuracy and precision of geographic assignments may be further improved by better understanding of the relationships between environmental and biological isotope variation; continued development and refinement of relevant isoscapes; and the eventual incorporation of a broader array of isotope proxy data.

| S-EPMC5319690 | biostudies-literature

Heme-Cu Binucleating Ligand Supports Heme/O2 and FeII-CuI/O2 Reactivity Providing High- and Low-Spin FeIII-Peroxo-CuII Complexes.

Project description:The focus of this study is in the description of synthetic heme/copper/O2 chemistry employing a heme-containing binucleating ligand which provides a tridentate chelate for copper ion binding. The addition of O2 (-80 °C, tetrahydrofuran (THF) solvent) to the reduced heme compound (PImH)FeII (1), gives the oxy-heme adduct, formally a heme-superoxide complex FeIII-(O2•-) (2) (resonance Raman spectroscopy (rR): νO-O, 1171 cm-1 (Δ18O2, -61 cm-1); νFe-O, 575 cm-1 (Δ18O2, -24 cm-1)). Simple warming of 2 to room temperature regenerates reduced complex 1; this reaction is reversible, as followed by UV-vis spectroscopy. Complex 2 is electron paramagnetic resonance (EPR)-silent and exhibits upfield-shifted pyrrole resonances (δ 9.12 ppm) in 2H NMR spectroscopy, indicative of a six-coordinate low-spin heme. The coordination of the tethered imidazolyl arm to the heme-superoxide complex as an axial base ligand is suggested. We also report the new fully reduced heme-copper complex [(PImH)FeIICuI]+ (3), where the copper ion is bound to the tethered tridentate portion of PImH. This reacts with O2 to give a distinctive low-temperature-stable, high-spin (S = 2, overall) peroxo-bridged complex [(PImH)FeIII-(O22-)-CuII]+ (3a): λmax, 420 (Soret), 545, 565 nm; δpyrr, 93 ppm; νO-O, 799 cm-1 (Δ18O2, -48 cm-1); νFe-O, 524 cm-1 (Δ18O2, -23 cm-1). To 3a, the addition of dicyclohexylimidazole (DCHIm), which serves as a heme axial base, leads to low-spin (S = 0 overall) species complex [(DCHIm)(PImH)FeIII-(O22-)-CuII]+ (3b): λmax, 425 (Soret), 538 nm; δpyrr, 10.2 ppm; νO-O, 817 cm-1 (Δ18O2, -55 cm-1); νFe-O, 610 cm-1 (Δ18O2, -26 cm-1). These investigations into the characterization of the O2-adducts from (PImH)FeII (1) with/without additional copper chelation advance our understanding of the dioxygen reactivity of heme-only and heme/Cu-ligand heterobinuclear system, thus potentially relevant to O2 reduction in heme-copper oxidases or fuel-cell chemistry.

| S-EPMC6916717 | biostudies-literature

Fe-heme conformations in ferric myoglobin.

Project description:X-ray absorption near-edge structure (XANES) spectra of ferric myoglobin from horse heart have been acquired as a function of pH (between 5.3 and 11.3). At pH = 11.3 temperature-dependent spectra (between 20 and 293 K) have been collected as well. Experimental data solve three main conformations of the Fe-heme: the first, at low pH, is related to high-spin aquomet-myoglobin (Mb+OH2). The other two, at pH 11.3, are related to hydroxymet-myoglobin (Mb+OH-), and are in thermal equilibrium, corresponding to high- and low-spin Mb+OH-. The structure of the three Fe-heme conformations has been assigned according to spin-resolved multiple scattering simulations and fitting of the XANES data. The chemical transition between Mb+OH2 and high-spin Mb+OH-, and the spin transition of Mb+OH-, are accompanied by changes of the Fe coordination sphere due to its movement toward the heme plane, coupled to an increase of the axial asymmetry.

| S-EPMC1299987 | biostudies-other

Superoxo, mu-peroxo, and mu-oxo complexes from heme/O2 and heme-Cu/O2 reactivity: copper ligand influences in cytochrome c oxidase models.

Project description:The O(2)-reaction chemistry of 1:1 mixtures of (F(8))Fe(II) (1; F(8) = tetrakis(2,6-diflurorophenyl)porphyrinate) and [(L(Me(2))N)Cu(I)](+) (2; L(Me(2))N = N,N-bis(2-[2-(N',N'-4-dimethylamino)pyridyl]ethyl)methylamine) is described, to model aspects of the chemistry occurring in cytochrome c oxidase. Spectroscopic investigations, along with stopped-flow kinetics, reveal that low-temperature oxygenation of 1/2 leads to rapid formation of a heme-superoxo species (F(8))Fe(III)-(O(2)(-)) (3), whether or not 2 is present. Complex 3 subsequently reacts with 2 to form [(F(8))Fe(III)-(O(2)(2-))-Cu(II)(L(Me(2))N)](+) (4), which thermally converts to [(F(8))Fe(III)-(O)-Cu(II)(L(Me(2))N)](+) (5), which has an unusually bent (Fe-O-Cu) bond moiety. Tridentate chelation, compared with tetradentate, is shown to dramatically lower the nu(O-O) values observed in 4 and give rise to the novel structural features in 5.

| S-EPMC152972 | biostudies-literature

Effective intermediate-spin iron in O2-transporting heme proteins.

Project description:Proteins carrying an iron-porphyrin (heme) cofactor are essential for biological O2 management. The nature of Fe-O2 bonding in hemoproteins is debated for decades. We used energy-sampling and rapid-scan X-ray K? emission and K-edge absorption spectroscopy as well as quantum chemistry to determine molecular and electronic structures of unligated (deoxy), CO-inhibited (carboxy), and O2-bound (oxy) hemes in myoglobin (MB) and hemoglobin (HB) solutions and in porphyrin compounds at 20-260 K. Similar metrical and spectral features revealed analogous heme sites in MB and HB and the absence of low-spin (LS) to high-spin (HS) conversion. Amplitudes of K? main-line emission spectra were directly related to the formal unpaired Fe(d) spin count, indicating HS Fe(II) in deoxy and LS Fe(II) in carboxy. For oxy, two unpaired Fe(d) spins and, thus by definition, an intermediate-spin iron center, were revealed by our static and kinetic X-ray data, as supported by (time-dependent) density functional theory and complete-active-space self-consistent-field calculations. The emerging Fe-O2 bonding situation includes in essence a ferrous iron center, minor superoxide character of the noninnocent ligand, significant double-bond properties of the interaction, and three-center electron delocalization as in ozone. It resolves the apparently contradictory classical models of Pauling, Weiss, and McClure/Goddard into a unifying view of O2 bonding, tuned toward reversible oxygen transport.

| S-EPMC5559043 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data