Measurement of Internal Substrate Binding in Dehaloperoxidase–Hemoglobin by Competition with the Heme–Fluoride Binding Equilibrium

Zhao, Jing; Moretto, Justin; Le, Peter; Franzen, Stefan

doi:10.1021/jp512996v

Cited by 17 publications

(16 citation statements)

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“…50 Plots of ν(Fe III −F) frequency versus ν(Fe II −His) frequency for the Clds studied here, along with a variety of other heme proteins for which literature data are available, (Figure 7A and Table S2) reveal linear and negative correlations between them. These correlations constitute experimental evidence for the effects predicted previously by DFT calculations 51 and provide more detailed insight into the roles of both distal and proximal heme environments on Fe III −F bonding. Although all the heme proteins on this plot have proximal His ligands, the protein environments that dictate their nonbonded interactions with the distal and proximal axial heme ligands vary considerably.…”

Section: Resultssupporting

confidence: 77%

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

et al. 2017

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O2-evolving chlorite dismutases (Clds) fall into two subfamilies, which efficiently convert ClO2− to O2 and Cl−. The Cld from Dechloromonas aromatica (DaCld) represents the chlorite-decomposing homopentameric enzymes found in perchlorate and chlorate respiring bacteria. The Cld from the Gram-negative, human pathogen Klebsiella pneumoniae (KpCld) is representative of the second subfamily, comprising homodimeric enzymes having truncated N-termini. Here steric and nonbonding properties of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic and spectroscopic behaviors of their fluorides, chlorides and hydroxides. Cooperative Cl− binding to KpCld drives formation of a hexacoordinate, high-spin aqua heme, whereas DaCld remains pentacoordinate and high-spin under analogous conditions. Fluoride coordinates to the heme iron in KpCld and DaCld, exhibiting ν(FeIII−F) bands at 385 and 390 cm−1, respectively. Correlation of these frequencies with their CT1 energies reveals strong H-bond-donation to the F− ligand, indicating that atoms directly coordinated to heme iron are accessible by distal H-bond donation. New vibrational frequency correlations between either ν(FeIII−F) or ν(FeIII−OH) and ν(FeII−His) of Clds and other heme proteins are reported. These correlations orthogonalize proximal and distal effects on the bonding between iron and exogenous π-donor ligands. The axial Fe−X vibrations and the relationships between them illuminate both similarities and differences in the H-bonding and electrostatic properties of the distal and proximal heme environments in pentameric and dimeric Clds. Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety.

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Section: Resultssupporting

confidence: 77%

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

et al. 2017

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“…Thus, a competition assay with the heme-fluoride binding equilibrium was employed to indirectly measure substrate binding (Figure S10). 52 In this method, substrates that bind within the DHP active site lead to a decreased binding affinity of fluoride to the heme ( K d F− = 2.5 ± 0.2 mM, pH 5). In the presence of 5 mM pyrrole, a ~2-fold increase in the K d F− to 5.2 ± 0.4 mM at pH was observed (Table 2), consistent with pyrrole binding to the active site of DHP.…”

Section: Resultsmentioning

confidence: 99%

“…Fluoride-binding studies were performed per literature protocol 52 to determine the extent of substrate binding. DHP B (50 μM) was incubated with 5 mM pyrrole, and 10 – 400 equiv.…”

Section: Methodsmentioning

confidence: 99%

Oxidation of pyrrole by dehaloperoxidase-hemoglobin: chemoenzymatic synthesis of pyrrolin-2-ones

McCombs

Smirnova

Ghiladi

2017

Catal. Sci. Technol.

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The use of oxidoreductases as biocatalysts in the syntheses of functionalized, monomeric pyrroles has been a challenge owing to, among a number of factors, undesired polypyrrole formation. Here, we have investigated the ability of dehaloperoxidase (DHP), the coelomic hemoglobin from the terebellid polychaete Amphitrite ornata, to catalyze the H2O2-dependent oxidation of pyrroles as a new class of substrate for this enzyme. Substrate oxidation was observed for all compounds employed (pyrrole, N-methylpyrrole, 2-methylpyrrole, 3-methylpyrrole and 2,5-dimethylpyrrole) under both aerobic and anaerobic conditions. Using pyrrole as a representative substrate, only a single oxidation product, 4-pyrrolin-2-one, was observed, and notably without formation of polypyrrole. Reactivity could be initiated from all three biologically relevant oxidation states for this catalytic globin: ferric, ferrous and oxyferrous. Isotope labeling studies determined that the O-atom incorporated into the 4-pyrrolin-2-one product was derived exclusively from H2O2, indicative of a peroxygenase mechanism. Consistent with this observation, single- and double-mixing stopped-flow UV-visible spectroscopic studies supported Compound I, but not Compounds ES or II, as the catalytically-relevant ferryl intermediate involved in pyrrole oxidation. Electrophilic addition of the ferryl oxygen to pyrrole is proposed as the mechanism of O-atom transfer. The results demonstrate the breadth of chemical reactivity afforded by dehaloperoxidase, and provide further evidence for establishing DHP as a multifunctional globin with practical applications as a biocatalyst.

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“…These are calculations with large basis sets and the enthalpies of solvation of pyridine and ␤-IP should be very small since they have no electrostatic component. The anionic component of the binding interactions by Cl − and Ac − can be accurately calculated using COSMO [28,46]. From a computational point of view it appears that there is little more that can be done to achieve better agreement with regard to these reactions.…”

Section: Tablementioning

confidence: 99%

Aerobic oxidation of β-isophorone by tetraphenylporphyrin catalysts in pyridine solution

Burns

Huang

Weare

et al. 2015

Journal of Molecular Catalysis A: Chemical

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a b s t r a c tA kinetic study was conducted using five metallo-tetraphenylporphyrins (MTPPs) as catalysts for the aerobic oxidation reaction of ␤-isophorone (␤-IP) to ketoisophorone (KIP). The oxidation reaction catalyzed by MTPPs (M = Cr, Mn, Fe, Co and Cu) was observed over a seven hour period under a range of experimental conditions. Changes in the specificity of conversion of reactant to the product, KIP, and the main side-product, ␣-isophorone (␣-IP), were observed at temperatures ranging from 60 • C to 75 • C, in solvents with varying compositions of pyridine and ␤-IP, with different MTPP catalysts, oxygen gas flow rates, and solution agitation frequencies. Control experiments show that MTPP catalysts modestly increase the rate of KIP formation, but significantly improve specificity through the apparent suppression of ␣-IP formation. Analysis revealed that MnTPP (CH 3 COO − ) produced the highest product specificity ratio [KIP]/ [␣-IP]. Given that all of the metals were in the 3+ oxidation state in this study and there was no observed binding by O 2 to any of the MTPP catalysts, the catalytic mechanism is suggested to involve the binding of ␤-IP to the MTPP metal center. Binding of ␤-IP is most favorable when pyridine is the trans ligand, but ␤-IP is also observed to weakly bind when trans to acetate in the MnTPP adduct. This conclusion is supported by electronic absorption spectroscopy, resonance Raman spectroscopy and density functional theory (DFT) calculations. The role played by the catalyst appears to be the activation of hydrogen abstraction following the substrate's ligation to the metal, rather than the more traditional role of MTPPs as O 2 activation catalysts by ligation of diatomic O 2 . ␤-IP oxidation is an example of a case where the catalyst appears to have a more important role for improving the specificity of the reaction (through decreasing side-product formation) rather than increasing the rate of product formation.

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Measurement of Internal Substrate Binding in Dehaloperoxidase–Hemoglobin by Competition with the Heme–Fluoride Binding Equilibrium

Cited by 17 publications

References 78 publications

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

Oxidation of pyrrole by dehaloperoxidase-hemoglobin: chemoenzymatic synthesis of pyrrolin-2-ones

Aerobic oxidation of β-isophorone by tetraphenylporphyrin catalysts in pyridine solution

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Measurement of Internal Substrate Binding in Dehaloperoxidase–Hemoglobin by Competition with the Heme–Fluoride Binding Equilibrium

Cited by 17 publications

References 78 publications

Active Sites of O2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

Active Sites of O2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

Oxidation of pyrrole by dehaloperoxidase-hemoglobin: chemoenzymatic synthesis of pyrrolin-2-ones

Aerobic oxidation of β-isophorone by tetraphenylporphyrin catalysts in pyridine solution

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Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations

Active Sites of O₂-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron–Ligand Vibrational Correlations