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Zhang X, Liu Y. Computational Insights into the Catalysis of the pH Dependence of Bromite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica ( DaCld). Inorg Chem 2024; 63:6776-6786. [PMID: 38572830 DOI: 10.1021/acs.inorgchem.4c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The heme-containing chlorite dismutases catalyze the rapid and efficient decomposition of chlorite (ClO2-) to yield Cl- and O2, and the catalytic efficiency of chlorite dismutase from Dechloromonas aromatica (DaCld) in catalyzing the decomposition of bromite (BrO2-) was dependent on pH, which was supposed to be caused by the conversion of active Cpd I to the inactive Cpd II by proton-coupled electron transfer (PCET) from the pocket Tyr118 to the propionate side chain of heme at high pH. However, the direct evidence of PCET and how the pH affects the efficiency of DaCld, as well as whether Cpd II is really inactive, are still poorly understood. Here, on the basis of the high-resolution crystal structures, the computational models in both acidic (pH 5.0) and alkaline (pH 9.0) environments were constructed, and a series of quantum mechanical/molecular mechanical calculations were performed. On the basis of our calculation results, the O-Br bond cleavage of BrO2- always follows the homolytic mode to generate Cpd II rather than Cpd I. It is different from the O-O cleavage of O2/H2O2 or peracetic acid catalyzed by the other heme-containing enzymes. Thus, in the subsequent O-O rebound reaction, it is the Fe(IV)═O in Cpd II that combines with the O-Br radical. Because the porphyrin ring in Cpd II does not bear an unpaired electron, the previously suggested PCET from Tyr118 to the propionate side chain of heme was not theoretically recognized in an alkaline environment. In addition, the O-O rebound step in an alkaline solution corresponds to an energy barrier that is larger than that in an acidic environment, which can well explain the pH dependence of the activity of DaCld. In addition, the protonation state of the propionic acid side chains of heme and the surrounding hydrogen bond networks were calculated to have a significant impact on the barriers of the O-O rebound step, which is mainly achieved by affecting the reactivity of the Fe(IV)═O group in Cpd II. In an acidic environment, the relatively weaker coordination of the O2 atom to Fe leads to its higher reactivity toward the O-O rebound reaction. These observations may provide useful information for understanding the catalysis of chlorite dismutases.
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Affiliation(s)
- Xianghui Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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2
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González-Delgado JM, Thompson PM, Andrałojć W, Gdaniec Z, Ghiladi RA, Franzen S. Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes. J Phys Chem B 2024; 128:3383-3397. [PMID: 38563384 DOI: 10.1021/acs.jpcb.3c07176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.
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Affiliation(s)
| | - Peter M Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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3
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Madhuresh NKD, Nguyen H, Franzen S. The divergent pH dependence of substrate turnover in dehaloperoxidases A and B. J Inorg Biochem 2023; 238:112029. [PMID: 36371913 DOI: 10.1016/j.jinorgbio.2022.112029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
The pH-dependent peroxidase activity in both dehaloperoxidases A and B was studied by a kinetic assay, stopped flow spectroscopy, resonance Raman spectroscopy, and high-performance liquid chromatography at pH 5.0, 6.0, and 7.0. At pH 7.0, both isozymes follow the peroxidase ping-pong kinetic model derived from the three-step reaction scheme using the steady-state approximation. However, deviation from standard saturation behavior is observed at pH < 6.0 and [TCP] > 0.7 mM, owing to multiple processes: a) self-inhibition of TCP by internal binding; b) oxidation of the product by a pH- and concentration-dependent secondary reaction; and c) formation of an inactive species known as compound RH in the absence of oxidizable substrate. Although DHP-A and DHP-B differ by only 5 amino acids, they show a complete trend reversal in their observed peroxidase kinetics and product yields. Although at pH 7.0 DHP-B had higher TCP oxidation activity than DHP-A as reported previously, as pH was lowered, DHP-A appeared to have a higher peroxidase activity than DHP-B. This is an unprecedented result. However, the fact that there are multiple processes contributing to both kinetics and yield of TCP oxidation complicates interpretation of these data. Deactivation via compound RH and self-inhibition are pH dependent reactions that compete with substrate oxidation. Compound RH formation was observed to be rapid at low pH. A complete set of control experiments were conducted to differentiate the various contributions to the observed enzyme kinetics.
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Affiliation(s)
| | - Hilbert Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America.
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4
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Yun D, de Serrano V, Ghiladi RA. Oxidation of bisphenol A (BPA) and related compounds by the multifunctional catalytic globin dehaloperoxidase. J Inorg Biochem 2023; 238:112020. [PMID: 36272837 DOI: 10.1016/j.jinorgbio.2022.112020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Dehaloperoxidase (DHP) from the marine polychaete Amphitrite ornata is a multifunctional enzyme that possesses peroxidase, peroxygenase, oxidase and oxygenase activities. Herein, we investigated the reactivity of DHP B with bisphenol A (BPA) and related compounds (bisphenol E, bisphenol F, tetrachlorobisphenol A, 2,2'-biphenol, 3,3'-biphenol, 4,4'-biphenol, and 3,3'-dibromo-4,4'-biphenol). As a previously unknown substrate for DHP B, BPA (as a representative substrate) is an endocrine disruptor widely used in polycarbonate and epoxy resins, thus resulting in human exposure. Reactivity studies with these substrates were investigated using high performance liquid chromatography (HPLC), and their corresponding oxidation products were determined by mass spectrometry (GC-MS/ LC-MS). BPA undergoes oxidation in the presence of DHP B and hydrogen peroxide yielding two cleavage products (4-isopropenylphenol and 4-(2-hydroxypropan-2-yl)phenol), and oligomers with varying degrees of oxidation. 18O-labeling studies confirmed that the O-atom incorporated into the products was derived exclusively from water, consistent with substrate oxidation via a peroxidase-based mechanism. The X-ray crystal structures of DHP bound with bisphenol E (1.48 Å), bisphenol F (1.75 Å), 2,2'-biphenol (1.90 Å) and 3,3'-biphenol (1.30 Å) showed substrate binding sites are in the distal pocket of the heme cofactor, similar to other previously studied DHP substrates. Stopped-flow UV-visible spectroscopy was utilized to investigate the mechanistic details and enzyme oxidation states during substrate turnover, and a reaction mechanism is proposed. The data presented here strongly suggest that DHP B can catalyze the oxidation of bisphenols and biphenols, thus providing evidence of how infaunal invertebrates can contribute to the biotransformation of these marine pollutants.
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Affiliation(s)
- Dongju Yun
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States.
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5
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Malewschik T, Carey LM, de Serrano V, Ghiladi RA. Bridging the functional gap between reactivity and inhibition in dehaloperoxidase B from Amphitrite ornata: Mechanistic and structural studies with 2,4- and 2,6-dihalophenols. J Inorg Biochem 2022; 236:111944. [PMID: 35969974 DOI: 10.1016/j.jinorgbio.2022.111944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
The multifunctional catalytic globin dehaloperoxidase (DHP) from the marine worm Amphitrite ornata was shown to catalyze the H2O2-dependent oxidation of 2,4- and 2,6-dihalophenols (DXP; X = F, Cl, Br). Product identification by LC-MS revealed multiple monomeric products with varying degrees of oxidation and/or dehalogenation, as well as oligomers with n up to 6. Mechanistic and 18O-labeling studies demonstrated sequential dihalophenol oxidation via peroxidase and peroxygenase activities. Binding studies established that 2,4-DXP (X = Cl, Br) have the highest affinities of any known DHP substrate. X-ray crystallography identified different binding positions for 2,4- and 2,6-DXP substrates in the hydrophobic distal pocket of DHP. Correlation between the number of halogens and the substrate binding orientation revealed a halogen-dependent binding motif for mono- (4-halophenol), di- (2,4- and 2,6-dihalophenol) and trihalophenols (2,4,6-trihalopenol). Taken together, the findings here on dihalophenol reactivity with DHP advance our understanding of how these compounds bridge the inhibitory and oxidative functions of their mono- and trihalophenol counterparts, respectively, and provide further insight into the protein structure-function paradigm relevant to multifunctional catalytic globins in comparison to their monofunctional analogs.
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Affiliation(s)
- Talita Malewschik
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Leiah M Carey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States.
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Moreno-Chicano T, Carey LM, Axford D, Beale JH, Doak RB, Duyvesteyn HME, Ebrahim A, Henning RW, Monteiro DCF, Myles DA, Owada S, Sherrell DA, Straw ML, Šrajer V, Sugimoto H, Tono K, Tosha T, Tews I, Trebbin M, Strange RW, Weiss KL, Worrall JAR, Meilleur F, Owen RL, Ghiladi RA, Hough MA. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. IUCRJ 2022; 9:610-624. [PMID: 36071813 PMCID: PMC9438502 DOI: 10.1107/s2052252522006418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.
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Affiliation(s)
- Tadeo Moreno-Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Leiah M. Carey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - R. Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Helen M. E. Duyvesteyn
- Division of Structural Biology (STRUBI), University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ali Ebrahim
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Robert W. Henning
- BioCARS, University of Chicago, Building 434B, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Diana C. F. Monteiro
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1102, USA
| | - Dean A. Myles
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Darren A. Sherrell
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Megan L. Straw
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Vukica Šrajer
- BioCARS, University of Chicago, Building 434B, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | | | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ivo Tews
- Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, United Kingdom
| | - Martin Trebbin
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203-1102, USA
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Kevin L. Weiss
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Flora Meilleur
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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Popescu C, Dinh T, Chen H, Miller D, Washburn A, McGuire A, Dumarieh R, D'Antonio J, Ghiladi RA. Mössbauer studies of the ferryl, ferrous and ferric states of dehaloperoxidase from A. ornata. J Inorg Biochem 2022; 234:111867. [DOI: 10.1016/j.jinorgbio.2022.111867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/13/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
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Hindson SA, Bunzel HA, Frank B, Svistunenko DA, Williams C, van der Kamp MW, Mulholland AJ, Pudney CR, Anderson JLR. Rigidifying a De Novo Enzyme Increases Activity and Induces a Negative Activation Heat Capacity. ACS Catal 2021; 11:11532-11541. [PMID: 34557328 PMCID: PMC8453482 DOI: 10.1021/acscatal.1c01776] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/29/2021] [Indexed: 12/22/2022]
Abstract
![]()
Conformational sampling
profoundly impacts the overall activity
and temperature dependence of enzymes. Peroxidases have emerged as
versatile platforms for high-value biocatalysis owing to their broad
palette of potential biotransformations. Here, we explore the role
of conformational sampling in mediating activity in the de
novo peroxidase C45. We demonstrate that 2,2,2-triflouoroethanol
(TFE) affects the equilibrium of enzyme conformational states, tending
toward a more globally rigid structure. This is correlated with increases
in both stability and activity. Notably, these effects are concomitant
with the emergence of curvature in the temperature-activity profile,
trading off activity gains at ambient temperature with losses at high
temperatures. We apply macromolecular rate theory (MMRT) to understand
enzyme temperature dependence data. These data point to an increase
in protein rigidity associated with a difference in the distribution
of protein dynamics between the ground and transition states. We compare
the thermodynamics of the de novo enzyme activity
to those of a natural peroxidase, horseradish peroxidase. We find
that the native enzyme resembles the rigidified de novo enzyme in terms of the thermodynamics of enzyme catalysis and the
putative distribution of protein dynamics between the ground and transition
states. The addition of TFE apparently causes C45 to behave more like
the natural enzyme. Our data suggest robust, generic strategies for
improving biocatalytic activity by manipulating protein rigidity;
for functional de novo protein catalysts in particular,
this can provide more enzyme-like catalysts without further rational
engineering, computational redesign, or directed evolution.
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Affiliation(s)
- Sarah A. Hindson
- Department of Biology and Biochemistry, Centre for Sustainable Chemical Technology, University of Bath, Bath BA2 7AY, U.K
| | - H. Adrian Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
- Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Bettina Frank
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, Bristol BS8 1TL, U.K
| | | | | | | | | | - Christopher R. Pudney
- Department of Biology and Biochemistry, Centre for Sustainable Chemical Technology, University of Bath, Bath BA2 7AY, U.K
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10
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Thompson MK, Shay MR, de Serrano V, Dumarieh R, Ghiladi RA, Franzen S. A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H2O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.
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Affiliation(s)
- Matthew K. Thompson
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Madeline R. Shay
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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Abstract
Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, USA.
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12
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Syryamina VN, Matveeva AG, Vasiliev YV, Savitsky A, Grishin YA. Improving B 1 field homogeneity in dielectric tube resonators for EPR spectroscopy via controlled shaping of the dielectric insert. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 311:106685. [PMID: 31981782 DOI: 10.1016/j.jmr.2020.106685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
We propose an approach for improving the homogeneity of microwave magnetic field amplitude in a dielectric tube resonator for electron paramagnetic resonance spectroscopy at X-band. The improvement is achieved by "shaping" (controllable variation of the outer diameter of a dielectric insert along its axial direction). Various shaping scenarios based on the principle of discrete solenoids and electromagnetic calculations have been considered. The dielectric insert having the most promising shape was manufactured from a bismuth germanate single crystal. The shaped insert increases the area at B1 > 0.9 B1max from 5.06 to 7.36 mm. Higher sensitivity and lower likelihood of quantitative errors have been achieved in pulse EPR experiments for "long" samples (whose length was comparable to that of the dielectric insert) in a shaped dielectric insert.
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Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya Str., 3, 630090 Novosibirsk, Russia; Novosibirsk State University, Pirogova Str., 2, 630090 Novosibirsk, Russia.
| | - Anna G Matveeva
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya Str., 3, 630090 Novosibirsk, Russia; Novosibirsk State University, Pirogova Str., 2, 630090 Novosibirsk, Russia
| | - Yan V Vasiliev
- Nikolaev Institute of Inorganic Chemistry, Acad. Lavrentiev Av., 3, 630090 Novosibirsk, Russia
| | - Anton Savitsky
- Physics Department, Technical University of Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Yuri A Grishin
- Voevodsky Institute of Chemical Kinetics and Combustion, Institutskaya Str., 3, 630090 Novosibirsk, Russia; Novosibirsk State University, Pirogova Str., 2, 630090 Novosibirsk, Russia
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13
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Zhang P, Yuan H, Xu J, Wang XJ, Gao SQ, Tan X, Lin YW. A Catalytic Binding Site Together with a Distal Tyr in Myoglobin Affords Catalytic Efficiencies Similar to Natural Peroxidases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b05080] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ping Zhang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Jiakun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
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14
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Malewschik T, de Serrano V, McGuire AH, Ghiladi RA. The multifunctional globin dehaloperoxidase strikes again: Simultaneous peroxidase and peroxygenase mechanisms in the oxidation of EPA pollutants. Arch Biochem Biophys 2019; 673:108079. [PMID: 31445024 DOI: 10.1016/j.abb.2019.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/25/2023]
Abstract
The multifunctional catalytic hemoglobin dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of EPA Priority Pollutants (4-Me-o-cresol, 4-Cl-m-cresol and pentachlorophenol) and EPA Toxic Substances Control Act compounds (o-, m-, p-cresol and 4-Cl-o-cresol). Biochemical assays (HPLC/LC-MS) indicated formation of multiple oxidation products, including the corresponding catechol, 2-methylbenzoquinone (2-MeBq), and oligomers with varying degrees of oxidation and/or dehalogenation. Using 4-Br-o-cresol as a representative substrate, labeling studies with 18O confirmed that the O-atom incorporated into the catechol was derived exclusively from H2O2, whereas the O-atom incorporated into 2-MeBq was from H2O, consistent with this single substrate being oxidized by both peroxygenase and peroxidase mechanisms, respectively. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the peroxygenase mechanism leading to catechol formation, and for Compounds I and ES in the peroxidase mechanism that yields the 2-MeBq product. The X-ray crystal structures of DHP bound with 4-F-o-cresol (1.42 Å; PDB 6ONG), 4-Cl-o-cresol (1.50 Å; PDB 6ONK), 4-Br-o-cresol (1.70 Å; PDB 6ONX), 4-NO2-o-cresol (1.80 Å; PDB 6ONZ), o-cresol (1.60 Å; PDB 6OO1), p-cresol (2.10 Å; PDB 6OO6), 4-Me-o-cresol (1.35 Å; PDB 6ONR) and pentachlorophenol (1.80 Å; PDB 6OO8) revealed substrate binding sites in the distal pocket in close proximity to the heme cofactor, consistent with both oxidation mechanisms. The findings establish cresols as a new class of substrate for DHP, demonstrate that multiple oxidation mechanisms may exist for a given substrate, and provide further evidence that different substituents can serve as functional switches between the different activities performed by dehaloperoxidase. More broadly, the results demonstrate the complexities of marine pollution where both microbial and non-microbial systems may play significant roles in the biotransformations of EPA-classified pollutants, and further reinforces that heterocyclic compounds of anthropogenic origin should be considered as environmental stressors of infaunal organisms.
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Affiliation(s)
- Talita Malewschik
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Ashlyn H McGuire
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, USA.
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15
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Svistunenko DA, Manole A. Tyrosyl radical in haemoglobin and haptoglobin-haemoglobin complex: how does haptoglobin make haemoglobin less toxic? J Biomed Res 2019; 34:281-291. [PMID: 32475850 PMCID: PMC7386409 DOI: 10.7555/jbr.33.20180084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the difficulties in creating a blood substitute on the basis of human haemoglobin (Hb) is the toxic nature of Hb when it is outside the safe environment of the red blood cells. The plasma protein haptoglobin (Hp) takes care of the Hb physiologically leaked into the plasma – it binds Hb and makes it much less toxic while retaining the Hb's high oxygen transporting capacity. We used Electron Paramagnetic Resonance (EPR) spectroscopy to show that the protein bound radical induced by H2O2 in Hb and Hp-Hb complex is formed on the same tyrosine residue(s), but, in the complex, the radical is found in a more hydrophobic environment and decays slower than in unbound Hb, thus mitigating its oxidative capacity. The data obtained in this study might set new directions in engineering blood substitutes for transfusion that would have the oxygen transporting efficiency typical of Hb, but which would be non-toxic.
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Affiliation(s)
- Dimitri A Svistunenko
- Biomedical EPR Facility, School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Andreea Manole
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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16
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Chaplin AK, Chicano TM, Hampshire BV, Wilson MT, Hough MA, Svistunenko DA, Worrall JAR. An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis. Chemistry 2019; 25:6141-6153. [PMID: 30945782 DOI: 10.1002/chem.201806290] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/27/2023]
Abstract
Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H2 O2 , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate. In the absence of substrate, the ferryl species decays to form transient protein-bound radicals on redox active amino acids. Identification of radical sites in DyPs has implications for their oxidative mechanism with substrate. Using a DyP from Streptomyces lividans, referred to as DtpA, which displays low reactivity towards synthetic dyes, activation with H2 O2 was explored. A Compound I EPR spectrum was detected, which in the absence of substrate decays to a protein-bound radical EPR signal. Using a newly developed version of the Tyrosyl Radical Spectra Simulation Algorithm, the radical EPR signal was shown to arise from a pristine tyrosyl radical and not a mixed Trp/Tyr radical that has been widely reported in DyP members exhibiting high activity with synthetic dyes. The radical site was identified as Tyr374, with kinetic studies inferring that although Tyr374 is not on the electron-transfer pathway from the dye RB19, its replacement with a Phe does severely compromise activity with other organic substrates. These findings hint at the possibility that alternative electron-transfer pathways for substrate oxidation are operative within the DyP family. In this context, a role for a highly conserved aromatic dyad motif is discussed.
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Affiliation(s)
- Amanda K Chaplin
- Present address: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tadeo Moreno Chicano
- Present address: Department of Molecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Bethany V Hampshire
- Present address: Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Michael T Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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17
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Reaction of O 2 with a diiron protein generates a mixed-valent Fe 2+/Fe 3+ center and peroxide. Proc Natl Acad Sci U S A 2019; 116:2058-2067. [PMID: 30659147 DOI: 10.1073/pnas.1809913116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The gene encoding the cyanobacterial ferritin SynFtn is up-regulated in response to copper stress. Here, we show that, while SynFtn does not interact directly with copper, it is highly unusual in several ways. First, its catalytic diiron ferroxidase center is unlike those of all other characterized prokaryotic ferritins and instead resembles an animal H-chain ferritin center. Second, as demonstrated by kinetic, spectroscopic, and high-resolution X-ray crystallographic data, reaction of O2 with the di-Fe2+ center results in a direct, one-electron oxidation to a mixed-valent Fe2+/Fe3+ form. Iron-O2 chemistry of this type is currently unknown among the growing family of proteins that bind a diiron site within a four α-helical bundle in general and ferritins in particular. The mixed-valent form, which slowly oxidized to the more usual di-Fe3+ form, is an intermediate that is continually generated during mineralization. Peroxide, rather than superoxide, is shown to be the product of O2 reduction, implying that ferroxidase centers function in pairs via long-range electron transfer through the protein resulting in reduction of O2 bound at only one of the centers. We show that electron transfer is mediated by the transient formation of a radical on Tyr40, which lies ∼4 Å from the diiron center. As well as demonstrating an expansion of the iron-O2 chemistry known to occur in nature, these data are also highly relevant to the question of whether all ferritins mineralize iron via a common mechanism, providing unequivocal proof that they do not.
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18
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Yin L, Yuan H, Liu C, He B, Gao SQ, Wen GB, Tan X, Lin YW. A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02979] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu−Lu Yin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Can Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
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19
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Deacon OM, Svistunenko DA, Moore GR, Wilson MT, Worrall JA. Naturally Occurring Disease-Related Mutations in the 40–57 Ω-Loop of Human Cytochrome c Control Triggering of the Alkaline Isomerization. Biochemistry 2018; 57:4276-4288. [DOI: 10.1021/acs.biochem.8b00520] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Oliver M. Deacon
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Dimitri A. Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Geoffrey R. Moore
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Michael T. Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Jonathan A.R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
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20
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McGuire AH, Carey LM, de Serrano V, Dali S, Ghiladi RA. Peroxidase versus Peroxygenase Activity: Substrate Substituent Effects as Modulators of Enzyme Function in the Multifunctional Catalytic Globin Dehaloperoxidase. Biochemistry 2018; 57:4455-4468. [DOI: 10.1021/acs.biochem.8b00540] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ashlyn H. McGuire
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Leiah M. Carey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Safaa Dali
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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21
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Carey LM, Gavenko R, Svistunenko DA, Ghiladi RA. How nature tunes isoenzyme activity in the multifunctional catalytic globin dehaloperoxidase from Amphitrite ornata. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:230-241. [DOI: 10.1016/j.bbapap.2017.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/05/2017] [Accepted: 11/07/2017] [Indexed: 01/29/2023]
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22
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Selective tuning of activity in a multifunctional enzyme as revealed in the F21W mutant of dehaloperoxidase B from Amphitrite ornata. J Biol Inorg Chem 2017; 23:209-219. [DOI: 10.1007/s00775-017-1520-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/17/2017] [Indexed: 11/25/2022]
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23
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Van Doorslaer S, Cuypers B. Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1392629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Antwerp, Belgium
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24
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McCombs NL, Smirnova T, Ghiladi RA. Oxidation of Pyrrole by Dehaloperoxidase-Hemoglobin: Chemoenzymatic Synthesis of Pyrrolin-2-Ones. Catal Sci Technol 2017; 7:3104-3118. [PMID: 29158890 PMCID: PMC5693384 DOI: 10.1039/c7cy00781g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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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Affiliation(s)
- Nikolette L McCombs
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204 USA. Tel: +1 919 513 0680
| | - Tatyana Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204 USA. Tel: +1 919 513 0680
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204 USA. Tel: +1 919 513 0680
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25
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Chaplin AK, Bernini C, Sinicropi A, Basosi R, Worrall JAR, Svistunenko DA. Tyrosine or Tryptophan? Modifying a Metalloradical Catalytic Site by Removal of the Cys-Tyr Cross-Link in the Galactose 6-Oxidase Homologue GlxA. Angew Chem Int Ed Engl 2017; 56:6502-6506. [DOI: 10.1002/anie.201701270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/13/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Amanda K. Chaplin
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Caterina Bernini
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Jonathan A. R. Worrall
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Dimitri A. Svistunenko
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
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26
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Chaplin AK, Bernini C, Sinicropi A, Basosi R, Worrall JAR, Svistunenko DA. Tyrosine or Tryptophan? Modifying a Metalloradical Catalytic Site by Removal of the Cys-Tyr Cross-Link in the Galactose 6-Oxidase Homologue GlxA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Amanda K. Chaplin
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Caterina Bernini
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Riccardo Basosi
- Department of Biotechnology, Chemistry and Pharmaceutical Sciences; University of Siena; Via A. Moro, 2 53100 Siena Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Jonathan A. R. Worrall
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
| | - Dimitri A. Svistunenko
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester Essex CO4 3SQ (U K
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27
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Bradley JM, Svistunenko DA, Moore GR, Le Brun NE. Tyr25, Tyr58 and Trp133 ofEscherichia colibacterioferritin transfer electrons between iron in the central cavity and the ferroxidase centre. Metallomics 2017; 9:1421-1428. [DOI: 10.1039/c7mt00187h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tyr58 and Trp133 play key roles in the formation and decay of the Tyr25 radical species ofE. coliBFR.
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Affiliation(s)
- Justin M. Bradley
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich Research Park
- Norwich
| | | | - Geoffrey R. Moore
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich Research Park
- Norwich
| | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich Research Park
- Norwich
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28
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McCombs NL, D’Antonio J, Barrios DA, Carey LM, Ghiladi RA. Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata. Biochemistry 2016; 55:2465-78. [DOI: 10.1021/acs.biochem.6b00143] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikolette L. McCombs
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204
| | - Jennifer D’Antonio
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204
| | - David A. Barrios
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204
| | - Leiah M. Carey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695-8204
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29
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Zhang Z, Santos AP, Zhou Q, Liang L, Wang Q, Wu T, Franzen S. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin. Biophys Chem 2016; 211:28-38. [DOI: 10.1016/j.bpc.2016.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/24/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
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30
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The reaction of oxyhemoglobin with nitric oxide: EPR evidence for an iron(III)-nitrate intermediate. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.07.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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The hydrogen-peroxide-induced radical behaviour in human cytochrome c-phospholipid complexes: implications for the enhanced pro-apoptotic activity of the G41S mutant. Biochem J 2015; 456:441-52. [PMID: 24099549 DOI: 10.1042/bj20130758] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have investigated whether the pro-apoptotic properties of the G41S mutant of human cytochrome c can be explained by a higher than wild-type peroxidase activity triggered by phospholipid binding. A key complex in mitochondrial apoptosis involves cytochrome c and the phospholipid cardiolipin. In this complex cytochrome c has its native axial Met(80) ligand dissociated from the haem-iron, considerably augmenting the peroxidase capability of the haem group upon H2O2 binding. By EPR spectroscopy we reveal that the magnitude of changes in the paramagnetic haem states, as well as the yield of protein-bound free radical, is dependent on the phospholipid used and is considerably greater in the G41S mutant. A high-resolution X-ray crystal structure of human cytochrome c was determined and, in combination with the radical EPR signal analysis, two tyrosine residues, Tyr(46) and Tyr(48), have been rationalized to be putative radical sites. Subsequent single and double tyrosine-to-phenylalanine mutations revealed that the EPR signal of the radical, found to be similar in all variants, including G41S and wild-type, originates not from a single tyrosine residue, but is instead a superimposition of multiple EPR signals from different radical sites. We propose a mechanism of multiple radical formations in the cytochrome c-phospholipid complexes under H2O2 treatment, consistent with the stabilization of the radical in the G41S mutant, which elicits a greater peroxidase activity from cytochrome c and thus has implications in mitochondrial apoptosis.
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32
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Zhao J, Moretto J, Le P, Franzen S. Measurement of Internal Substrate Binding in Dehaloperoxidase–Hemoglobin by Competition with the Heme–Fluoride Binding Equilibrium. J Phys Chem B 2015; 119:2827-38. [DOI: 10.1021/jp512996v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Justin Moretto
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Peter Le
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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33
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Sun S, Sono M, Du J, Dawson JH. Evidence of the Direct Involvement of the Substrate TCP Radical in Functional Switching from Oxyferrous O2 Carrier to Ferric Peroxidase in the Dual-Function Hemoglobin/Dehaloperoxidase from Amphitrite ornata. Biochemistry 2014; 53:4956-69. [DOI: 10.1021/bi5002757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shengfang Sun
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Masanori Sono
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jing Du
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - John H. Dawson
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- School
of Medicine, University of South Carolina, Columbia, South Carolina 29208, United States
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34
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Barrios DA, D'Antonio J, McCombs NL, Zhao J, Franzen S, Schmidt AC, Sombers LA, Ghiladi RA. Peroxygenase and oxidase activities of dehaloperoxidase-hemoglobin from Amphitrite ornata. J Am Chem Soc 2014; 136:7914-25. [PMID: 24791647 PMCID: PMC4063182 DOI: 10.1021/ja500293c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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The marine globin dehaloperoxidase-hemoglobin
(DHP) from Amphitrite ornata was found to catalyze
the H2O2-dependent oxidation of monohaloindoles,
a previously
unknown class of substrate for DHP. Using 5-Br-indole as a representative
substrate, the major monooxygenated products were found to be 5-Br-2-oxindole
and 5-Br-3-oxindolenine. Isotope labeling studies confirmed that the
oxygen atom incorporated was derived exclusively from H2O2, indicative of a previously unreported peroxygenase
activity for DHP. Peroxygenase activity could be initiated from either
the ferric or oxyferrous states with equivalent substrate conversion
and product distribution. It was found that 5-Br-3-oxindole, a precursor
of the product 5-Br-3-oxindolenine, readily reduced the ferric enzyme
to the oxyferrous state, demonstrating an unusual product-driven reduction
of the enzyme. As such, DHP returns to the globin-active oxyferrous
form after peroxygenase activity ceases. Reactivity with 5-Br-3-oxindole
in the absence of H2O2 also yielded 5,5′-Br2-indigo above the expected reaction stoichiometry under aerobic
conditions, and O2-concentration studies demonstrated dioxygen
consumption. Nonenzymatic and anaerobic controls both confirmed the
requirements for DHP and molecular oxygen in the catalytic generation
of 5,5′-Br2-indigo, and together suggest a newly
identified oxidase activity for DHP.
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Affiliation(s)
- David A Barrios
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
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35
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Zhao J, Zhao J, Franzen S. The Regulatory Implications of Hydroquinone for the Multifunctional Enzyme Dehaloperoxidase-Hemoglobin from Amphitrite ornata. J Phys Chem B 2013; 117:14615-24. [DOI: 10.1021/jp407663n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Junjie Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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36
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Dumarieh R, D'Antonio J, Deliz-Liang A, Smirnova T, Svistunenko DA, Ghiladi RA. Tyrosyl radicals in dehaloperoxidase: how nature deals with evolving an oxygen-binding globin to a biologically relevant peroxidase. J Biol Chem 2013; 288:33470-82. [PMID: 24100039 DOI: 10.1074/jbc.m113.496497] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dehaloperoxidase (DHP) from Amphitrite ornata, having been shown to catalyze the hydrogen peroxide-dependent oxidation of trihalophenols to dihaloquinones, is the first oxygen binding globin that possesses a biologically relevant peroxidase activity. The catalytically competent species in DHP appears to be Compound ES, a reactive intermediate that contains both a ferryl heme and a tyrosyl radical. By simulating the EPR spectra of DHP activated by H2O2, Thompson et al. (Thompson, M. K., Franzen, S., Ghiladi, R. A., Reeder, B. J., and Svistunenko, D. A. (2010) J. Am. Chem. Soc. 132, 17501-17510) proposed that two different radicals, depending on the pH, are formed, one located on either Tyr-34 or Tyr-28 and the other on Tyr-38. To provide additional support for these simulation-based assignments and to deduce the role(s) that tyrosyl radicals play in DHP, stopped-flow UV-visible and rapid-freeze-quench EPR spectroscopic methods were employed to study radical formation in DHP when three tyrosine residues, Tyr-28, Tyr-34, and Tyr-38, were replaced either individually or in combination with phenylalanines. The results indicate that radicals form on all three tyrosines in DHP. Evidence for the formation of DHP Compound I in several tyrosine mutants was obtained. Variants that formed Compound I showed an increase in the catalytic rate for substrate oxidation but also an increase in heme bleaching, suggesting that the tyrosines are necessary for protecting the enzyme from oxidizing itself. This protective role of tyrosines is likely an evolutionary adaptation allowing DHP to avoid self-inflicted damage in the oxidative environment.
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Affiliation(s)
- Rania Dumarieh
- From the Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204 and
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37
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The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2020-9. [DOI: 10.1016/j.bbapap.2013.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 11/23/2022]
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38
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Zhao J, Franzen S. Kinetic Study of the Inhibition Mechanism of Dehaloperoxidase-Hemoglobin A by 4-Bromophenol. J Phys Chem B 2013; 117:8301-9. [DOI: 10.1021/jp3116353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
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39
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Zhao J, de Serrano V, Zhao J, Le P, Franzen S. Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata. Biochemistry 2013; 52:2427-39. [DOI: 10.1021/bi301307f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Junjie Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Peter Le
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
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40
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Plummer A, Thompson MK, Franzen S. Role of Polarity of the Distal Pocket in the Control of Inhibitor Binding in Dehaloperoxidase-Hemoglobin. Biochemistry 2013; 52:2218-27. [DOI: 10.1021/bi301509r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ashlee Plummer
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
| | - Matthew K. Thompson
- Department
of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee
37232, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina
27695, United States
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41
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Schkolnik G, Utesch T, Zhao J, Jiang S, Thompson MK, Mroginski MA, Hildebrandt P, Franzen S. Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics – application of the vibrational Stark effect to understand enzyme kinetics. Biochem Biophys Res Commun 2013; 430:1011-5. [DOI: 10.1016/j.bbrc.2012.12.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 11/17/2022]
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42
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Zhao J, de Serrano V, Dumarieh R, Thompson M, Ghiladi RA, Franzen S. The Role of the Distal Histidine in H2O2 Activation and Heme Protection in both Peroxidase and Globin Functions. J Phys Chem B 2012; 116:12065-77. [DOI: 10.1021/jp300014b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Zhao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Matt Thompson
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
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43
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Reeder BJ, Svistunenko DA, Cooper CE, Wilson MT. Engineering Tyrosine-Based Electron Flow Pathways in Proteins: The Case of Aplysia Myoglobin. J Am Chem Soc 2012; 134:7741-9. [DOI: 10.1021/ja211745g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brandon J. Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ,
United Kingdom
| | - Dimitri A. Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ,
United Kingdom
| | - Chris E. Cooper
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ,
United Kingdom
| | - Michael T. Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ,
United Kingdom
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44
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Franzen S, Thompson MK, Ghiladi RA. The dehaloperoxidase paradox. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:578-88. [DOI: 10.1016/j.bbapap.2011.12.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 12/20/2011] [Accepted: 12/23/2011] [Indexed: 12/01/2022]
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45
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Svistunenko DA, Worrall JAR, Chugh SB, Haigh SC, Ghiladi RA, Nicholls P. Ferric haem forms of Mycobacterium tuberculosis catalase-peroxidase probed by EPR spectroscopy: Their stability and interplay with pH. Biochimie 2012; 94:1274-80. [PMID: 22381358 DOI: 10.1016/j.biochi.2012.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 02/16/2012] [Indexed: 11/26/2022]
Abstract
Low temperature EPR spectroscopy was used to characterise Mycobacterium tuberculosis catalase-peroxidase in its resting ferric haem state. Several high spin ferric haem forms and no low spin forms were found in the enzyme samples frozen in methanol on dry ice. The EPR spectra depended not only on the pH but also on the buffer type. As a general trend, the higher the pH, the greater the 'rhombic' fraction of the high spin ferric haem that was observed. The rhombic form was characterised by well separated two lines in the g = 6 region whereas in the 'axial' form the two lines overlap. This pH dependence of the equilibrium of axial and rhombic ferric haem forms is also seen in rapidly freeze-quenched samples. Different high spin ferric haem forms were monitored during a 3 week storage of the enzyme at 4 °C. For some forms, extremal dependences, i.e. those progressing via maxima or minima over storage time, were found. This indicates that the mechanism of the time-dependent transition from one high spin ferric haem form to another must be more complex than a simple single site oxidation.
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Affiliation(s)
- Dimitri A Svistunenko
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom.
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46
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Franzen S, Sasan K, Sturgeon BE, Lyon BJ, Battenburg BJ, Gracz H, Dumariah R, Ghiladi R. Nonphotochemical Base-Catalyzed Hydroxylation of 2,6-Dichloroquinone by H2O2 Occurs by a Radical Mechanism. J Phys Chem B 2012; 116:1666-76. [DOI: 10.1021/jp208536x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Bradley E. Sturgeon
- Department of Chemistry, Monmouth College, Monmouth, Illinois 61462, United States
| | - Blake J. Lyon
- Department of Chemistry, Monmouth College, Monmouth, Illinois 61462, United States
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47
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D'Antonio J, Ghiladi RA. Reactivity of deoxy- and oxyferrous dehaloperoxidase B from Amphitrite ornata: identification of compound II and its ferrous-hydroperoxide precursor. Biochemistry 2011; 50:5999-6011. [PMID: 21619067 DOI: 10.1021/bi200311u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. The bifunctional nature of DHP as a globin peroxidase appears to be at odds with the traditional starting oxidation state for each individual activity. Namely, reversible oxygen binding is only mediated via a ferrous heme in globins, and peroxidase activity is initiated from ferric centers and to the exclusion of the oxyferrous oxidation state from the peroxidase cycle. Thus, to address what appears to be a paradox, herein we report the details of our investigations into the DHP catalytic cycle when initiated from the deoxy- and oxyferrous states using biochemical assays, stopped-flow UV-visible, and rapid-freeze-quench electron paramagnetic resonance spectroscopies, and anaerobic methods. We demonstrate the formation of Compound II directly from deoxyferrous DHP B upon its reaction with hydrogen peroxide and show that this occurs both in the presence and in the absence of trihalophenol. Prior to the formation of Compound II, we have identified a new species that we have preliminarily attributed to a ferrous-hydroperoxide precursor that undergoes heterolysis to generate the aforementioned ferryl intermediate. Taken together, the results demonstrate that the oxyferrous state in DHP is a peroxidase competent starting species, and an updated catalytic cycle for DHP is proposed in which the ferric oxidation state is not an obligatory starting point for the peroxidase catalytic cycle of dehaloperoxidase. The data presented herein provide a link between the peroxidase and oxygen transport activities, which furthers our understanding of how this bifunctional enzyme is able to unite its two inherent functions in one system.
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Affiliation(s)
- Jennifer D'Antonio
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
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48
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Igamberdiev AU, Bykova NV, Hill RD. Structural and functional properties of class 1 plant hemoglobins. IUBMB Life 2011; 63:146-52. [DOI: 10.1002/iub.439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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49
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Nicoletti FP, Thompson MK, Franzen S, Smulevich G. Degradation of sulfide by dehaloperoxidase-hemoglobin from Amphitrite ornata. J Biol Inorg Chem 2011; 16:611-9. [DOI: 10.1007/s00775-011-0762-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/26/2011] [Indexed: 10/18/2022]
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