1
|
Aktar MS, de Serrano V, Ghiladi R, Franzen S. Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B. J Inorg Biochem 2023; 247:112332. [PMID: 37480762 DOI: 10.1016/j.jinorgbio.2023.112332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
The dehaloperoxidase-hemoglobin (DHP), first isolated from the coelom of a marine terebellid polychaete, Amphitrite ornata, is an example of a multi-functional heme enzyme. Long known for its reversible oxygen (O2) binding, further studies have established DHP activity as a peroxidase, oxidase, oxygenase, and peroxygenase. The specific reactivity depends on substrate binding at various internal and external binding sites. This study focuses on comparison of the binding and reactivity of the substrate 2,4-dichlorophenol (DCP) in the isoforms DHPA and B. There is strong interest in the degradation of DCP because of its wide use in the chemical industry, presence in waste streams, and particular reactivity to form dioxins, some of the most toxic compounds known. The catalytic efficiency is 3.5 times higher for DCP oxidation in DHPB than DHPA by a peroxidase mechanism. However, DHPA and B both show self-inhibition even at modest concentrations of DCP. This phenomenon is analogous to the self-inhibition of 2,4,6-trichlorophenol (TCP) at higher concentration. The activation energies of the electron transfer steps in DCP in DHPA and DHPB are 19.3 ± 2.5 and 24.3 ± 3.2 kJ/mol, respectively, compared to 37.2 ± 6.5 kJ/mol in horseradish peroxidase (HRP), which may be a result of the more facile electron transfer of an internally bound substrate in DHPA. The x-ray crystal structure of DHPA bound with DCP determined at 1.48 Å resolution, shows tight substrate binding inside the heme pocket of DHPA (PDB 8EJN). This research contributes to the studies of DHP as a naturally occurring bioremediation enzyme capable of oxidizing a wide range of environmental pollutants.
Collapse
Affiliation(s)
- Mst Sharmin Aktar
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Reza Ghiladi
- 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.
| |
Collapse
|
2
|
Zhang X, Liu Y. Direct Electrophilic Attack of Compound I on the Indole Ring in the Peroxygenase Mechanism of Dehaloperoxidase DHP B in Degrading Haloindole: Electron Transfer Promotes the Reaction. Inorg Chem 2023; 62:13230-13240. [PMID: 37561650 DOI: 10.1021/acs.inorgchem.3c01425] [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: 08/12/2023]
Abstract
The H2O2-dependent degradation of haloindole catalyzed by the dehaloperoxidase (DHP) from Amphitrite ornate has been reported to employ the peroxygenase mechanism, and the two oxidized products 5-halo-2-oxindole and 5-halo-3-oxindole have a similar amount. According to a previous experimental study, compound I (Cpd I) was suggested to be responsible for triggering the reaction, and the reaction may undergo three possible intermediates; however, the reaction details are still unclear. To clarify the reaction mechanism of DHP, the computational model was constructed on the basis of the high-resolution crystal structure, and a series of the quantum mechanical/molecular mechanical calculations were performed. Based on our calculation results, it is confirmed that the reaction starts from the direct electrophilic attack of Cpd I on the indole ring of the substrate, and the resulted intermediate contains both a carbocation and an oxygen anion, whereas the common hydrogen abstraction by Cpd I was calculated to correspond to a relatively higher barrier. In addition, a net electron transfer from the substrate to the iron center is observed during the attack of Cpd I on the indole ring; therefore, the carbocation/oxygen anion intermediate can easily undergo an intramolecular hydride transfer to form the product 5-halo-2-oxindole or isomerize to the epoxide intermediate which finally generates another product 5-halo-3-oxindole. It is the zwitterionic characteristic of the intermediate that makes the intermolecular hydride transfer quite easy, and it is the high electron affinity of the iron center that promotes the single-electron oxidation of the reaction intermediate. Our calculations well explain the formation of two oxidized products 5-halo-2-oxindole and 5-halo-3-oxindole.
Collapse
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
| |
Collapse
|
3
|
D'Alonzo D, De Fenza M, Pavone V, Lombardi A, Nastri F. Selective Oxidation of Halophenols Catalyzed by an Artificial Miniaturized Peroxidase. Int J Mol Sci 2023; 24:ijms24098058. [PMID: 37175773 PMCID: PMC10178546 DOI: 10.3390/ijms24098058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The development of artificial enzymes for application in sustainable technologies, such as the transformation of environmental pollutants or biomass, is one of the most challenging goals in metalloenzyme design. In this work, we describe the oxidation of mono-, di-, tri- and penta-halogenated phenols catalyzed by the artificial metalloenzyme Fe-MC6*a. It promoted the dehalogenation of 4-fluorophenol into the corresponding 1,4-benzoquinone, while under the same experimental conditions, 4-chloro, 4-bromo and 4-iodophenol were selectively converted into higher molecular weight compounds. Analysis of the 4-chlorophenol oxidation products clarified that oligomers based on C-O bonds were exclusively formed in this case. All results show that Fe-MC6*a holds intriguing enzymatic properties, as it catalyzes halophenol oxidation with substrate-dependent chemoselectivity.
Collapse
Affiliation(s)
- Daniele D'Alonzo
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
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
| |
Collapse
|
10
|
Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation. J Inorg Biochem 2018; 181:65-73. [DOI: 10.1016/j.jinorgbio.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 12/11/2017] [Accepted: 01/07/2018] [Indexed: 11/18/2022]
|
11
|
Bindings of NO, CO, and O 2 to multifunctional globin type dehaloperoxidase follow the 'sliding scale rule'. Biochem J 2017; 474:3485-3498. [PMID: 28899945 DOI: 10.1042/bcj20170515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023]
Abstract
Dehaloperoxidase-hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O2 were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed in DHP, which is similar to observations in SWMb, but in contrast with many heme sensor proteins. The weak affinity of DHP for O2 is mainly due to a fast O2 dissociation rate, in accordance with a longer εN-Fe distance between the heme iron and distal histidine in DHP than that in Mb, and an open-distal pocket that permits ligand escape. Binding affinities in DHP show the same 3-4 orders separation between the pairs NO/CO and CO/O2, consistent with the 'sliding scale rule' hypothesis. Strong gaseous ligand discrimination by DHP is very different from that observed in typical peroxidases, which show poor gaseous ligand selectivity, correlating with a neutral proximal imidazole ligand rather than an imidazolate. The present study provides useful insights into the rationale for DHP to function both as mono-oxygenase and oxidase, and is the first example of a globin peroxidase shown to follow the 'sliding scale rule' hypothesis in gaseous ligand discrimination.
Collapse
|
12
|
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
| |
Collapse
|
13
|
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]
|
14
|
Zhao J, Lu C, Franzen S. Distinct Enzyme–Substrate Interactions Revealed by Two Dimensional Kinetic Comparison between Dehaloperoxidase-Hemoglobin and Horseradish Peroxidase. J Phys Chem B 2015; 119:12828-37. [DOI: 10.1021/acs.jpcb.5b07126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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
| | - Chang Lu
- Department
of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Stefan Franzen
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department
of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| |
Collapse
|
15
|
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
| |
Collapse
|
16
|
Le P, Zhao J, Franzen S. Correlation of Heme Binding Affinity and Enzyme Kinetics of Dehaloperoxidase. Biochemistry 2014; 53:6863-77. [DOI: 10.1021/bi5005975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Le
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - 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
| |
Collapse
|
17
|
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
![]()
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.
Collapse
Affiliation(s)
- David A Barrios
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Zhao J, de Serrano V, Franzen S. A model for the flexibility of the distal histidine in dehaloperoxidase-hemoglobin A based on X-ray crystal structures of the carbon monoxide adduct. Biochemistry 2014; 53:2474-82. [PMID: 24670063 PMCID: PMC4203366 DOI: 10.1021/bi5001905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Dehaloperoxidase
hemoglobin A (DHP A) is a multifunctional hemoglobin
that appears to have evolved oxidative pathways for the degradation
of xenobiotics as a protective function that complements the oxygen
transport function. DHP A possesses at least two internal binding
sites, one for substrates and one for inhibitors, which include various
halogenated phenols and indoles. Herein, we report the X-ray crystallographic
structure of the carbonmonoxy complex (DHPCO). Unlike other DHP structures
with 6-coordinated heme, the conformation of the distal histidine
(H55) in DHPCO is primarily external or solvent exposed, despite the
fact that the heme Fe is 6-coordinated. As observed generally in globins,
DHP exhibits two distal histidine conformations (one internal and
one external). In previous structural studies, we have shown that
the distribution of H55 conformations is weighted strongly toward
the external position when the DHP heme Fe is 5-coordinated. The large
population of the external conformation of the distal histidine observed
in DHPCO crystals at pH 6.0 indicates that some structural factor
in DHP must account for the difference from other globins, which exhibit
a significant external conformation only when pH < 4.5. While the
original hypothesis suggested that interaction with a heme-Fe-bound
ligand was the determinant of H55 conformation, the current study
forces a refinement of that hypothesis. The external or open conformation
of H55 is observed to have interactions with two propionate groups
in heme, at distances of 3.82 and 2.73 Å, respectively. A relatively
weak hydrogen bonding interaction between H55 and CO, combined with
strong interactions with heme propionate (position 6), is hypothesized
to strengthen the external conformation of H55. Density function theory
(DFT) calculations were conducted to test whether there is a weaker
hydrogen bond interaction between H55 and heme bonded CO or O2. Molecular dynamics simulations were conducted to examine
how the tautomeric forms of H55 affect the dynamic motions of the
distal histidine that govern the switching between open and closed
conformations. The calculations support the modified hypothesis suggesting
a competition between the strength of interactions with heme ligand
and the heme propionates as the factors that determine the conformation
of the distal histidine.
Collapse
Affiliation(s)
- Junjie Zhao
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | | | | |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Zhao J, Srajer V, Franzen S. Functional consequences of the open distal pocket of dehaloperoxidase-hemoglobin observed by time-resolved X-ray crystallography. Biochemistry 2013; 52:7943-50. [PMID: 24116924 DOI: 10.1021/bi401118q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using time-resolved X-ray crystallography, we contrast a bifunctional dehaloperoxidase-hemoglobin (DHP) with previously studied examples of myoglobin and hemoglobin to understand the functional role of the distal pocket of globins. One key functional difference between DHP and other globins is the requirement that H2O2 enter the distal pocket of oxyferrous DHP to displace O2 from the heme Fe atom and thereby activate the heme for the peroxidase function. The open architecture of DHP permits more than one molecule to simultaneously enter the distal pocket of the protein above the heme to facilitate the unique peroxidase cycle starting from the oxyferrous state. The time-resolved X-ray data show that the distal pocket of DHP lacks a protein valve found in the two other globins that have been studied previously. The photolyzed CO ligand trajectory in DHP does not have a docking site; rather, the CO moves immediately to the Xe-binding site. From there, CO can escape but can also recombine an order of magnitude more rapidly than in other globins. The contrast with DHP dynamics and function more precisely defines the functional role of the multiple conformational states of myoglobin. Taken together with the high reduction potential of DHP, the open distal site helps to explain how a globin can also function as a peroxidase.
Collapse
Affiliation(s)
- Junjie Zhao
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | | | | |
Collapse
|
21
|
Wang C, Lovelace LL, Sun S, Dawson JH, Lebioda L. Complexes of Dual-Function Hemoglobin/Dehaloperoxidase with Substrate 2,4,6-Trichlorophenol Are Inhibitory and Indicate Binding of Halophenol to Compound I. Biochemistry 2013; 52:6203-10. [DOI: 10.1021/bi400627w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chunxue Wang
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Leslie L. Lovelace
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Shengfang Sun
- 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 29209, United States
| | - Lukasz Lebioda
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Center
for Colon Cancer Research, University of South Carolina, Columbia, South Carolina 29209, United States
| |
Collapse
|
22
|
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
| |
Collapse
|
23
|
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
| |
Collapse
|
24
|
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
| |
Collapse
|