1
|
Aktar MS, de Serrano V, Ghiladi RA, Franzen S. Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B. Biochemistry 2024; 63:1761-1773. [PMID: 38959050 DOI: 10.1021/acs.biochem.4c00179] [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: 07/04/2024]
Abstract
Dehalperoxidase (DHP) has diverse catalytic activities depending on the substrate binding conformation, pH, and dynamics in the distal pocket above the heme. According to our hypothesis, the molecular structure of the substrate and binding orientation in DHP guide enzymatic function. Enzyme kinetic studies have shown that the catalytic activity of DHP B is significantly higher than that of DHP A despite 96% sequence homology. There are more than 30 substrate-bound structures with DHP B, each providing insight into the nature of enzymatic binding at the active site. By contrast, the only X-ray crystallographic structures of small molecules in a complex with DHP A are phenols. This study is focused on investigating substrate binding in DHP A to compare with DHP B structures. Fifteen substrates were selected that were known to bind to DHP B in the crystal to test whether soaking substrates into DHP A would yield similar structures. Five of these substrates yielded X-ray crystal structures of substrate-bound DHP A, namely, 2,4-dichlorophenol (1.48 Å, PDB: 8EJN), 2,4-dibromophenol (1.52 Å, PDB: 8VSK), 4-nitrophenol (2.03 Å, PDB: 8VKC), 4-nitrocatechol (1.40 Å, PDB: 8VKD), and 4-bromo-o-cresol (1.64 Å, PDB: 8VZR). For the remaining substrates that bind to DHP B, such as cresols, 5-bromoindole, benzimidazole, 4,4-biphenol, 4.4-ethylidenebisphenol, 2,4-dimethoxyphenol, and guaiacol, the electron density maps in DHP A are not sufficient to determine the presence of the substrates, much less their orientation. In our hands, only phenols, 4-Br-o-cresol, and 4-nitrocatechol can be soaked into crystalline DHP A. None of the larger substrates were observed to bind. A minimum of seven hanging drops were selected for soaking with more than 50 crystals screened for each substrate. The five high-quality examples of direct comparison of modes of binding in DHP A and B for the same substrate provide further support for the hypothesis that the substrate-binding conformation determines the enzyme function of DHP.
Collapse
Affiliation(s)
- Mst Sharmin Aktar
- 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
| | - 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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris. Int J Mol Sci 2023; 24:ijms24043973. [PMID: 36835381 PMCID: PMC9961634 DOI: 10.3390/ijms24043973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Plant hemoglobins, often referred to as phytoglobins, play important roles in abiotic stress tolerance. Several essential small physiological metabolites can be bound to these heme proteins. In addition, phytoglobins can catalyze a range of different oxidative reactions in vivo. These proteins are often oligomeric, but the degree and relevance of subunit interactions are largely unknown. In this study, we delineate which residues are involved in dimer formation of a sugar beet phytoglobin type 1.2 (BvPgb1.2) using NMR relaxation experiments. E. coli cells harboring a phytoglobin expression vector were cultivated in isotope-labeled (2H, 13C and 15N) M9 medium. The triple-labeled protein was purified to homogeneity using two chromatographic steps. Two forms of BvPgb1.2 were examined, the oxy-form and the more stable cyanide-form. Using three-dimensional triple-resonance NMR experiments, sequence-specific assignments for CN-bound BvPgb1.2 were achieved for 137 backbone amide cross-peaks in the 1H-15N TROSY spectrum, which amounts to 83% of the total number of 165 expected cross-peaks. A large proportion of the non-assigned residues are located in α-helixes G and H, which are proposed to be involved in protein dimerization. Such knowledge around dimer formation will be instrumental for developing a better understanding of phytoglobins' roles in planta.
Collapse
|
4
|
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
|
5
|
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]
|
6
|
Schoen M, Evans R, Gubbins KE, Rabe JP, Thommes M, Jackson G. Gerhard Findenegg (1938–2019). Mol Phys 2021. [DOI: 10.1080/00268976.2021.1953272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Martin Schoen
- Technische Universität Berlin, Fakultät für Mathematik und Naturwissenschaften, Berlin, Germany
| | - Robert Evans
- H. H. Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Keith E. Gubbins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Jürgen P. Rabe
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Thommes
- Department of Chemical and Bioeengineering, Institute of Separation Science and Technology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - George Jackson
- Department of Chemical Engineering, Imperial College London, London, UK
| |
Collapse
|
7
|
Fu Y, Jiang Z, Feng W. A peroxidase coordinating to Zn (II) preventing heme bleaching and resistant to the interference of H 2 O 2. Biotechnol Prog 2020; 37:e3075. [PMID: 32869526 DOI: 10.1002/btpr.3075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 08/10/2020] [Accepted: 08/27/2020] [Indexed: 01/14/2023]
Abstract
Dehaloperoxidase (DHP) catalyzes detoxifying halophenols. It is a heme-containing enzyme using H2 O2 as the oxidant. Heme bleaching from the active site is of great concern. In addition, the interference of DHP by H2 O2 leads to the inactivation of the enzyme. To solve these two problems, DHP is coordinated to Zn (II) in PBS buffer to form a biomineralized composite (DHP&Zn-CP). DHP&Zn-CP was characterized by measuring SEM and confocal images, as well as energy dispersive X-ray spectrometry mapping. Fluorescence spectra demonstrated that DHP&Zn-CP can prevent heme bleaching. Two-dimensional FTIR spectra were measured, dynamically providing insight into the structural change of DHP along the coordination process. Raman spectra were performed to analyze the structural change. The optical spectra confirmed that the forming of DHP&Zn-CP had a little effect on the structures of DHP. For the dehalogenation of 2,4,6-trichlorophenol, DHP&Zn-CP can tolerate the presence of H2 O2 and is resistant to the interference by H2 O2 . The catalytic efficiency of DHP&Zn-CP is much higher than that of free DHP.
Collapse
Affiliation(s)
- Yaqi Fu
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Zhengfeng Jiang
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Wei Feng
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|