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Nageswari P, Swathi K. In silico docking and Molecular Dynamic (MD) simulations studies of selected phytochemicals against Human Glycolate Oxidase (hGOX) and Oxalate oxidase (OxO). Drug Res (Stuttg) 2023; 73:459-464. [PMID: 37487522 DOI: 10.1055/a-2088-3889] [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: 07/26/2023]
Abstract
Globally, Urolithiasis is the most prevalent urological problem which affects the populations across the ages and races. In recent years, several phytochemicals are being investigated to improve the efficacy and safety of anti-urolithiasis formulations. To develop drugs based on traditional medicines, it is essential to understand the molecular mechanism of action of these drugs. We present the results of in silico docking and molecular dynamic (MD) simulation studies on selected phytochemical including catechin, epicatechin, gallic acid, gallocatechin, epigallocatechin, epigallocatechin 3-o-gallate, 4-methoxy-nor-securine, nor-securinine, and fisetin with human glycolate oxidase (hGOX) and oxalate oxidase (OxO). Gallic acid, gallocatechin and fisetin showed better docking scores than the rest. In MD simulation analysis, stable interactions of the gallic acid with hGOX and OxO; gallocatechin and fisetin with hGOX were observed. It was found that, gallic acid stably interacts withTYR26, LYS 236, ARG 315, and ASP 291 residues of hGOX. On other hand, gallic acid stably interacs with GLU 58 residue of OxO. Gallocatechin, forms stable interactions with TYR 26, ASP 170, ARG 167 and THR 161 of HGOX. In MD simulations, fisetin stably interacted with TYR 26, TRP110 and ARG 263 as we predicted in molecular docking. None of the interactions was formed during the MD simulation of OxO with gallocatechin and fisetin. Together, these results suggest that gallic acid, gallocatechin and fisetin are the potential candidates for the development of phytochemicals for the management of urolithiasis in humans.
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Affiliation(s)
- Patnam Nageswari
- Institute of Pharmaceutical Technology, Sri Padmavati Mahila Viswavidyalayam, Tirupati, Sri Padmavathi Mahila Viswavidyalayam, India
| | - K Swathi
- Institute of Pharmaceutical Technology, Sri Padmavati Mahila ViswavidyalayamSri Padmavathi Mahila Viswavidyalayam, India
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2
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Thermally stable manganese(III) peroxido complexes with hindered N3 tripodal ligands: Structures and their physicochemical properties. J Inorg Biochem 2021; 225:111597. [PMID: 34547605 PMCID: PMC10019377 DOI: 10.1016/j.jinorgbio.2021.111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 11/20/2022]
Abstract
Mononuclear manganese(III) peroxido complexes are candidates for the reaction intermediates in manganese containing proteins, such as manganese superoxide dismutase (Mn-SOD) etc. In this study, manganese(III) peroxido complexes [Mn(O2)(L3)] and [Mn(O2)(L10)] ligated by anionic N3 type ligands with sterically hindered substituents, hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate (L3-) and hydrotris(3-adamantyl-5-isopropyl-1-pyrazolyl)borate (L10-), respectively, were structurally characterized. These complexes are the first examples of structurally characterized five-coordinate manganese(III) peroxido complexes. Their characteristic ν(OO) and ν(MnO) stretchings were determined by using H218O2 for the first time. Theoretical calculations were performed to obtain further insight into their structural parameters. The decomposed products were obtained as [{MnIII(μ-O)(L3)}2MnIV] and [MnIII(OH){L10(O)}] from [Mn(O2)(L3)] and [Mn(O2)(L10)], respectively.
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3
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Bagha UK, Satpathy JK, Mukherjee G, Sastri CV, de Visser SP. A comprehensive insight into aldehyde deformylation: mechanistic implications from biology and chemistry. Org Biomol Chem 2021; 19:1879-1899. [PMID: 33406196 DOI: 10.1039/d0ob02204g] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aldehyde deformylation is an important reaction in biology, organic chemistry and inorganic chemistry and the process has been widely applied and utilized. For instance, in biology, the aldehyde deformylation reaction has wide differences in biological function, whereby cyanobacteria convert aldehydes into alkanes or alkenes, which are used as natural products for, e.g., defense mechanisms. By contrast, the cytochromes P450 catalyse the biosynthesis of hormones, such as estrogen, through an aldehyde deformylation reaction step. In organic chemistry, the aldehyde deformylation reaction is a common process for replacing functional groups on a molecule, and as such, many different synthetic methods and procedures have been reported that involve an aldehyde deformylation step. In bioinorganic chemistry, a variety of metal(iii)-peroxo complexes have been synthesized as biomimetic models and shown to react efficiently with aldehydes through deformylation reactions. This review paper provides an overview of the various aldehyde deformylation reactions in organic chemistry, biology and biomimetic model systems, and shows a broad range of different chemical reaction mechanisms for this process. Although a nucleophilic attack at the carbonyl centre is the consensus reaction mechanism, several examples of an alternative electrophilic reaction mechanism starting with hydrogen atom abstraction have been reported as well. There is still much to learn and to discover on aldehyde deformylation reactions, as deciphered in this review paper.
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Affiliation(s)
- Umesh Kumar Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | | | - Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and the Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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4
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Chaudhary K, Kumar K, Venkatesu P, Masram DT. Protein immobilization on graphene oxide or reduced graphene oxide surface and their applications: Influence over activity, structural and thermal stability of protein. Adv Colloid Interface Sci 2021; 289:102367. [PMID: 33545443 DOI: 10.1016/j.cis.2021.102367] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/06/2021] [Accepted: 01/20/2021] [Indexed: 12/20/2022]
Abstract
Due to the essential role of biological macromolecules in our daily life; it is important to control the stability and activity of such macromolecules. Therefore, the most promising route for enhancement in stability and activity is immobilizing proteins on different support materials. Furthermore, large surface area and surface functional groups are the important features that are required for a better support system. These features of graphene oxide (GO) and reduced graphene oxide (RGO) makes them ideal support materials for protein immobilization. Studies show the successful formation of GO/RGO-protein complexes with enhancement in structural/thermal stability due to various interactions at the nano-bio interface and their utilization in various functional applications. The present review focuses on protein immobilization using GO/RGO as solid support materials. Moreover, we also emphasized on basic underlying mechanism and interactions (hydrophilic, hydrophobic, electrostatic, local protein-protein, hydrogen bonding and van der Walls) between protein and GO/RGO which influences structural stability and activity of enzymes/proteins. Furthermore, GO/RGO-protein complexes are utilized in various applications such as biosensors, bioimaging and theranostic agent, targeted drug delivery agents, and nanovectors for drug and protein delivery.
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Cruz WT, Bezerra EHS, Ramos MV, Rocha BAM, Medina MC, Demarco D, Carvalho CPS, Oliveira JS, Sousa JS, Souza PFN, Freire VN, da Silva FMS, Freitas CDT. Crystal structure and specific location of a germin-like protein with proteolytic activity from Thevetia peruviana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110590. [PMID: 32771148 DOI: 10.1016/j.plantsci.2020.110590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Peruvianin-I is a cysteine peptidase (EC 3.4.22) purified from Thevetia peruviana. Previous studies have shown that it is the only germin-like protein (GLP) with proteolytic activity described so far. In this work, the X-ray crystal structure of peruvianin-I was determined to a resolution of 2.15 Å (PDB accession number: 6ORM) and its specific location was evaluated by different assays. Its overall structure shows an arrangement composed of a homohexamer (a trimer of dimers) where each monomer exhibits a typical β-barrel fold and two glycosylation sites (Asn55 and Asn144). Analysis of its active site confirmed the absence of essential amino acids for typical oxalate oxidase activity of GLPs. Details of the active site and molecular docking results, using a specific cysteine peptidase inhibitor (iodoacetamide), were used to discuss a plausible mechanism for proteolytic activity of peruvianin-I. Histological analyses showed that T. peruviana has articulated anastomosing laticifers, i.e., rows of cells which merge to form continuous tubes throughout its green organs. Moreover, peruvianin-I was detected exclusively in the latex. Because latex peptidases have been described as defensive molecules against insects, we hypothesize that peruvianin-I contributes to protect T. peruviana plants against herbivory.
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Affiliation(s)
- Wallace T Cruz
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil
| | - Eduardo H S Bezerra
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil
| | - Márcio V Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil
| | - Bruno A M Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil
| | - Maria C Medina
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, CEP 05.508-090, São Paulo, São Paulo, Brazil
| | - Diego Demarco
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, CEP 05.508-090, São Paulo, São Paulo, Brazil
| | - Cristina Paiva S Carvalho
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil
| | - Jefferson S Oliveira
- Departamento de Biomedicina, Universidade Federal do Delta do Parnaíba, Campus Ministro Reis Velloso, Parnaíba, Piauí, Brazil
| | - Jeanlex S Sousa
- Departamento de Física, Universidade Federal de Ceará, Fortaleza, Brazil
| | - Pedro F N Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil
| | - Valder N Freire
- Departamento de Física, Universidade Federal de Ceará, Fortaleza, Brazil
| | | | - Cleverson D T Freitas
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, CEP 60.440-554, Fortaleza, Ceará, Brazil.
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6
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Parham JD, Wijeratne GB, Mayfield JR, Jackson TA. Steric control of dioxygen activation pathways for Mn II complexes supported by pentadentate, amide-containing ligands. Dalton Trans 2019; 48:13034-13045. [PMID: 31406966 PMCID: PMC6733413 DOI: 10.1039/c9dt02682g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dioxygen activation at manganese centers is well known in nature, but synthetic manganese systems capable of utilizing O2 as an oxidant are relatively uncommon. These present investigations probe the dioxygen activation pathways of two mononuclear MnII complexes supported by pentacoordinate amide-containing ligands, [MnII(dpaq)](OTf) and the sterically modified [MnII(dpaq2Me)](OTf). Dioxygen titration experiments demonstrate that [MnII(dpaq)](OTf) reacts with O2 to form [MnIII(OH)(dpaq)](OTf) according to a 4 : 1 Mn : O2 stoichiometry. This stoichiometry is consistent with a pathway involving comproportionation between a MnIV-oxo species and residual MnII complex to form a (μ-oxo)dimanganese(iii,iii) species that is hydrolyzed by water to give the MnIII-hydroxo product. In contrast, the sterically modified [MnII(dpaq2Me)](OTf) complex was found to react with O2 according to a 2 : 1 Mn : O2 stoichiometry. This stoichiometry is indicative of a pathway in which a MnIV-oxo intermediate abstracts a hydrogen atom from solvent instead of undergoing comproportionation with the MnII starting complex. Isotopic labeling experiments, in which the oxygenation of the MnII complexes was carried out in deuterated solvent, supported this change in pathway. The oxygenation of [MnII(dpaq)](OTf) did not result in any deuterium incorporation in the MnIII-hydroxo product, while the oxygenation of [MnII(dpaq2Me)](OTf) in d3-MeCN showed [MnIII(OD)(dpaq2Me)]+ formation. Taken together, these observations highlight the use of steric effects as a means to select which intermediates form along dioxygen activation pathways.
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Affiliation(s)
- Joshua D Parham
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, USA.
| | - Gayan B Wijeratne
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, USA.
| | - Jaycee R Mayfield
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, USA.
| | - Timothy A Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, USA.
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Structural and enzymatic characterization of Peruvianin‑I, the first germin-like protein with proteolytic activity. Int J Biol Macromol 2019; 126:1167-1176. [DOI: 10.1016/j.ijbiomac.2019.01.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/04/2019] [Accepted: 01/05/2019] [Indexed: 11/21/2022]
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8
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Tamura M, Tanabe M, Valkonen JPT, Akita M. Sunagoke Moss ( Racomitrium japonicum) Used for Greening Roofs Is Severely Damaged by Sclerotium delphinii and Protected by a Putative Bacillus amyloliquefaciens Isolate. Front Microbiol 2019; 10:372. [PMID: 30873147 PMCID: PMC6403164 DOI: 10.3389/fmicb.2019.00372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/12/2019] [Indexed: 12/29/2022] Open
Abstract
Mosses are ecologically important plants also used for greening, gardening, and decorative purposes. Knowledge of the microbial flora associated with mosses is expected to be important for control and preservation of global and local environments. However, the moss-associated microbial flora is often poorly known. Moss-associated fungi and bacteria may promote plant growth and pest control, but they may be alternative hosts for pathogens of vascular plants. In this study, the fungus Sclerotinia delphinii was identified for the first time as a pathogen that causes severe damage to Sunagoke moss (Racomitrium japonicum). This moss is used for greening roofs and walls of buildings in urban environments owing to its notable tolerance of environmental stresses. Inoculation with the S. delphinii strain SR1 of the mono- and dicotyledonous seed plants Hordeum vulgare, Brassica rapa var. pekinensis, Lactuca sativa, and Spinacia oleracea, in addition to the liverwort Marchantia polymorpha and the moss Physcomitrella patens, showed that the fungus has a wide host range. Colonization with SR1 progressed more rapidly in non-vascular than in vascular plant species. Studies with P. patens under controlled conditions showed that SR1 secreted a fluid during colonization. Treatment with the secretion induced production of reactive oxygen species in the moss. Endogenous peroxidase partially inhibited SR1 colonization of P. patens. A bacterial isolate, most likely Bacillus amyloliquefaciens, that coexists with R. japonicum was antagonistic to SR1 growth. Taken together, the present results suggest that fungal colonization of mosses may be prevented by a peroxidase secreted by the moss and an antagonistic bacterium coexisting in the moss habitat. The findings suggest that there is potential to apply biological control measures for protection of mosses against fungal pathogens.
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Affiliation(s)
- Mako Tamura
- Department of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Minatsu Tanabe
- Department of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Motomu Akita
- Department of Biotechnological Science, Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
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9
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Production of Oxalate Oxidase from Endophytic Ochrobactrum intermedium CL6. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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10
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Denler MC, Wijeratne GB, Rice DB, Colmer HE, Day VW, Jackson TA. Mn III-Peroxo adduct supported by a new tetradentate ligand shows acid-sensitive aldehyde deformylation reactivity. Dalton Trans 2018; 47:13442-13458. [PMID: 30183042 PMCID: PMC6176719 DOI: 10.1039/c8dt02300j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The new tetradentate L7BQ ligand (L7BQ = 1,4-di(quinoline-8-yl)-1,4-diazepane) has been synthesized and shown to support MnII and MnIII-peroxo complexes. X-ray crystallography of the [MnII(L7BQ)(OTf)2] complex shows a monomeric MnII center with the L7BQ ligand providing four donor nitrogen atoms in the equatorial field, with two triflate ions bound in the axial positions. When this species is treated with H2O2 and Et3N at -40 °C, a MnIII-peroxo adduct, [MnIII(O2)(L7BQ)]+ is formed. The formation of this new intermediate is supported by a variety of spectroscopic techniques, including electronic absorption, Mn K-edge X-ray absorption and electron paramagnetic resonance methods. Evaluation of extended X-ray absorption fine structure data for [MnIII(O2)(L7BQ)]+ resolved Mn-O bond distances of 1.85 Å, which are on the short end of those previously reported for crystallographically characterized MnIII-peroxo adducts. An analysis of the X-ray pre-edge region of [MnIII(O2)(L7BQ)]+ revealed a large pre-edge area of 20.8 units. Time-dependent density functional theory computations indicate that the pre-edge intensity is due to Mn 4p-3d mixing caused by geometric distortions from centrosymmetry induced by both the peroxo and L7BQ ligands. The reactivity of [MnIII(O2)(L7BQ)]+ towards aldehydes was assessed through reaction with cyclohexanecarboxaldehyde and 2-phenylpropionaldehyde. From these experiments, it was determined that [MnIII(O2)(L7BQ)]+ only reacts with aldehydes in the presence of acid. Specifically, the addition of cyclohexanecarboxylic acid to [MnIII(O2)(L7BQ)]+ converts the MnIII-peroxo adduct to a new intermediate that could be responsible for the observed aldehyde deformylation activity. These observations underscore the challenges in identifying the reactive metal species in aldehyde deformylation reactions.
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Affiliation(s)
- Melissa C Denler
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA.
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Jena P, Acharya AN, Mundlapati VR, Dash AC, Biswal HS. Kinetics and mechanistic study of the reduction of
$$\hbox {Mn}^{\mathrm{III}}$$
Mn
III
by oxalate in Salophen scaffold: relevance to oxalate oxidase. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1514-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Chopra G, Chopra N, Kaur D. Quantum chemical study of hydrogen-bonded complexes of serine with water and $$\hbox {H}_{2}\hbox {O}_{2}$$ H 2 O 2. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1506-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Syiemlieh I, Kumar A, Kurbah SD, Lal RA. Synthesis, characterization and structure assessment of mononuclear and binuclear low-spin manganese(II) complexes derived from oxaloyldihydrazones, 1,10-phenanthroline and 2,2′-bipyridine. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Deshpande AR, Pochapsky TC, Ringe D. The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Chem Rev 2017; 117:10474-10501. [PMID: 28731690 DOI: 10.1021/acs.chemrev.7b00117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe2+ or Ni2+) in the active site. The Fe2+-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni2+-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.
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Affiliation(s)
- Aditi R Deshpande
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Thomas C Pochapsky
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Dagmar Ringe
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
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15
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Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes. Essays Biochem 2017; 61:259-270. [PMID: 28487402 DOI: 10.1042/ebc20160070] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/05/2017] [Accepted: 03/17/2017] [Indexed: 02/06/2023]
Abstract
Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX). Spectroscopic measurements and/or computational studies suggest that Mn(III)/Mn(II) are the catalytically active oxidation states of the metal, and the importance of 'second-shell' hydrogen bonding interactions with metal ligands has been demonstrated for a number of examples. The ability of these enzymes to modulate the redox properties of the Mn(III)/Mn(II) couple, thereby allowing them to generate substrate-based radicals, appears essential for accessing diverse chemistries of fundamental importance to organisms in all branches of life.
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Kumar K, Devarabhat P. Chemical Modification of Oxalate Oxidase Produced from Ochrobactrum intermedium CL6 Gave New Insight on its Catalytic Prowess. ACTA ACUST UNITED AC 2016. [DOI: 10.3923/ajb.2017.9.15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes. J Biol Inorg Chem 2016; 22:407-424. [PMID: 27853875 DOI: 10.1007/s00775-016-1402-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
The active sites of metalloenzymes that catalyze O2-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O2 at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O2 reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O2 activation at these three "overlooked" metals.
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18
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Twahir UT, Ozarowski A, Angerhofer A. Redox Cycling, pH Dependence, and Ligand Effects of Mn(III) in Oxalate Decarboxylase from Bacillus subtilis. Biochemistry 2016; 55:6505-6516. [DOI: 10.1021/acs.biochem.6b00891] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Umar T. Twahir
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Alexander Angerhofer
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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Identification of manganese efficiency candidate genes in winter barley (Hordeum vulgare) using genome wide association mapping. BMC Genomics 2016; 17:775. [PMID: 27716061 PMCID: PMC5050567 DOI: 10.1186/s12864-016-3129-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Manganese (Mn) has several essential functions in plants, including a role as cofactor in the oxygen evolving complex (OEC) of photosystem II (PSII). Manganese deficiency is a major plant nutritional disorder in winter cereals resulting in significant yield reductions and winter kill in more severe cases. Among the winter cereals, genotypes of winter barley are known to differ considerably in tolerance to Mn deficiency, but the genes controlling the Mn deficiency trait remains elusive. RESULTS Experiments were conducted using 248 barley varieties, cultivated in six distinct environments prone to induce Mn deficiency. High-throughput phenotyping for Mn deficiency was performed by chlorophyll a (Chl a) fluorescence analysis to quantify the quantum yield efficiency of PSII. High-throughput phenotyping in combination with ICP-OES based multi-element analyses allowed detection of marker-trait associations by genome wide association (GWA) mapping. Several key candidate genes were identified, including PSII subunit proteins, germin like proteins and Mn superoxide dismutase. The putative roles of the encoded proteins in Mn dependent metabolic processes are discussed. CONCLUSIONS Fifty-four candidate genes were identified by Chl a fluorescence phenotyping and association genetics. Tolerance of plants to Mn deficiency, which is referred to as Mn efficiency, appeared to be a complex trait involving many genes. Moreover, the trait appeared to be highly dependent on the environmental conditions in field. This study provides the basis for an improved understanding of the parameters influencing Mn efficiency and is valuable in future plant breeding aiming at producing new varieties with improved tolerance to cultivation in soil prone to induce Mn deficiency.
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Kim S, Park G, Cho EJ, You Y. Coreactant Strategy for the Photoredox Catalytic Generation of Trifluoromethyl Radicals under Low-Energy Photoirradiation. J Org Chem 2016; 81:7072-9. [DOI: 10.1021/acs.joc.6b00966] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Eun Jin Cho
- Department
of Chemistry, Chung-Ang University, Seoul 06974, Republic of Korea
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21
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Preparation, structures and properties of manganese complexes containing amine–(amido or amidato)–phenolato type ligands. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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22
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Zhu W, Easthon LM, Reinhardt LA, Tu C, Cohen SE, Silverman DN, Allen KN, Richards NGJ. Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase. Biochemistry 2016; 55:2163-73. [PMID: 27014926 PMCID: PMC4854488 DOI: 10.1021/acs.biochem.6b00043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Oxalate
decarboxylase (OxDC) catalyzes the conversion of oxalate
into formate and carbon dioxide in a remarkable reaction that requires
manganese and dioxygen. Previous studies have shown that replacing
an active-site loop segment Ser161-Glu162-Asn163-Ser164 in the N-terminal domain of OxDC with
the cognate residues Asp161-Ala162-Ser-163-Asn164 of an evolutionarily related, Mn-dependent
oxalate oxidase gives a chimeric variant (DASN) that exhibits significantly
increased oxidase activity. The mechanistic basis for this change
in activity has now been investigated using membrane inlet mass spectrometry
(MIMS) and isotope effect (IE) measurements. Quantitative analysis
of the reaction stoichiometry as a function of oxalate concentration,
as determined by MIMS, suggests that the increased oxidase activity
of the DASN OxDC variant is associated with only a small fraction
of the enzyme molecules in solution. In addition, IE measurements
show that C–C bond cleavage in the DASN OxDC variant proceeds
via the same mechanism as in the wild-type enzyme, even though the
Glu162 side chain is absent. Thus, replacement of the loop
residues does not modulate the chemistry of the enzyme-bound Mn(II)
ion. Taken together, these results raise the possibility that the
observed oxidase activity of the DASN OxDC variant arises from an
increased level of access of the solvent to the active site during
catalysis, implying that the functional role of Glu162 is
to control loop conformation. A 2.6 Å resolution X-ray crystal
structure of a complex between oxalate and the Co(II)-substituted
ΔE162 OxDC variant, in which Glu162 has been deleted
from the active site loop, reveals the likely mode by which the substrate
coordinates the catalytically active Mn ion prior to C–C bond
cleavage. The “end-on” conformation of oxalate observed
in the structure is consistent with the previously published V/K IE data and provides an empty coordination
site for the dioxygen ligand that is thought to mediate the formation
of Mn(III) for catalysis upon substrate binding.
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Affiliation(s)
- Wen Zhu
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
| | - Lindsey M Easthon
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - Laurie A Reinhardt
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53726, United States
| | - Chingkuang Tu
- Department of Pharmacology & Therapeutics, University of Florida , Gainesville, Florida 32610, United States
| | - Steven E Cohen
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - David N Silverman
- Department of Pharmacology & Therapeutics, University of Florida , Gainesville, Florida 32610, United States
| | - Karen N Allen
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | - Nigel G J Richards
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States
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23
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Scouting new sigma receptor ligands: Synthesis, pharmacological evaluation and molecular modeling of 1,3-dioxolane-based structures and derivatives. Eur J Med Chem 2016; 112:1-19. [DOI: 10.1016/j.ejmech.2016.01.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/13/2016] [Accepted: 01/30/2016] [Indexed: 11/23/2022]
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24
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Colmer HE, Howcroft AW, Jackson TA. Formation, Characterization, and O-O Bond Activation of a Peroxomanganese(III) Complex Supported by a Cross-Clamped Cyclam Ligand. Inorg Chem 2016; 55:2055-69. [PMID: 26908013 DOI: 10.1021/acs.inorgchem.5b02398] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although there have been reports describing the nucleophilic reactivity of peroxomanganese(III) intermediates, as well as their conversion to high-valent oxo-bridged dimers, it remains a challenge to activate peroxomanganese(III) species for conversion to high-valent, mononuclear manganese complexes. Herein, we report the generation, characterization, and activation of a peroxomanganese(III) adduct supported by the cross-clamped, macrocyclic Me2EBC ligand (4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane). This ligand is known to support high-valent, mononuclear Mn(IV) species with well-defined spectroscopic properties, which provides an opportunity to identify mononuclear Mn(IV) products from O-O bond activation of the corresponding Mn(III)-peroxo adduct. The peroxomanganese(III) intermediate, [Mn(III)(O2)(Me2EBC)](+), was prepared at low-temperature by the addition of KO2 to [Mn(II)(Cl)2(Me2EBC)] in CH2Cl2, and this complex was characterized by electronic absorption, electron paramagnetic resonance (EPR), and Mn K-edge X-ray absorption (XAS) spectroscopies. The electronic structure of the [Mn(III)(O2)(Me2EBC)](+) intermediate was examined by density functional theory (DFT) and time-dependent (TD) DFT calculations. Detailed spectroscopic investigations of the decay products of [Mn(III)(O2)(Me2EBC)](+) revealed the presence of mononuclear Mn(III)-hydroxo species or a mixture of mononuclear Mn(IV) and Mn(III)-hydroxo species. The nature of the observed decay products depended on the amount of KO2 used to generate [Mn(III)(O2)(Me2EBC)](+). The Mn(III)-hydroxo product was characterized by Mn K-edge XAS, and shifts in the pre-edge transition energies and intensities relative to [Mn(III)(O2)(Me2EBC)](+) provide a marker for differences in covalency between peroxo and nonperoxo ligands. To the best of our knowledge, this work represents the first observation of a mononuclear Mn(IV) center upon decay of a nonporphyrinoid Mn(III)-peroxo center.
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Affiliation(s)
- Hannah E Colmer
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Anthony W Howcroft
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
| | - Timothy A Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas , Lawrence, Kansas 66045, United States
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25
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Fukuzumi S. Artificial photosynthesis for production of hydrogen peroxide and its fuel cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:604-611. [PMID: 26365231 DOI: 10.1016/j.bbabio.2015.08.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/21/2015] [Accepted: 08/29/2015] [Indexed: 01/14/2023]
Abstract
The reducing power released from photosystem I (PSI) via ferredoxin enables the reduction of NADP(+) to NADPH, which is essential in the Calvin-Benson cycle to make sugars in photosynthesis. Alternatively, PSI can reduce O2 to produce hydrogen peroxide as a fuel. This article describes the artificial version of the photocatalytic production of hydrogen peroxide from water and O2 using solar energy. Hydrogen peroxide is used as a fuel in hydrogen peroxide fuel cells to make electricity. The combination of the photocatalytic H2O2 production from water and O2 using solar energy with one-compartment H2O2 fuel cells provides on-site production and usage of H2O2 as a more useful and promising solar fuel than hydrogen. This article is part of a Special Issue entitled Biodesign for Bioenergetics--The design and engineering of electronc transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, ALCA and SENTAN, Japan Science and Technology Agency (JST), Osaka University, Suita, Osaka 565-0871, Japan; Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea; Faculty of Science and Technology, Meijo University and ALCA and SENTAN, Japan Science and Technology Agency (JST), Tempaku, Nagoya, Aichi 468-8502, Japan.
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26
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Inhibition of ferric ion to oxalate oxidase shed light on the substrate binding site. Biometals 2015; 28:861-8. [DOI: 10.1007/s10534-015-9871-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 06/18/2015] [Indexed: 11/26/2022]
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27
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Kim J, Shin B, Kim H, Lee J, Kang J, Yanagisawa S, Ogura T, Masuda H, Ozawa T, Cho J. Steric Effect on the Nucleophilic Reactivity of Nickel(III) Peroxo Complexes. Inorg Chem 2015; 54:6176-83. [DOI: 10.1021/acs.inorgchem.5b00294] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jalee Kim
- Department of Emerging
Materials Science, DGIST, Daegu 711-873, Korea
| | - Bongki Shin
- Department of Emerging
Materials Science, DGIST, Daegu 711-873, Korea
| | - Hyunjeong Kim
- Department of Emerging
Materials Science, DGIST, Daegu 711-873, Korea
| | - Junhyung Lee
- Department of Emerging
Materials Science, DGIST, Daegu 711-873, Korea
| | - Joongoo Kang
- Department of Emerging
Materials Science, DGIST, Daegu 711-873, Korea
| | - Sachiko Yanagisawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Hideki Masuda
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Tomohiro Ozawa
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Jaeheung Cho
- Department of Emerging
Materials Science, DGIST, Daegu 711-873, Korea
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28
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Sakamoto A, Nishimura T, Miyaki YI, Watanabe S, Takagi H, Izumi S, Shimada H. In vitro and in vivo evidence for oxalate oxidase activity of a germin-like protein from azalea. Biochem Biophys Res Commun 2015; 458:536-542. [PMID: 25677624 DOI: 10.1016/j.bbrc.2015.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/01/2015] [Indexed: 11/16/2022]
Abstract
Germins and germin-like proteins (GLPs) comprise large families of extracellular plant glycoproteins that are structurally similar, yet they have been reported to have distinct biochemical activities: oxalate oxidase and superoxide dismutase activities, respectively. We expressed an azalea GLP (RmGLP2) in cultured cells of tobacco, and determined that the extracellular protein fraction and the recombinant RmGLP2 protein purified from these cells catalyzed the oxidation of oxalate. Notably, this activity is purportedly restricted to germin and has not been demonstrated for a GLP. Although the specific activity of the purified RmGLP2 protein was low compared with that of a previously characterized barley germin/oxalate oxidase, tobacco cells expressing RmGLP2 exhibited significantly reduced oxalate levels. Thus, RmGLP2 represents the first reported GLP with oxalate oxidase activity.
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Affiliation(s)
- Atsushi Sakamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Takashi Nishimura
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Yoh-Ichi Miyaki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Shunsuke Watanabe
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Hiroshi Takagi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Shunsuke Izumi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Hiroshi Shimada
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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29
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Twahir UT, Stedwell CN, Lee CT, Richards NGJ, Polfer NC, Angerhofer A. Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4. Free Radic Biol Med 2015; 80:59-66. [PMID: 25526893 PMCID: PMC4355160 DOI: 10.1016/j.freeradbiomed.2014.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 01/02/2023]
Abstract
This contribution describes the trapping of the hydroperoxyl radical at a pH of 4 during turnover of wild-type oxalate decarboxylase and its T165V mutant using the spin-trap BMPO. Radicals were detected and identified by a combination of EPR and mass spectrometry. Superoxide, or its conjugate acid, the hydroperoxyl radical, is expected as an intermediate in the decarboxylation and oxidation reactions of the oxalate monoanion, both of which are promoted by oxalate decarboxylase. Another intermediate, the carbon dioxide radical anion was also observed. The quantitative yields of superoxide trapping are similar in the wild type and the mutant while it is significantly different for the trapping of the carbon dioxide radical anion. This suggests that the two radicals are released from different sites of the protein.
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Affiliation(s)
- Umar T Twahir
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Cory T Lee
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Nigel G J Richards
- Department of Chemistry & Chemical Biology, Indiana University Purdue University, Indianapolis, Indianapolis, IN 46202, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Alexander Angerhofer
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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30
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Pawlak PL, Panda M, Li J, Banerjee A, Averill DJ, Nikolovski B, Shay BJ, Brennessel WW, Chavez FA. Oxalate Oxidase Model Studies - Substrate Reactivity. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201402835] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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Colmer HE, Geiger RA, Leto DF, Wijeratne GB, Day VW, Jackson TA. Geometric and electronic structure of a peroxomanganese(III) complex supported by a scorpionate ligand. Dalton Trans 2014; 43:17949-63. [PMID: 25312785 PMCID: PMC4237624 DOI: 10.1039/c4dt02483d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A monomeric Mn(II) complex has been prepared with the facially-coordinating Tp(Ph2) ligand, (Tp(Ph2) = hydrotris(3,5-diphenylpyrazol-1-yl)borate). The X-ray crystal structure shows three coordinating solvent molecules resulting in a six-coordinate complex with Mn-ligand bond lengths that are consistent with a high-spin Mn(II) ion. Treatment of this Mn(II) complex with excess KO2 at room temperature resulted in the formation of a Mn(III)-O2 complex that is stable for several days at ambient conditions, allowing for the determination of the X-ray crystal structure of this intermediate. The electronic structure of this peroxomanganese(III) adduct was examined by using electronic absorption, electron paramagnetic resonance (EPR), low-temperature magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. Density functional theory (DFT), time-dependent (TD)-DFT, and multireference ab initio CASSCF/NEVPT2 calculations were used to assign the electronic transitions and further investigate the electronic structure of the peroxomanganese(III) species. The lowest ligand-field transition in the electronic absorption spectrum of the Mn(III)-O2 complex exhibits a blue shift in energy compared to other previously characterized peroxomanganese(III) complexes that results from a large axial bond elongation, reducing the metal-ligand covalency and stabilizing the σ-antibonding Mn dz(2) MO that is the donor MO for this transition.
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Affiliation(s)
- Hannah E Colmer
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA.
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32
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Karmakar T, Balasubramanian S. Elucidating the interaction of H 2 O 2 with polar amino acids – Quantum chemical calculations. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.08.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Čechová D, Martišková A, Padělková Z, Gal’a L, Dlháň L, Valigura D, Valko M, Boča R, Moncol J. Manganese(II) one-dimensional coordination polymers with nitrobenzoato or nitrosalicylato bridges: Syntheses, crystal structures, and magnetic properties. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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34
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Moomaw EW, Uberto R, Tu C. Membrane inlet mass spectrometry reveals that Ceriporiopsis subvermispora bicupin oxalate oxidase is inhibited by nitric oxide. Biochem Biophys Res Commun 2014; 450:750-4. [PMID: 24953692 DOI: 10.1016/j.bbrc.2014.06.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
Abstract
Membrane inlet mass spectrometry (MIMS) uses a semipermeable membrane as an inlet to a mass spectrometer for the measurement of the concentration of small uncharged molecules in solution. We report the use of MIMS to characterize the catalytic properties of oxalate oxidase (E.C. 1.2.3.4) from Ceriporiopsis subvermispora (CsOxOx). Oxalate oxidase is a manganese dependent enzyme that catalyzes the oxygen-dependent oxidation of oxalate to carbon dioxide in a reaction that is coupled with the formation of hydrogen peroxide. CsOxOx is the first bicupin enzyme identified that catalyzes this reaction. The MIMS method of measuring OxOx activity involves continuous, real-time direct detection of oxygen consumption and carbon dioxide production from the ion currents of their respective mass peaks. (13)C2-oxalate was used to allow for accurate detection of (13)CO2 (m/z 45) despite the presence of adventitious (12)CO2. Steady-state kinetic constants determined by MIMS are comparable to those obtained by a continuous spectrophotometric assay in which H2O2 production is coupled to the horseradish peroxidase catalyzed oxidation of 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonic acid). Furthermore, we used MIMS to determine that NO inhibits the activity of the CsOxOx with a KI of 0.58±0.06 μM.
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Affiliation(s)
- Ellen W Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USA.
| | - Richard Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
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35
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Serra IA, Bernardo L, Spadafora A, Faccioli P, Canton C, Mazzuca S. The Citrus clementina putative allergens: from proteomic analysis to structural features. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:8949-8958. [PMID: 23927767 DOI: 10.1021/jf4023367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Several allergens have been identified and characterized in the genus Citrus, which belongs to the germin-like proteins (GPLs), profilins, and non-specific lipid transfer proteins (nsLTPs). In this work, in silico sequence analysis, protein purification, mass spectrometry identification, and the spectral counting method were integrated to identify new putative allergens of Citrus clementina and their expression level in the fruit peel. The in silico analysis revealed fifteen new sequences belonging to GLPs (Cit cl 1), and two more belonging to nsLTPs (Cit cl 3). No other new sequences were found as regards profilins (Cit cl 2). Each putative allergen from fruit peel was obtained using different protein extraction methods, and the protein sequences of the putative allergens were identified by means of LTQ-Orbitrap XL mass spectrometer. The spectral counting strategy revealed that Cit cl 1 had a higher expression level than Cit cl 2 and Cit cl 3. To predict the quaternary structure and deduced function of Cit cl 1, its primary sequence was used as a template to search a homologous protein structure in the RCSB PDB Database, getting high correspondence with the oxalate oxidase protein in barley.
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Affiliation(s)
- Ilia Anna Serra
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende (CS), Italy
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36
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Uberto R, Moomaw EW. Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PLoS One 2013; 8:e74477. [PMID: 24040257 PMCID: PMC3765361 DOI: 10.1371/journal.pone.0074477] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/01/2013] [Indexed: 12/11/2022] Open
Abstract
The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional clustering. Networks based only on cupin domains and networks based on the whole proteins provide complementary information. Domain-clustering supports phylogenetic conclusions that the N- and C-terminal domains of bicupin proteins evolved independently. Interestingly, although many functionally similar enzymatic cupin members bind the same active site metal ion, the structure and sequence clustering does not correlate with the identity of the bound metal. It is anticipated that the application of PSNs to this superfamily will inform experimental work and influence the functional annotation of databases.
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Affiliation(s)
- Richard Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ellen W. Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
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37
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Leto DF, Chattopadhyay S, Day VW, Jackson TA. Reaction landscape of a pentadentate N5-ligated Mn(II) complex with O2˙- and H2O2 includes conversion of a peroxomanganese(III) adduct to a bis(μ-oxo)dimanganese(III,IV) species. Dalton Trans 2013; 42:13014-25. [PMID: 23872704 DOI: 10.1039/c3dt51277k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein we describe the chemical reactivity of the mononuclear [Mn(II)(N4py)(OTf)](OTf) (1) complex with hydrogen peroxide and superoxide. Treatment of 1 with one equivalent superoxide at -40 °C in MeCN formed the peroxomanganese(III) adduct, [Mn(III)(O2)(N4py)](+) (2) in ~30% yield. Complex 2 decayed over time and the formation of the bis(μ-oxo)dimanganese(III,IV) complex, [Mn(III)Mn(IV)(μ-O)2(N4py)2](3+) (3) was observed. When 2 was formed in higher yields (~60%) using excess superoxide, the [Mn(III)(O2)(N4py)](+) species thermally decayed to Mn(II) species and 3 was formed in no greater than 10% yield. Treatment of [Mn(III)(O2)(N4py)](+) with 1 resulted in the formation of 3 in ~90% yield, relative to the concentration of [Mn(III)(O2)(N4py)](+). This reaction mimics the observed chemistry of Mn-ribonucleotide reductase, as it features the conversion of two Mn(II) species to an oxo-bridged Mn(III)Mn(IV) compound using O2(-) as oxidant. Complex 3 was independently prepared through treatment of 1 with H2O2 and base at -40 °C. The geometric and electronic structures of 3 were probed using electronic absorption, electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), variable-temperature, variable-field MCD (VTVH-MCD), and X-ray absorption (XAS) spectroscopies. Complex 3 was structurally characterized by X-ray diffraction (XRD), which revealed the N4py ligand bound in an unusual tetradentate fashion.
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Affiliation(s)
- Domenick F Leto
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA.
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Yamada Y, Nomura A, Miyahigashi T, Ohkubo K, Fukuzumi S. Acetate Induced Enhancement of Photocatalytic Hydrogen Peroxide Production from Oxalic Acid and Dioxygen. J Phys Chem A 2013; 117:3751-60. [DOI: 10.1021/jp312795f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yusuke Yamada
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, ALCA, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871,
Japan
| | - Akifumi Nomura
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, ALCA, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871,
Japan
| | - Takamitsu Miyahigashi
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, ALCA, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871,
Japan
| | - Kei Ohkubo
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, ALCA, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871,
Japan
| | - Shunichi Fukuzumi
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, ALCA, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871,
Japan
- Department of Bioinspired
Science, Ewha Womans University, Seoul
120-750, Korea
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Moomaw EW, Hoffer E, Moussatche P, Salerno JC, Grant M, Immelman B, Uberto R, Ozarowski A, Angerhofer A. Kinetic and spectroscopic studies of bicupin oxalate oxidase and putative active site mutants. PLoS One 2013; 8:e57933. [PMID: 23469254 PMCID: PMC3585803 DOI: 10.1371/journal.pone.0057933] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 01/29/2013] [Indexed: 01/02/2023] Open
Abstract
Ceriporiopsis subvermispora oxalate oxidase (CsOxOx) is the first bicupin enzyme identified that catalyzes manganese-dependent oxidation of oxalate. In previous work, we have shown that the dominant contribution to catalysis comes from the monoprotonated form of oxalate binding to a form of the enzyme in which an active site carboxylic acid residue must be unprotonated. CsOxOx shares greatest sequence homology with bicupin microbial oxalate decarboxylases (OxDC) and the 241-244DASN region of the N-terminal Mn binding domain of CsOxOx is analogous to the lid region of OxDC that has been shown to determine reaction specificity. We have prepared a series of CsOxOx mutants to probe this region and to identify the carboxylate residue implicated in catalysis. The pH profile of the D241A CsOxOx mutant suggests that the protonation state of aspartic acid 241 is mechanistically significant and that catalysis takes place at the N-terminal Mn binding site. The observation that the D241S CsOxOx mutation eliminates Mn binding to both the N- and C- terminal Mn binding sites suggests that both sites must be intact for Mn incorporation into either site. The introduction of a proton donor into the N-terminal Mn binding site (CsOxOx A242E mutant) does not affect reaction specificity. Mutation of conserved arginine residues further support that catalysis takes place at the N-terminal Mn binding site and that both sites must be intact for Mn incorporation into either site.
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Affiliation(s)
- Ellen W Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America.
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Li T, Huo L, Pulley C, Liu A. Decarboxylation mechanisms in biological system. Bioorg Chem 2012; 43:2-14. [PMID: 22534166 DOI: 10.1016/j.bioorg.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/04/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
Abstract
This review examines the mechanisms propelling cofactor-independent, organic cofactor-dependent and metal-dependent decarboxylase chemistry. Decarboxylation, the removal of carbon dioxide from organic acids, is a fundamentally important reaction in biology. Numerous decarboxylase enzymes serve as key components of aerobic and anaerobic carbohydrate metabolism and amino acid conversion. In the past decade, our knowledge of the mechanisms enabling these crucial decarboxylase reactions has continued to expand and inspire. This review focuses on the organic cofactors biotin, flavin, NAD, pyridoxal 5'-phosphate, pyruvoyl, and thiamin pyrophosphate as catalytic centers. Significant attention is also placed on the metal-dependent decarboxylase mechanisms.
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Affiliation(s)
- Tingfeng Li
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
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Zhang Y, Zhang J, Huang X, Zhou X, Wu H, Guo S. Assembly of graphene oxide-enzyme conjugates through hydrophobic interaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:154-159. [PMID: 22038754 DOI: 10.1002/smll.201101695] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Indexed: 05/27/2023]
Abstract
Biochemical and biomedical applications of graphene oxide (GO) critically rely on the interaction of biomolecules with it. It has been previously reported that the biological activity of the GO-enzyme conjugate decreases due to electrostatic interaction between the enzymes and GO. Herein, the immobilization of horseradish peroxidase (HRP) and oxalate oxidase (OxOx) on chemically reduced graphene oxide (CRGO) are reported. The enzymes can be adsorbed onto CRGO directly with a tenfold higher enzyme loading than that on GO, and maximum enzyme loadings reach 1.3 and 12 mg mg(-1) for HRP and OxOx, respectively. Significantly, the more CRGO is reduced, the higher the enzyme loading. The CRGO-HRP conjugates also exhibit higher enzyme activity and stability than GO-HRP. Excellent properties of the CRGO-enzyme conjugates are attributed to hydrophobic interaction between the enzymes and the CRGO. The hydrophobic interaction mode of the CRGO-enzyme conjugates can be applied to other hydrophobic proteins, and thus could dramatically improve the performance of immobilized proteins. The results indicate that CRGO is a potential substrate for efficient enzyme immobilization, and is an ideal candidate as a macromolecule carrier and biosensor.
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Affiliation(s)
- Yan Zhang
- National Key Laboratory of Micro/Nano Fabrication Technology, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Research Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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Yamada Y, Miyahigashi T, Ohkubo K, Fukuzumi S. Photocatalytic hydrogen evolution from carbon-neutral oxalate with 2-phenyl-4-(1-naphthyl)quinolinium ion and metal nanoparticles. Phys Chem Chem Phys 2012; 14:10564-71. [DOI: 10.1039/c2cp41906h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Geiger RA, Leto DF, Chattopadhyay S, Dorlet P, Anxolabéhère-Mallart E, Jackson TA. Geometric and Electronic Structures of Peroxomanganese(III) Complexes Supported by Pentadentate Amino-Pyridine and -Imidazole Ligands. Inorg Chem 2011; 50:10190-203. [DOI: 10.1021/ic201168j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert A. Geiger
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
| | - Domenick F. Leto
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
| | - Swarup Chattopadhyay
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
| | - Pierre Dorlet
- Laboratoire Stress Oxydant et Détoxication, CNRS URA 2096 and CEA/iBiTec-S/SB2SM, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Elodie Anxolabéhère-Mallart
- Laboratoire d’Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, F-75205 Paris Cedex 13, France
| | - Timothy A. Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
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Moussatche P, Angerhofer A, Imaram W, Hoffer E, Uberto K, Brooks C, Bruce C, Sledge D, Richards NGJ, Moomaw EW. Characterization of Ceriporiopsis subvermispora bicupin oxalate oxidase expressed in Pichia pastoris. Arch Biochem Biophys 2011; 509:100-7. [PMID: 21376010 PMCID: PMC3078958 DOI: 10.1016/j.abb.2011.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/23/2011] [Accepted: 02/24/2011] [Indexed: 01/16/2023]
Abstract
Oxalate oxidase (E.C. 1.2.3.4) catalyzes the oxygen-dependent oxidation of oxalate to carbon dioxide in a reaction that is coupled with the formation of hydrogen peroxide. Although there is currently no structural information available for oxalate oxidase from Ceriporiopsis subvermispora (CsOxOx), sequence data and homology modeling indicate that it is the first manganese-containing bicupin enzyme identified that catalyzes this reaction. Interestingly, CsOxOx shares greatest sequence homology with bicupin microbial oxalate decarboxylases (OxDC). We show that CsOxOx activity directly correlates with Mn content and other metals do not appear to be able to support catalysis. EPR spectra indicate that the Mn is present as Mn(II), and are consistent with the coordination environment expected from homology modeling with known X-ray crystal structures of OxDC from Bacillus subtilis. EPR spin-trapping experiments support the existence of an oxalate-derived radical species formed during turnover. Acetate and a number of other small molecule carboxylic acids are competitive inhibitors for oxalate in the CsOxOx catalyzed reaction. The pH dependence of this reaction suggests that the dominant contribution to catalysis comes from the monoprotonated form of oxalate binding to a form of the enzyme in which an active site carboxylic acid residue must be unprotonated.
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Affiliation(s)
- Patricia Moussatche
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Alexander Angerhofer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Witcha Imaram
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Eric Hoffer
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| | - Kelsey Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
| | - Christopher Brooks
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Crystal Bruce
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Daniel Sledge
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
| | - Nigel G. J. Richards
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200
| | - Ellen W. Moomaw
- Department of Chemistry, Gainesville State College, 3820 Mundy Mill Road, Oakwood, GA 30566-3414
- Department of Chemistry and Biochemistry, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144-5588
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Singla M, Mathur P. Oxidation of alcohols using a manganese (II) complex based on a pentakis benzimidazole amide ligand. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 74:536-543. [PMID: 19660981 DOI: 10.1016/j.saa.2009.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 05/13/2009] [Accepted: 07/01/2009] [Indexed: 05/28/2023]
Abstract
A pentakis benzimidazole based penta-amide ligand diethylenetriamine-N,N,N',N',N''-pentakis(2-methyl benzimidazolyl)penta-amide [GBDTPA] has been synthesized and utilized to prepare Mn (II) complexes of general composition [Mn(2)(GBDTPA)X(4)], where X is an exogenous anionic ligand (X = Cl(-), NO(3)(-) and Br(-)). The oxidation of alcohols has been investigated using [Mn(2)(GBDTPA)Cl(4)] as the catalyst and TBHP as an alternate source of oxygen. The respective aldehydic products have been isolated and characterized by (1)H NMR.
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Affiliation(s)
- Manisha Singla
- Department of Chemistry, Delhi University, Delhi 110007, India.
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Groni S, Hureau C, Guillot R, Blondin G, Blain G, Anxolabéhère-Mallart E. Characterizations of chloro and aqua Mn(II) mononuclear complexes with amino-pyridine ligands. Comparison of their electrochemical properties with those of Fe(II) counterparts. Inorg Chem 2009; 47:11783-97. [PMID: 19007154 DOI: 10.1021/ic8015172] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution behavior of mononuclear Mn(II) complexes, namely, [(L(5)(2))MnCl](+) (1), [(L(5)(3))MnCl](+) (2), [(L(5)(2))Mn(OH(2))](2+) (3), [(L(5)(3))Mn(OH(2))](2+) (4), and [(L(6)(2))Mn(OH(2))](2+) (6), with L(5)(2/3) and L(6)(2) being penta- and hexadentate amino-pyridine ligands, is investigated in MeCN using EPR, UV-vis spectroscopies, and electrochemistry. The addition of one chloride ion onto species 6 leads to the formation of the complex [(L(6)(2))MnCl](+) (5) that is X-ray characterized. EPR and UV-vis spectra indicate that structure and redox states of complexes 1-6 are maintained in MeCN solution. Chloro complexes 1, 2, and 5 show reversible Mn(II)/Mn(III) process at 0.95, 1.02, and 1.05 V vs SCE, respectively, whereas solvated complexes 3, 4, and 6 show an irreversible anodic peak around 1.5 V vs SCE. Electrochemical oxidations of 1 and 5 leading to the Mn(III) complexes [(L(5)(2))MnCl](2+) (7) and [(L(6)(2))MnCl](2+) (8) are successful. The UV-vis signatures of 7 and 8 show features associated with chloro to Mn(III) LMCT and d-d transitions. The X-ray characterization of the heptacoordinated Mn(III) species 8 is also reported. The analogous electrochemical generation of the corresponding Mn(III) complex was not possible when starting from 2. The new mixed-valence di-mu-oxo [(L(5)(2))Mn(muO)(2)Mn(L(5)(2))](3+) species (9) can be obtained from 3, whereas the sister [(L(5)(3))Mn(muO)(2)Mn(L(5)(3))](3+) species can not be generated from 4. Such different responses upon oxidations are commented on with the help of comparison with related Mn/Fe complexes and are discussed in relation with the size of the metallacycle formed between the diamino bridge and the metal center (5- vs 6-membered). Lastly, a comparison between redox potentials of the studied Mn(II) complexes with those of Fe(II) analogues is drawn and completed with previously reported data on Mn/Fe isostructural systems. This gives us the opportunity to get some indirect insights into the metal specificity encountered in enzymes among which superoxide dismutase is the archetypal model.
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Affiliation(s)
- Sihem Groni
- Equipe de Chimie Inorganique, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Sud 11, UMR 8182 CNRS, Orsay F-91405, France
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Agarwal G, Rajavel M, Gopal B, Srinivasan N. Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PLoS One 2009; 4:e5736. [PMID: 19478949 PMCID: PMC2684688 DOI: 10.1371/journal.pone.0005736] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 04/27/2009] [Indexed: 01/22/2023] Open
Abstract
Background The members of cupin superfamily exhibit large variations in their sequences, functions, organization of domains, quaternary associations and the nature of bound metal ion, despite having a conserved β-barrel structural scaffold. Here, an attempt has been made to understand structure-function relationships among the members of this diverse superfamily and identify the principles governing functional diversity. The cupin superfamily also contains proteins for which the structures are available through world-wide structural genomics initiatives but characterized as “hypothetical”. We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function. Methodology/Principal Findings A 3-D structure-based phylogenetic approach was undertaken. Interestingly, a dendrogram generated solely on the basis of structural dissimilarity measure at the level of domain folds was found to cluster functionally similar members. This clustering also reflects an independent evolution of the two domains in bicupins. Close examination of structural superposition of members across various functional clusters reveals structural variations in regions that not only form the active site pocket but are also involved in interaction with another domain in the same polypeptide or in the oligomer. Conclusions/Significance Structure-based phylogeny of cupins can influence identification of functions of proteins of yet unknown function with cupin fold. This approach can be extended to other proteins with a common fold that show high evolutionary divergence. This approach is expected to have an influence on the function annotation in structural genomics initiatives.
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Affiliation(s)
- Garima Agarwal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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48
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Biochemical characterization and mutational analysis of the mononuclear non-haem Fe2+ site in Dke1, a cupin-type dioxygenase from Acinetobacter johnsonii. Biochem J 2009; 418:403-11. [PMID: 18973472 DOI: 10.1042/bj20081161] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
beta-diketone-cleaving enzyme Dke1 is a homotetrameric Fe2+-dependent dioxygenase from Acinetobacter johnsonii. The Dke1protomer adopts a single-domain beta-barrel fold characteristic of the cupin superfamily of proteins and features a mononuclear non-haem Fe2+ centre where a triad of histidine residues, His-62, His-64 and His-104, co-ordinate the catalytic metal. To provide structure-function relationships for the peculiar metal site of Dke1 in relation to the more widespread 2-His-1-Glu/Asp binding site for non-haem Fe2+,we replaced each histidine residue individually with glutamate and asparagine and compared binding of Fe2+ and four non-native catalytically inactive metals with purified apo-forms of wild-type and mutant enzymes. Results from anaerobic equilibrium microdialysis (Fe2+) and fluorescence titration (Fe2+, Cu2+, Ni2+, Mn2+ and Zn2+) experiments revealed the presence of two broadly specific metal-binding sites in native Dke1 that bind Fe2+ with a dissociation constant (Kd) of 5 microM (site I) and approximately 0.3 mM (site II). Each mutation, except for the substitution of asparagine for His-104, disrupted binding of Fe2+, but not that of the other bivalent metal ions, at site I,while leaving metal binding at site II largely unaffected. Dke1 mutants harbouring glutamate substitutions were completely inactive and not functionally complemented by external Fe2+.The Fe2+ catalytic centre activity (kcat) of mutants with asparagine substitution of His-62 and His-104 was decreased 140- and 220-fold respectively, compared with the kcat value of 8.5 s(-1) for the wild-type enzyme in the reaction with pentane-2,4-dione.The H64N mutant was not catalytically competent, except in the presence of external Fe2+ (1 mM) which elicited about 1/1000 of wild-type activity. Therefore co-ordination of Fe2+ by Dke1 requires an uncharged metallocentre, and three histidine ligands are needed for the assembly of a fully functional catalytic site. Oxidative inactivation of Dke1 was shown to involve conversion of enzyme-bound Fe2+ into Fe3+, which is then released from the metal centre.
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Joosten RP, Womack T, Vriend G, Bricogne G. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:176-85. [PMID: 19171973 PMCID: PMC2631631 DOI: 10.1107/s0907444908037591] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 11/12/2008] [Indexed: 11/17/2022]
Abstract
The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data.
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Affiliation(s)
- Robbie P. Joosten
- CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Thomas Womack
- Global Phasing, Sheraton House, Castle Park, Cambridge CB3 0AX, England
| | - Gert Vriend
- CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Gérard Bricogne
- Global Phasing, Sheraton House, Castle Park, Cambridge CB3 0AX, England
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Scarpellini M, Gätjens J, Martin OJ, Kampf JW, Sherman SE, Pecoraro VL. Modeling the resting state of oxalate oxidase and oxalate decarboxylase enzymes. Inorg Chem 2008; 47:3584-93. [PMID: 18399627 DOI: 10.1021/ic701953g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In view of the biological and commercial interest in models for Oxalate Decarboxylases (OxDC) and Oxalate Oxidases (OxOx), we have synthesized and characterized three new Mn (II) complexes ( 1- 3) employing N3O-donor amino-carboxylate ligands (TCMA, 1,4,7-triazacyclononane- N-acetic acid; K (i) Pr 2TCMA, potassium 1,4-diisopropyl-1,4,7-triazacyclononane- N-acetate; and KBPZG, potassium N,N-bis(3,5-dimethylpyrazolyl methyl)glycinate). These complexes were characterized by several techniques including X-ray crystallographic analysis, X-band electron paramagnetic resonance (EPR), electrospray ionization mass spectrometry (ESI-MS), and cyclic voltammetry. The crystal structures of 1 and 3 revealed that both form infinite polymeric chains of Mn (II) complexes linked by the pendant carboxylate arms of the TCMA (-) and the BPZG (-) ligands in a syn-antipattern. Complex 2 crystallizes as a mononuclear Mn (II) cation, six-coordinate in a distorted octahedral geometry. Although complexes 1 and 3 crystallize as polymeric chains, all compounds present the same N3O-donor set atoms around the metal center as observed in the crystallographically characterized OxDC and OxOx. Moreover, complex 2 also contains two water molecules coordinated to the Mn center as observed in the active site of OxDC and OxOx. ESI-MS spectrometry, combined with EPR, were useful techniques to establish that complexes 1- 3 are present as mononuclear Mn (II) species in solution. Finally, complexes 1- 3 are able to model the resting state active sites, with special attention focused on complex 2 which provides the first exact first coordination sphere ligand structural model for the resting states of both OxDC and OxOx.
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Affiliation(s)
- Marciela Scarpellini
- Willard H. Dow Laboratories, Department of Chemistry, University of Michigan, 930 North University, Ann Arbor, MI 48109, USA
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