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Igwe CL, Müller DF, Gisperg F, Pauk JN, Kierein M, Elshazly M, Klausser R, Kopp J, Spadiut O, Přáda Brichtová E. Online monitoring of protein refolding in inclusion body processing using intrinsic fluorescence. Anal Bioanal Chem 2024; 416:3019-3032. [PMID: 38573344 PMCID: PMC11045631 DOI: 10.1007/s00216-024-05249-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Inclusion bodies (IBs) are protein aggregates formed as a result of overexpression of recombinant protein in E. coli. The formation of IBs is a valuable strategy of recombinant protein production despite the need for additional processing steps, i.e., isolation, solubilization and refolding. Industrial process development of protein refolding is a labor-intensive task based largely on empirical approaches rather than knowledge-driven strategies. A prerequisite for knowledge-driven process development is a reliable monitoring strategy. This work explores the potential of intrinsic tryptophan and tyrosine fluorescence for real-time and in situ monitoring of protein refolding. In contrast to commonly established process analytical technology (PAT), this technique showed high sensitivity with reproducible measurements for protein concentrations down to 0.01 g L- 1 . The change of protein conformation during refolding is reflected as a shift in the position of the maxima of the tryptophan and tyrosine fluorescence spectra as well as change in the signal intensity. The shift in the peak position, expressed as average emission wavelength of a spectrum, was correlated to the amount of folding intermediates whereas the intensity integral correlates to the extent of aggregation. These correlations were implemented as an observation function into a mechanistic model. The versatility and transferability of the technique were demonstrated on the refolding of three different proteins with varying structural complexity. The technique was also successfully applied to detect the effect of additives and process mode on the refolding process efficiency. Thus, the methodology presented poses a generic and reliable PAT tool enabling real-time process monitoring of protein refolding.
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Affiliation(s)
- Chika Linda Igwe
- Competence Center CHASE GmbH, Hafenstraße 47-51, Linz, 4020, Austria
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Don Fabian Müller
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Florian Gisperg
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
- Christian Doppler Laboratory for Inclusion Body Processing 4.0, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Jan Niklas Pauk
- Competence Center CHASE GmbH, Hafenstraße 47-51, Linz, 4020, Austria
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Matthias Kierein
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Mohamed Elshazly
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
- Christian Doppler Laboratory for Inclusion Body Processing 4.0, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Robert Klausser
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
- Christian Doppler Laboratory for Inclusion Body Processing 4.0, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Julian Kopp
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
- Christian Doppler Laboratory for Inclusion Body Processing 4.0, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
- Christian Doppler Laboratory for Inclusion Body Processing 4.0, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria
| | - Eva Přáda Brichtová
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria.
- Christian Doppler Laboratory for Inclusion Body Processing 4.0, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstraße 1A, Vienna, 1060, Austria.
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2
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Swoboda A, Zwölfer S, Duhović Z, Bürgler M, Ebner K, Glieder A, Kroutil W. Multistep Biooxidation of 5-(Hydroxymethyl)furfural to 2,5-Furandicarboxylic Acid with H 2O 2 by Unspecific Peroxygenases. CHEMSUSCHEM 2024:e202400156. [PMID: 38568785 DOI: 10.1002/cssc.202400156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/05/2024]
Abstract
5-(Hydroxymethyl)furfural (HMF) is a key platform chemical derived from renewable biomass sources, holding great potential as starting material for the synthesis of valuable compounds, thereby replacing petrochemical-derived counterparts. Among these valorised compounds, 2,5-furandicarboxylic acid (FDCA) has emerged as a versatile building block. Here we demonstrate the biocatalytic synthesis of FDCA from HMF via a one-pot three-step oxidative cascade performed via two operative steps under mild reaction conditions employing two unspecific peroxygenases (UPOs) using hydrogen peroxide as the only oxidant. The challenge of HMF oxidation by UPOs is the chemoselectivity of the first step, as one of the two possible oxidation products is only a poor substrate for further oxidation. The unspecific peroxygenase from Marasmius oreades (MorUPO) was found to oxidize 100 mM of HMF to 5-formyl-2-furoic acid (FFCA) with 95 % chemoselectivity. In the sequential one-pot cascade employing MorUPO (TON up to 13535) and the UPO from Agrocybe aegerita (AaeUPO, TON up to 7079), 100 mM of HMF were oxidized to FDCA reaching up to 99 % conversion and yielding 861 mg isolated pure crystalline FDCA, presenting the first example of a gram scale biocatalytic synthesis of FDCA involving UPOs.
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Affiliation(s)
- Alexander Swoboda
- Austrian Center of Industrial Biotechnology (ACIB GmbH), c/o Department of Chemistry, University of Graz, Heinrichstraße 28, 8010, Graz, Austria
| | - Silvie Zwölfer
- Department of Chemistry, University of Graz, Heinrichstraße 28, 8010, Graz, Austria
| | - Zerina Duhović
- Austrian Center of Industrial Biotechnology (ACIB GmbH), c/o Department of Chemistry, University of Graz, Heinrichstraße 28, 8010, Graz, Austria
| | - Moritz Bürgler
- Bisy GmbH, Wünschendorf 292, 8200, Hofstätten an der Raab, Austria
| | - Katharina Ebner
- Bisy GmbH, Wünschendorf 292, 8200, Hofstätten an der Raab, Austria
| | - Anton Glieder
- Bisy GmbH, Wünschendorf 292, 8200, Hofstätten an der Raab, Austria
| | - Wolfgang Kroutil
- Austrian Center of Industrial Biotechnology (ACIB GmbH), c/o Department of Chemistry, University of Graz, Heinrichstraße 28, 8010, Graz, Austria
- Department of Chemistry, University of Graz, Heinrichstraße 28, 8010, Graz, Austria
- BioTechMed Graz, 8010, Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010, Graz, Austria
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3
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Alpdağtaş S, Jankowski N, Urlacher VB, Koschorreck K. Identification of redox activators for continuous reactivation of glyoxal oxidase from Trametes versicolor in a two-enzyme reaction cascade. Sci Rep 2024; 14:5932. [PMID: 38467766 PMCID: PMC10928124 DOI: 10.1038/s41598-024-56429-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
Glyoxal oxidases, belonging to the group of copper radical oxidases (CROs), oxidize aldehydes to carboxylic acids, while reducing O2 to H2O2. Their activity on furan derivatives like 5-hydroxymethylfurfural (HMF) makes these enzymes promising biocatalysts for the environmentally friendly synthesis of the bioplastics precursor 2,5-furandicarboxylic acid (FDCA). However, glyoxal oxidases suffer from inactivation, which requires the identification of suitable redox activators for efficient substrate conversion. Furthermore, only a few glyoxal oxidases have been expressed and characterized so far. Here, we report on a new glyoxal oxidase from Trametes versicolor (TvGLOX) that was expressed at high levels in Pichia pastoris (reclassified as Komagataella phaffii). TvGLOX was found to catalyze the oxidation of aldehyde groups in glyoxylic acid, methyl glyoxal, HMF, 2,5-diformylfuran (DFF) and 5-formyl-2-furancarboxylic acid (FFCA), but barely accepted alcohol groups as in 5-hydroxymethyl-2-furancarboxylic acid (HMFCA), preventing formation of FDCA from HMF. Various redox activators were tested for TvGLOX reactivation during catalyzed reactions. Among them, a combination of horseradish peroxidase and its substrate 2,2'-azino-di-(3-ethylbenzthiazoline sulfonic acid) (ABTS) most efficiently reactivated TvGLOX. Through continuous reactivation of TvGLOX in a two-enzyme system employing a recombinant Moesziomyces antarcticus aryl-alcohol oxidase (MaAAO) almost complete conversion of 8 mM HMF to FDCA was achieved within 24 h.
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Affiliation(s)
- Saadet Alpdağtaş
- Department of Biology, Van Yuzuncu Yil University, Van, 65080, Turkey
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Nina Jankowski
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Katja Koschorreck
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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4
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Copper radical oxidases: galactose oxidase, glyoxal oxidase, and beyond! Essays Biochem 2022; 67:597-613. [PMID: 36562172 DOI: 10.1042/ebc20220124] [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: 10/14/2022] [Revised: 10/14/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
The copper radical oxidases (CROs) are an evolutionary and functionally diverse group of enzymes established by the historically significant galactose 6-oxidase and glyoxal oxidase from fungi. Inducted in 2013, CROs now constitute Auxiliary Activity Family 5 (AA5) in the Carbohydrate-Active Enzymes (CAZy) classification. CROs catalyse the two-electron oxidation of their substrates using oxygen as the final electron acceptor and are particularly distinguished by a cross-linked tyrosine-cysteine co-factor that is integral to radical stabilization. Recently, there has been a significant increase in the biochemically and structurally characterized CROs, which has revealed an expanded natural diversity of catalytic activities in the family. This review provides a brief historical introduction to CRO biochemistry and structural biology as a foundation for an update on current advances in CRO enzymology, biotechnology, and biology across kingdoms of life.
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5
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Duke JA, Paschall AV, Glushka J, Lees A, Moremen KW, Avci FY. Harnessing galactose oxidase in the development of a chemoenzymatic platform for glycoconjugate vaccine design. J Biol Chem 2022; 298:101453. [PMID: 34838818 PMCID: PMC8689215 DOI: 10.1016/j.jbc.2021.101453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 12/02/2022] Open
Abstract
In the preparation of commercial conjugate vaccines, capsular polysaccharides (CPSs) must undergo chemical modification to generate the reactive groups necessary for covalent attachment to a protein carrier. One of the most common approaches employed for this derivatization is sodium periodate (NaIO4) oxidation of vicinal diols found within CPS structures. This procedure is largely random and structurally damaging, potentially resulting in significant changes in the CPS structure and therefore its antigenicity. Additionally, periodate activation of CPS often gives rise to heterogeneous conjugate vaccine products with variable efficacy. Here, we explore the use of an alternative agent, galactose oxidase (GOase) isolated from Fusarium sp. in a chemoenzymatic approach to generate a conjugate vaccine against Streptococcus pneumoniae. Using a colorimetric assay and NMR spectroscopy, we found that GOase generated aldehyde motifs on the CPS of S. pneumoniae serotype 14 (Pn14p) in a site-specific and reversible fashion. Direct comparison of Pn14p derivatized by either GOase or NaIO4 illustrates the functionally deleterious role chemical oxidation can have on CPS structures. Immunization with the conjugate synthesized using GOase provided a markedly improved humoral response over the traditional periodate-oxidized group. Further, functional protection was validated in vitro by measure of opsonophagocytic killing and in vivo through a lethality challenge in mice. Overall, this work introduces a strategy for glycoconjugate development that overcomes limitations previously known to play a role in the current approach of vaccine design.
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Affiliation(s)
- Jeremy A Duke
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Molecular Medicine, University of Georgia, Athens, Georgia, USA
| | - Amy V Paschall
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Molecular Medicine, University of Georgia, Athens, Georgia, USA
| | - John Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Andrew Lees
- Fina Biosolutions, LLC, Rockville, Maryland, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Fikri Y Avci
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA; Center for Molecular Medicine, University of Georgia, Athens, Georgia, USA.
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6
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Figueiredo C, De Lacey AL, Pita M. Electrochemical studies of galactose oxidase. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | | | - Marcos Pita
- Instituto de Catálisis y Petroleoquímica CSIC Madrid Spain
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7
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Vuong TV, Master ER. Enzymatic upgrading of heteroxylans for added-value chemicals and polymers. Curr Opin Biotechnol 2021; 73:51-60. [PMID: 34311175 DOI: 10.1016/j.copbio.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/27/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023]
Abstract
Xylan is one of the most abundant, natural polysaccharides, and much recent interest focuses on upgrading heteroxylan to make use of its unique structures and chemistries. Significant progress has been made in the discovery and application of novel enzymes for debranching and modifying heteroxylans. Debranching enzymes include acetylxylan esterases, α-l-arabinofuranosidases and α-dglucuronidases that release side groups from the xylan backbone to recover both biochemicals and less substituted xylans for polymer applications in food packaging or drug delivery systems. Besides esterases and hydrolases, many oxidoreductases including carbohydrate oxidases, lytic polysaccharide monooxygenases, laccases and peroxidases have been also applied to alter different types of xylans for improved physical and chemical properties. This review will highlight the recent discovery and application of enzymes for upgrading xylans for use as added-value chemicals and in functional polymers.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.
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8
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Kunert R, Philouze C, Berthiol F, Jarjayes O, Storr T, Thomas F. Distorted copper(ii) radicals with sterically hindered salens: electronic structure and aerobic oxidation of alcohols. Dalton Trans 2020; 49:12990-13002. [PMID: 32909589 DOI: 10.1039/d0dt02524k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sterically hindered salen ligands featuring biphenyl and tetramethyl putrescine linkers were synthesized and chelated to copper. The resulting complexes CuLbp,tBu, CuLbp,OMe, CuLpu,tBu and CuLpu,OMe were structurally characterized, showing a significanty tetrahedrally distorted metal center. The complexes show two reversible oxidation waves in the range 0.2 to 0.8 V vs. Fc+/Fc. A further reduction wave is detected in the range -1.4 to -1.7 V vs. Fc+/Fc. It is reversible for CuLbp,tBu and CuLbp,OMe and assigned to the CuII/CuI redox couple. One-electron oxidation of CuLbp,OMe, CuLpu,tBu and CuLpu,OMe was performed chemically and electrochemically. It is accompanied by a quenching of the EPR resonances. Phenoxyl radical formation was established by X-Ray diffraction on the cations [CuLbp,OMe]+ and [CuLpu,OMe]+, whereby the coordination sphere is elongated upon oxidation with quinoidal distributions of bond distances. The cations exhibit a NIR band of moderate intensity in their optical spectrum, supporting their classification as class II mixed-valent radical species according to the Robin Day classification. The proposed electronic structures are supported by DFT calculations. The cations [CuLbp,OMe]+, [CuLpu,tBu]+ and [CuLpu,OMe]+ were active towards aerobic oxidation of the unactivated alcohol 2-phenylethanol, with TON numbers up to 58 within 3 h.
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Affiliation(s)
- R Kunert
- Univ. Grenoble Alpes, CNRS, DCM, 38000 Grenoble, France.
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9
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Xu S, Sun F, Wu R. A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation. Anal Chem 2020; 92:9807-9814. [PMID: 32574038 PMCID: PMC7437014 DOI: 10.1021/acs.analchem.0c01284] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
O-GlcNAcylation has gradually been recognized as a critically important protein post-translational modification in mammalian cells. Besides regulation of gene expression, its crosstalk with protein phosphorylation is vital for cell signaling. Despite its importance, comprehensive analysis of O-GlcNAcylation is extraordinarily challenging due to the low abundances of many O-GlcNAcylated proteins and the complexity of biological samples. Here, we developed a novel chemoenzymatic method based on a wild-type galactosyltransferase and uridine diphosphate galactose (UDP-Gal) for global and site-specific analysis of protein O-GlcNAcylation. This method integrates enzymatic reactions and hydrazide chemistry to enrich O-GlcNAcylated peptides. All reagents used are more easily accessible and cost-effective as compared to the engineered enzyme and click chemistry reagents. Biological triplicate experiments were performed to validate the effectiveness and the reproducibility of this method, and the results are comparable with the previous chemoenzymatic method using the engineered enzyme and click chemistry. Moreover, because of the promiscuity of the galactosyltransferase, 18 unique O-glucosylated peptides were identified on the EGF domain from nine proteins. Considering that effective and approachable methods are critical to advance glycoscience research, the current method without any sample restrictions can be widely applied for global analysis of protein O-GlcNAcylation in different samples.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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10
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Characterization of a New Glyoxal Oxidase from the Thermophilic Fungus Myceliophthora thermophila M77: Hydrogen Peroxide Production Retained in 5-Hydroxymethylfurfural Oxidation. Catalysts 2018. [DOI: 10.3390/catal8100476] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Myceliophthora thermophyla is a thermophilic industrially relevant fungus that secretes an assortment of hydrolytic and oxidative enzymes for lignocellulose degradation. Among them is glyoxal oxidase (MtGLOx), an extracellular oxidoreductase that oxidizes several aldehydes and α-hydroxy carbonyl substrates coupled to the reduction of O2 to H2O2. This copper metalloprotein belongs to a class of enzymes called radical copper oxidases (CRO) and to the “auxiliary activities” subfamily AA5_1 that is based on the Carbohydrate-Active enZYmes (CAZy) database. Only a few members of this family have been characterized to date. Here, we report the recombinant production, characterization, and structure-function analysis of MtGLOx. Electron Paramagnetic Resonance (EPR) spectroscopy confirmed MtGLOx to be a radical-coupled copper complex and small angle X-ray scattering (SAXS) revealed an extended spatial arrangement of the catalytic and four N-terminal WSC domains. Furthermore, we demonstrate that methylglyoxal and 5-hydroxymethylfurfural (HMF), a fermentation inhibitor, are substrates for the enzyme.
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Enzymatic Preparation of 2,5-Furandicarboxylic Acid (FDCA)-A Substitute of Terephthalic Acid-By the Joined Action of Three Fungal Enzymes. Microorganisms 2018; 6:microorganisms6010005. [PMID: 29315223 PMCID: PMC5874619 DOI: 10.3390/microorganisms6010005] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/05/2018] [Accepted: 01/06/2018] [Indexed: 12/03/2022] Open
Abstract
Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different reaction steps was evaluated and apparent kinetic data (Michaelis-Menten constants, turnover numbers, specific constants) were calculated for different enzyme-substrate ratios and enzyme combinations. Finally, the target product, 2,5-furandicarboxylic acid (FDCA), was prepared in a multi-enzyme cascade reaction combining three fungal oxidoreductases at micro-scale. Furthermore, an oxidase-like reaction is proposed for heme-containing peroxidases, such as UPO, horseradish peroxidase, or catalase, causing the conversion of 5-formyl-2-furancarboxylic acid into FDCA in the absence of exogenous hydrogen peroxide.
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12
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Carro J, Ferreira P, Rodríguez L, Prieto A, Serrano A, Balcells B, Ardá A, Jiménez‐Barbero J, Gutiérrez A, Ullrich R, Hofrichter M, Martínez AT. 5‐hydroxymethylfurfural conversion by fungal aryl‐alcohol oxidase and unspecific peroxygenase. FEBS J 2015; 282:3218-29. [DOI: 10.1111/febs.13177] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/05/2014] [Accepted: 12/10/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Juan Carro
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Patricia Ferreira
- Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos Zaragoza Spain
| | - Leonor Rodríguez
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Ana Serrano
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Beatriz Balcells
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Ana Ardá
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Jesús Jiménez‐Barbero
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla Consejo Superior de Investigaciones Científicas Seville Spain
| | - René Ullrich
- Department of Bio‐ and Environmental Sciences International Institute of Zittau Germany
| | - Martin Hofrichter
- Department of Bio‐ and Environmental Sciences International Institute of Zittau Germany
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas Consejo Superior de Investigaciones Científicas Madrid Spain
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13
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Expression, purification, and characterization of galactose oxidase of Fusarium sambucinum in E. coli. Protein Expr Purif 2014; 108:73-79. [PMID: 25543085 PMCID: PMC4370742 DOI: 10.1016/j.pep.2014.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/14/2014] [Accepted: 12/16/2014] [Indexed: 11/01/2022]
Abstract
A gene encoding a galactose oxidase (GalOx) was isolated from Fusarium sambucinum cultures and overexpressed in Escherichia coli yielding 4.4mg enzyme per L of growth culture with a specific activity of 159Umg(-1). By adding a C-terminal His-tag the enzyme could be easily purified with a single affinity chromatography step with high recovery rate (90%). The enzyme showed a single band on SDS-PAGE with an apparent molecular mass of 68.5kDa. The pH optimum for the oxidation of galactose was in the range of pH 6-7.5. Optimum temperature for the enzyme activity was 35°C, with a half-life of 11.2min, 5.3min, and 2.7min for incubation at 40°C, 50°C, and 60°C, respectively. From all tested substrates, the highest relative activity was found for 1-methyl-β-galactopyranoside (226Umg(-1)) and the highest catalytic efficiency (kcat/Km) for melibiose (2700mM(-1)s(-1)). The enzyme was highly specific for molecular oxygen as an electron acceptor, and showed no appreciable activity with a range of alternative acceptors investigated. Different chemicals were tested for their effect on GalOx activity. The activity was significantly reduced by EDTA, NaN3, and KCN.
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14
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Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes. Fungal Genet Biol 2014; 72:124-130. [DOI: 10.1016/j.fgb.2014.05.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 11/20/2022]
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Paukner R, Staudigl P, Choosri W, Sygmund C, Halada P, Haltrich D, Leitner C. Galactose oxidase from Fusarium oxysporum--expression in E. coli and P. pastoris and biochemical characterization. PLoS One 2014; 9:e100116. [PMID: 24967652 PMCID: PMC4072685 DOI: 10.1371/journal.pone.0100116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 05/22/2014] [Indexed: 11/20/2022] Open
Abstract
A gene coding for galactose 6-oxidase from Fusarium oxysporum G12 was cloned together with its native preprosequence and a C-terminal His-tag, and successfully expressed both in Escherichia coli and Pichia pastoris. The enzyme was subsequently purified and characterized. Among all tested substrates, the highest catalytic efficiency (kcat/Km) was found with 1-methyl-β-D-galactopyranoside (2.2 mM−1 s−1). The Michaelis constant (Km) for D-galactose was determined to be 47 mM. Optimal pH and temperature for the enzyme activity were 7.0 and 40°C, respectively, and the enzyme was thermoinactivated at temperatures above 50°C. GalOx contains a unique metalloradical complex consisting of a copper atom and a tyrosine residue covalently attached to the sulphur of a cysteine. The correct formation of this thioether bond during the heterologous expression in E. coli and P. pastoris could be unequivocally confirmed by MALDI mass spectrometry, which offers a convenient alternative to prove this Tyr-Cys crosslink, which is essential for the catalytic activity of GalOx.
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Affiliation(s)
- Regina Paukner
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Petra Staudigl
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Withu Choosri
- Department of Food Technology, Ramkhamhaeng University, Bangkok, Thailand
| | - Christoph Sygmund
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Petr Halada
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dietmar Haltrich
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Leitner
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- * E-mail:
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16
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Kochem A, Gellon G, Leconte N, Baptiste B, Philouze C, Jarjayes O, Orio M, Thomas F. Stable anilinyl radicals coordinated to nickel: X-ray crystal structure and characterization. Chemistry 2013; 19:16707-21. [PMID: 24281814 DOI: 10.1002/chem.201303228] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Indexed: 11/11/2022]
Abstract
Two anilinosalen and a mixed phenol-anilinosalen ligands involving sterically hindered anilines moieties were synthesized. Their nickel(II) complexes 1, 2, and 3 were prepared and characterized. They could be readily one-electron oxidized (E(1/2)=-0.30, -0.26 and 0.10 V vs. Fc(+)/Fc, respectively) into anilinyl radicals species [1](+), [2](+), and [3](+), respectively. The radical complexes are extremely stable and were isolated as single crystals. X-ray crystallographic structures reveal that the changes in bond length resulting from oxidation do not exceed 0.02 Å within the ligand framework in the symmetrical [1](+) and [2](+). No quinoid bond pattern was present. In contrast, larger structural rearrangements were evidenced for the unsymmetrical [3](+), with shortening of one C(ortho)-C(meta) bond. Radical species [1](+) and [2](+) exhibit a strong absorption band at around 6000 cm(-1) (class III mixed valence compounds). This band is significantly less intense than [3](+), consistent with a rather localized anilinyl radical character, and thus a classification of this species as class II mixed-valence compound. Magnetic and electronic properties, as well as structural parameters, have been computed by DFT methods.
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Affiliation(s)
- Amélie Kochem
- Département de Chimie Moléculaire, Chimie Inorganique Redox Biomimétique (CIRE), UMR-5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9 (France), Fax: (+33) 476-51-4836
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17
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Byun JC, Mun DH, Park KM. Synthesis and Characterization of Copper(II) Complexes with Tetraazadiphenol Macrocyclic Ligand Having Cyclohexane Rings. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.1.255] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Synthesis, characterisation of a complex of Cu(II) with a multidentate macrocyclic ligand and its interactions with anions. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.05.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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de Biazio GR, Leite GGS, Tessmann DJ, Barbosa-Tessmann IP. A new PCR approach for the identification of Fusarium graminearum. Braz J Microbiol 2008; 39:554-60. [PMID: 24031265 PMCID: PMC3768439 DOI: 10.1590/s1517-838220080003000028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 12/24/2007] [Accepted: 07/13/2008] [Indexed: 11/22/2022] Open
Abstract
The main objective of this work was to develop a PCR protocol for the identification of Fusarium graminearum, based on a pair of primers targeted to a segment of the 3´coding region of the gaoA gene that codes for the enzyme galactose oxidase (GO). This region has low homology with the same region of GO genes from other fungi. Genomic DNA from 17 strains of Fusarium spp. isolated from diseased cereals, from several other Fusarium species, and from other fungi genera was analyzed in a PCR assay using this primer set. The 17 strains of Fusarium spp. were also analyzed for the GO enzyme production in submerse fermentation in a new formulated liquid medium. All strains that were morphologically and molecularly identified as F. graminearum were able to secrete the enzyme and had a positive result in the used PCR protocol. No DNA fragment was amplified using genomic DNA from other Fusarium species and species of other fungi genera. The results suggest that the proposed PCR protocol is specific and can be considered as a new molecular tool for the identification of F. graminearum. In addition, the new formulated medium is a cheap alternative for screening for GO screening production by F. graminearum.
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Affiliation(s)
| | | | - Dauri José Tessmann
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, PR, Brasil
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20
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Espagne E, Lespinet O, Malagnac F, Da Silva C, Jaillon O, Porcel BM, Couloux A, Aury JM, Ségurens B, Poulain J, Anthouard V, Grossetete S, Khalili H, Coppin E, Déquard-Chablat M, Picard M, Contamine V, Arnaise S, Bourdais A, Berteaux-Lecellier V, Gautheret D, de Vries RP, Battaglia E, Coutinho PM, Danchin EG, Henrissat B, Khoury RE, Sainsard-Chanet A, Boivin A, Pinan-Lucarré B, Sellem CH, Debuchy R, Wincker P, Weissenbach J, Silar P. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 2008; 9:R77. [PMID: 18460219 PMCID: PMC2441463 DOI: 10.1186/gb-2008-9-5-r77] [Citation(s) in RCA: 233] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 02/12/2008] [Accepted: 05/06/2008] [Indexed: 12/13/2022] Open
Abstract
A 10X draft sequence of Podospora anserina genome shows highly dynamic evolution since its divergence from Neurospora crassa. Background The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. Results We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown. Conclusion The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.
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Affiliation(s)
- Eric Espagne
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay cedex, France
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21
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The tandem of free radicals and methylglyoxal. Chem Biol Interact 2008; 171:251-71. [DOI: 10.1016/j.cbi.2007.11.009] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 11/02/2007] [Accepted: 11/19/2007] [Indexed: 11/19/2022]
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Crawford DJ, Hoskins AA, Friedman LJ, Gelles J, Moore MJ. Visualizing the splicing of single pre-mRNA molecules in whole cell extract. RNA (NEW YORK, N.Y.) 2008; 14:170-9. [PMID: 18025254 PMCID: PMC2151038 DOI: 10.1261/rna.794808] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Accepted: 10/11/2007] [Indexed: 05/23/2023]
Abstract
The excision of introns from nascent eukaryotic transcripts is catalyzed by the spliceosome, a highly complex and dynamic macromolecular machine composed of RNA and protein. Because of its complexity, biochemical analysis of the spliceosome has been previously limited to bulk assays in largely unfractionated cell extracts. We now report development of methodologies for studying the splicing of isolated single pre-mRNA molecules in real time. In this system, a fluorescently tagged pre-mRNA is tethered to a glass surface via its 3'-end. Splicing can be observed in Saccharomyces cerevisiae whole cell extract by monitoring loss of intron-specific fluorescence with a multi-wavelength total internal reflection fluorescence (TIRF) microscope. To prolong fluorophore lifetime, two enzyme-based O2 scavenging systems compatible with splicing were also developed. This work provides a powerful new approach for elucidating the mechanisms of spliceosome function and demonstrates the feasibility of utilizing TIRF microscopy for biochemical studies of single molecules in highly complex environments.
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Affiliation(s)
- Daniel J Crawford
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02453, USA
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23
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Rokhsana D, Dooley DM, Szilagyi RK. Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures. J Biol Inorg Chem 2007; 13:371-83. [PMID: 18057969 DOI: 10.1007/s00775-007-0325-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 11/14/2007] [Indexed: 12/01/2022]
Abstract
A systematic in silico approach has been employed to generate sound, experimentally validated active-site models for galactose oxidase (GO) using a hybrid density functional, B(38HF)P86. GO displays three distinct oxidation states: oxidized [Cu(II)-Y*]; semireduced [Cu(II)-Y]; and reduced [Cu(I)-Y]. Only the [Cu(II)-Y*] and the [Cu(I)-Y] states are assumed to be involved in the catalytic cycle, but their structures have not yet been determined. We have developed several models (1-7) for the [Cu(II)-Y*] state that were evaluated by comparison of our computational results with experimental data. An extended model system (6) that includes solvent molecules and second coordination sphere residues (R330, Y405, and W290) is essential to obtain an experimentally correct electronic structure of the active site. The optimized structure of 6 resulted in a five-coordinate Cu site with a protein radical centered on the Tyr-Cys cofactor. We further validated our converged model with the largest model (7) that included additional outer-sphere residues (Q406, H334, Y329, G513, and T580) and water molecules. Adding these residues did not affect significantly the active site's electronic and geometric structures. Using both 6 and 7, we explored the redox dependence of the active-site structure. We obtained four- and three-coordinate Cu sites for [Cu(II)-Y] and [Cu(I)-Y] states, respectively, that corroborate well with the experimental data. The relative energies of these states were validated by a comparison with experimental redox potentials. Collectively, our computational GO models well reproduce the physicochemical characteristics of the individual states, including their redox behaviors.
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Affiliation(s)
- Dalia Rokhsana
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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24
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Rogers MS, Tyler EM, Akyumani N, Kurtis CR, Spooner RK, Deacon SE, Tamber S, Firbank SJ, Mahmoud K, Knowles PF, Phillips SEV, McPherson MJ, Dooley DM. The stacking tryptophan of galactose oxidase: a second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis. Biochemistry 2007; 46:4606-18. [PMID: 17385891 PMCID: PMC2532978 DOI: 10.1021/bi062139d] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The function of the stacking tryptophan, W290, a second-coordination sphere residue in galactose oxidase, has been investigated via steady-state kinetics measurements, absorption, CD and EPR spectroscopy, and X-ray crystallography of the W290F, W290G, and W290H variants. Enzymatic turnover is significantly slower in the W290 variants. The Km for D-galactose for W290H is similar to that of the wild type, whereas the Km is greatly elevated in W290G and W290F, suggesting a role for W290 in substrate binding and/or positioning via the NH group of the indole ring. Hydrogen bonding between W290 and azide in the wild type-azide crystal structure are consistent with this function. W290 modulates the properties and reactivity of the redox-active tyrosine radical; the Y272 tyrosyl radicals in both the W290G and W290H variants have elevated redox potentials and are highly unstable compared to the radical in W290F, which has properties similar to those of the wild-type tyrosyl radical. W290 restricts the accessibility of the Y272 radical site to solvent. Crystal structures show that Y272 is significantly more solvent exposed in the W290G variant but that W290F limits solvent access comparable to the wild-type indole side chain. Spectroscopic studies indicate that the Cu(II) ground states in the semireduced W290 variants are very similar to that of the wild-type protein. In addition, the electronic structures of W290X-azide complexes are also closely similar to the wild-type electronic structure. Azide binding and azide-mediated proton uptake by Y495 are perturbed in the variants, indicating that tryptophan also modulates the function of the catalytic base (Y495) in the wild-type enzyme. Thus, W290 plays multiple critical roles in enzyme catalysis, affecting substrate binding, the tyrosyl radical redox potential and stability, and the axial tyrosine function.
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Affiliation(s)
- Melanie S. Rogers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Ejan M. Tyler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Nana Akyumani
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Christian R. Kurtis
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - R. Kate Spooner
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah E. Deacon
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sunita Tamber
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Susan J. Firbank
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Khaled Mahmoud
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter F. Knowles
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon E. V. Phillips
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David M. Dooley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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25
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Kersten P, Cullen D. Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genet Biol 2007; 44:77-87. [PMID: 16971147 DOI: 10.1016/j.fgb.2006.07.007] [Citation(s) in RCA: 251] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 07/20/2006] [Indexed: 11/17/2022]
Abstract
The US Department of Energy has assembled a high quality draft genome of Phanerochaete chrysosporium, a white rot Basidiomycete capable of completely degrading all major components of plant cell walls including cellulose, hemicellulose and lignin. Hundreds of sequences are predicted to encode extracellular enzymes including an impressive number of oxidative enzymes potentially involved in lignocellulose degradation. Herein, we summarize the number, organization, and expression of genes encoding peroxidases, copper radical oxidases, FAD-dependent oxidases, and multicopper oxidases. Possibly relevant to extracellular oxidative systems are genes involved in posttranslational processes and a large number of hypothetical proteins.
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Affiliation(s)
- Phil Kersten
- Forest Products Laboratory, USDA, One Gifford Pinchot Drive, Madison, WI 53705, USA
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26
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Kujawa M, Volc J, Halada P, Sedmera P, Divne C, Sygmund C, Leitner C, Peterbauer C, Haltrich D. Properties of pyranose dehydrogenase purified from the litter-degrading fungus Agaricus xanthoderma. FEBS J 2007; 274:879-94. [PMID: 17227387 DOI: 10.1111/j.1742-4658.2007.05634.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We purified an extracellular pyranose dehydrogenase (PDH) from the basidiomycete fungus Agaricus xanthoderma using ammonium sulfate fractionation and ion-exchange and hydrophobic interaction chromatography. The native enzyme is a monomeric glycoprotein (5% carbohydrate) containing a covalently bound FAD as its prosthetic group. The PDH polypeptide consists of 575 amino acids and has a molecular mass of 65 400 Da as determined by MALDI MS. On the basis of the primary structure of the mature protein, PDH is a member of the glucose-methanol-choline oxidoreductase family. We constructed a homology model of PDH using the 3D structure of glucose oxidase from Aspergillus niger as a template. This model suggests a novel type of bi-covalent flavinylation in PDH, 9-S-cysteinyl, 8-alpha-N3-histidyl FAD. The enzyme exhibits a broad sugar substrate tolerance, oxidizing structurally different aldopyranoses including monosaccharides and oligosaccharides as well as glycosides. Its preferred electron donor substrates are D-glucose, D-galactose, L-arabinose, and D-xylose. As shown by in situ NMR analysis, D-glucose and D-galactose are both oxidized at positions C2 and C3, yielding the corresponding didehydroaldoses (diketoaldoses) as the final reaction products. PDH shows no detectable activity with oxygen, and its reactivity towards electron acceptors is rather limited, reducing various substituted benzoquinones and complexed metal ions. The azino-bis-(3-ethylbenzthiazolin-6-sulfonic acid) cation radical and the ferricenium ion are the best electron acceptors, as judged by the catalytic efficiencies (k(cat)/K(m)). The enzyme may play a role in lignocellulose degradation.
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Affiliation(s)
- Magdalena Kujawa
- Division of Food Biotechnology, Department of Food Sciences and Technology, BOKU - University of Natural Resources and Applied Life Sciences, Vienna, Austria
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27
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Selective isotopic labeling of recombinant proteins using amino acid auxotroph strains. Methods Mol Biol 2007; 389:175-88. [PMID: 17951643 DOI: 10.1007/978-1-59745-456-8_13] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Labeling proteins with stable isotopes is important for many analytical and structural techniques, including NMR spectroscopy and mass spectrometry. Nonselective labeling, which uniformly labels all amino acids in the protein, may be accomplished with readily available wild-type expression hosts. However, there are often advantages to labeling a specific amino acid, and residue-selective labeling generally requires the use of an expression strain that is auxotrophic for the amino acid in order to efficiently incorporate the isotopic label. The behavior of an auxotrophic strain may be complicated by the regulatory properties of the biosynthetic pathway, by secondary nutritional requirements resulting from disruption of a biosynthetic pathway, and from acquired sensitivity to environmental factors resulting from build-up of metabolic intermediates. As a result, it is important to characterize the phenotype of the each auxotrophic strain in order to optimize its performance as an expression host for selective labeling of proteins. The application of aromatic auxotroph strains of Pichia pastoris to labeling tyrosines in a recombinant protein (galactose oxidase) will be used to illustrate selective-labeling methods.
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28
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Whittaker MM, Whittaker JW. Streptomyces coelicolor oxidase (SCO2837p): A new free radical metalloenzyme secreted by Streptomyces coelicolor A3(2). Arch Biochem Biophys 2006; 452:108-18. [PMID: 16884677 DOI: 10.1016/j.abb.2006.06.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 06/10/2006] [Accepted: 06/20/2006] [Indexed: 11/23/2022]
Abstract
The SCO2837 open-reading frame is located within the conserved central core region of the Streptomyces coelicolor A3(2) genome, which contains genes required for essential cellular functions. SCO2837 protein (SCO2837p) expressed by Pichia pastoris is a copper metalloenzyme, catalyzing the oxidation of simple alcohols to aldehydes and reduction of dioxygen to hydrogen peroxide. Distinct optical absorption spectra are observed for oxidized and one-electron reduced holoenzyme, and a free radical EPR signal is present in the oxidized apoprotein, characteristic of the Tyr-Cys redox cofactor previously reported for fungal secretory radical copper oxidases, galactose oxidase and glyoxal oxidase, with which it shares weak sequence similarity. SCO2837p was detected in the growth medium of both S. coelicolor and a recombinant expression host (Streptomyces lividans TK64) by Western blotting, with the expression level dependent on the nature of the carbon source. This represents the first characterized example of a prokaryotic radical copper oxidase.
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Affiliation(s)
- Mei M Whittaker
- Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, OR 97006-8291, USA
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29
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Neumann R, Khenkin AM. Molecular oxygen and oxidation catalysis by phosphovanadomolybdates. Chem Commun (Camb) 2006:2529-38. [PMID: 16779469 DOI: 10.1039/b600711m] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The history of aerobic catalytic oxidation mediated by a subclass of polyoxometalates, the phosphovanadomolybdates of the Keggin structure, [PV(x)Mo(12-x)O40](3+x)-, is described. In the earlier research it was shown that phosphovanadomolybdates catalyze oxydehydrogenation reactions through an electron-transfer oxidation of a substrate by the polyoxometalate that is then reoxidized by oxygen. These aerobic oxidations are selective and synthetically useful in various transformations, notably diene aromatization, phenol dimerization and alcohol oxidation. Oxygen transfer from the polyoxometalate to arenes and alkylarenes was also discussed as a homogeneous analog of a Mars-van Krevelen oxidation. "Second generation" catalysts include binary complexes of the polyoxometalate and a organometallic compound useful, for example, for methane oxidation and nanoparticles stabilized by polyoxometalates effective for aerobic alkene epoxidation.
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Affiliation(s)
- Ronny Neumann
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100.
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30
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Nairn AK, Archibald SJ, Bhalla R, Gilbert BC, Maclean EJ, Teat SJ, Walton PH. (N-Benzyl-bis-N',N''-salicylidene)-cis-1,3,5-triaminocyclohexane copper(II): a novel catalyst for the aerobic oxidation of benzyl alcohol. Dalton Trans 2005:172-6. [PMID: 16357974 DOI: 10.1039/b512296c] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Reaction of Cu(BF(4))(2).6H(2)O with the N(3)O(2) donor ligand H(2)L (where H(2)L = N-benzyl-N',N''-di-tert-butyl-disalicyl-triaminocyclohexane) results in the formation of a novel Cu(II)L complex, 1. X-Ray crystallography of it shows the Cu(II) centre coordinated by two phenolate oxygens and two imine nitrogens in a distorted square plane with an elongated bond to the amine nitrogen (2.512 A) in the axial position. EPR spectroscopy gives g values of g(1) = 2.277, g(2) = 2.100, g(3) = 2.025, and A(1) = 15.6 mT which are consistent with the distorted square pyramidal coordination environment determined from the X-ray structure. UV/visible and electrochemical analysis of shows that it undergoes two reversible processes assigned to the successive oxidation of the phenolate oxygens to phenoxyl radicals, the first at E((1/2)) = 0.89 V (DeltaE = 81 mV, vs. Ag/AgCl) and the second at E((1/2)) = 1.13V (DeltaE = 84 mV, vs. Ag/AgCl). Chemical oxidation results in the formation of a species, assigned as [1](+)(.) which is EPR silent due to antiferromagnetic coupling between the Cu(II) centre and the bound phenoxyl radical. The oxidised species catalyses the oxidation of benzyl alcohol to benzaldehyde.
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Affiliation(s)
- Alison K Nairn
- Department of Chemistry, University of York, Heslington, York, UK YO10 5DD
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Jeschke G. EPR techniques for studying radical enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:91-102. [PMID: 15721608 DOI: 10.1016/j.bbabio.2004.02.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Accepted: 02/26/2004] [Indexed: 11/26/2022]
Abstract
EPR studies on radical enzymes are reviewed under the aspects of the information that they can provide and of the techniques that are used. An overview of organic radicals derived from amino acids, modified amino acids, and cofactors is given and g tensor data are compiled. The information accessible from a spectroscopic point of view is contrasted with the information required to understand enzyme structure and function, and some precautions are discussed that must be taken to derive the latter kind of information from the former. Structural dynamics is identified as an aspect that has rarely been addressed in the past although it is highly relevant for enzyme function. It is proposed that techniques introduced recently on other classes of proteins could help to close this gap.
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Affiliation(s)
- G Jeschke
- Max Planck Institute for Polymer Research, Postfach 3148, Mainz D-55021, Germany.
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32
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Swain MD, Benson DE. Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs. Proteins 2005; 59:64-71. [PMID: 15696544 DOI: 10.1002/prot.20403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-derived cofactors that are composed of covalently crosslinked amino acid side chains are of increasing importance in protein science. These crosslinked protein-derived cofactors (CPDC) are formed either through direct oxidation by metal/O(2)-derived intermediates or through outer sphere oxidation by highly oxidizing cofactors. CPDCs that are formed by outer sphere oxidation do not require side-chain precursors to be coordinated by a metal center, and therefore are more difficult to identify than those formed by direct oxidation. To better understand the propensity for CPDC formation by outer sphere oxidation, the geometrical preferences of CPDCs were examined. The Dezymer algorithm has been used to identify all putative CPDC-forming mutations in 500 proteins. Geometrically, although chemically unrelated, these CPDCs were found to be similar to disulfide-bonded cysteine pairs. Additionally, the percentage of near-sequence pairs (i and i +1 to i and i + 5) increased as the average C(alpha)-C(alpha) distance between the amino acid pairs increased. This survey also examined the protein databank for proteins with pre-attack conformations for CPDCs, using non-bonded contacts reported by Procheck. A total of 323 unique proteins was identified, with 55 being near-sequence amino acid pairs. The high geometric propensity of near-sequence amino acid pairs for forming CPDCs is significant due to difficulties associated with detection by structural or mass spectrometric methods.
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Affiliation(s)
- Marla D Swain
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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33
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Phanerochaete chrysosporium Genomics. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1874-5334(05)80016-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Fukuzumi S, Shimoosako K, Suenobu T, Watanabe Y. Mechanisms of Hydrogen-, Oxygen-, and Electron-Transfer Reactions of Cumylperoxyl Radical. J Am Chem Soc 2003; 125:9074-82. [PMID: 15369364 DOI: 10.1021/ja035156o] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rates of hydrogen-transfer reactions from a series of para-substituted N,N-dimethylanilines to cumylperoxyl radical and oxygen-transfer reactions from cumylperoxyl radical to a series of sulfides and phosphines have been determined in propionitrile (EtCN) and pentane at low temperatures by use of ESR. The observed rate constants exhibit first-order and second-order dependence with respect to concentrations of N,N-dimethylanilines. This indicates that the hydrogen- and oxygen-transfer reactions proceed via 1:1 charge-transfer (CT) complexes formed between the substrates and cumylperoxyl radical. The primary kinetic isotope effects are determined by comparing the rates of N,N-dimethylanilines and the corresponding N,N-bis(trideuteriomethyl)anilines. The isotope effect profiles are quite different from those reported for the P-450 model oxidation of the same series of substrates. Rates of electron-transfer reactions from ferrocene derivatives to cumylperoxyl radical have also been determined by use of ESR. The catalytic effects of Sc(OTf)(3) (OTf = triflate) on the electron-transfer reactions are compared with those of Sc(OTf)(3) on the hydrogen- and oxygen-transfer reactions. Such comparison provides strong evidence that the hydrogen- and oxygen- transfer reactions of cumylperoxyl radical proceed via a one-step hydrogen atom and oxygen atom transfer rather than via an electron transfer from substrates to cumylperoxyl radical.
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Affiliation(s)
- Shunichi Fukuzumi
- Contribution from the Department of Material and Life Science, Graduate School of Engineering, Osaka University, CREST, Japan Science and Technology Corporation (JST), Suita, Osaka 565-0871, Japan.
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Whittaker MM, Whittaker JW. Cu(I)-dependent biogenesis of the galactose oxidase redox cofactor. J Biol Chem 2003; 278:22090-101. [PMID: 12672814 DOI: 10.1074/jbc.m300112200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Galactose oxidase is a copper metalloenzyme containing a novel protein-derived redox cofactor in its active site, formed by cross-linking two residues, Cys228 and Tyr272. Previous studies have shown that formation of the tyrosyl-cysteine (Tyr-Cys) cofactor is a self-processing step requiring only copper and dioxygen. We have investigated the biogenesis of cofactor-containing galactose oxidase from pregalactose oxidase lacking the Tyr-Cys cross-link but having a fully processed N-terminal sequence, using both Cu(I) and Cu(II). Mature galactose oxidase forms rapidly following exposure of a pregalactose oxidase-Cu(I) complex to dioxygen (t(1/2) = 3.9s at pH7). In contrast, when Cu(II) is used in place of Cu(I) the maturation process requires several hours (t(1/2) = 5.1 h). EDTA prevents reaction of pregalactose oxidase with Cu(II) but does not interfere with the Cu(I)-dependent biogenesis reaction. The yield of cross-link corresponds to the amount of copper added, although a fraction of the pregalactose oxidase protein is unable to undergo this cross-linking reaction. The latter component, which may have an altered conformation, does not interfere with analysis of cofactor biogenesis at low copper loading. The biogenesis product has been quantitatively characterized, and mechanistic studies have been developed for the Cu(I)-dependent reaction, which forms oxidized, mature galactose oxidase and requires two molecules of O2. Transient kinetics studies of the biogenesis reaction have revealed a pH sensitivity that appears to reflect ionization of a protein group (pKa = 7.3) at intermediate pH resulting in a rate acceleration and protonation of an early oxygenated intermediate at lower pH competing with commitment to cofactor formation. These spectroscopic, kinetic, and biochemical results lead to new insights into the biogenesis mechanism.
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Affiliation(s)
- Mei M Whittaker
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006, USA
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