1
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Taborda A, Frazão T, Rodrigues MV, Fernández-Luengo X, Sancho F, Lucas MF, Frazão C, Melo EP, Ventura MR, Masgrau L, Borges PT, Martins LO. Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms. Nat Commun 2023; 14:7289. [PMID: 37963862 PMCID: PMC10646112 DOI: 10.1038/s41467-023-42000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
C-glycosides are natural products with important biological activities but are recalcitrant to degradation. Glycoside 3-oxidases (G3Oxs) are recently identified bacterial flavo-oxidases from the glucose-methanol-coline (GMC) superfamily that catalyze the oxidation of C-glycosides with the concomitant reduction of O2 to H2O2. This oxidation is followed by C-C acid/base-assisted bond cleavage in two-step C-deglycosylation pathways. Soil and gut microorganisms have different oxidative enzymes, but the details of their catalytic mechanisms are largely unknown. Here, we report that PsG3Ox oxidizes at 50,000-fold higher specificity (kcat/Km) the glucose moiety of mangiferin to 3-keto-mangiferin than free D-glucose to 2-keto-glucose. Analysis of PsG3Ox X-ray crystal structures and PsG3Ox in complex with glucose and mangiferin, combined with mutagenesis and molecular dynamics simulations, reveal distinctive features in the topology surrounding the active site that favor catalytically competent conformational states suitable for recognition, stabilization, and oxidation of the glucose moiety of mangiferin. Furthermore, their distinction to pyranose 2-oxidases (P2Oxs) involved in wood decay and recycling is discussed from an evolutionary, structural, and functional viewpoint.
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Grants
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Fundação para a Ciência e Tecnologia, Portugal, grants 2022.02027.PTDC, UIDB/04612/2020 and UIDP/04612/2020, LA/P/0087/2020, PTDC/BII-BBF/29564/2017, and AAC 01/SAICT/2016 Fundação para a Ciência e Tecnologia, Portugal, Ph.D. fellowships 2020.07928, 2022.13872, and 2022.09426 Ministry of Science and Innovation, Spain, grant PID2021-126897NB-I00 and fellowship PRE2019-088412, funded by the MCIN/AEI/10.13039/501100011033/ FEDER, EU
- Fundação para a Ciência e Tecnologia (FCT), Portugal, grants UIDB/04326/2020, UIDP/043226/2020 and LA/P/0101/2020
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Affiliation(s)
- André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Tomás Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Miguel V Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | | | - Ferran Sancho
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | | | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Eduardo P Melo
- Centro de Ciências do Mar, Universidade do Algarve, 8005-139, Faro, Portugal
| | - M Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Laura Masgrau
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
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2
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Sucharitakul J, Buckel W, Chaiyen P. Rapid kinetics reveal surprising flavin chemistry in bifurcating electron transfer flavoprotein from Acidaminococcus fermentans. J Biol Chem 2020; 296:100124. [PMID: 33239361 PMCID: PMC7948398 DOI: 10.1074/jbc.ra120.016017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Electron bifurcation uses free energy from exergonic redox reactions to power endergonic reactions. β-FAD of the electron transfer flavoprotein (EtfAB) from the anaerobic bacterium Acidaminococcus fermentans bifurcates the electrons of NADH, sending one to the low-potential ferredoxin and the other to the high-potential α-FAD semiquinone (α-FAD•−). The resultant α-FAD hydroquinone (α-FADH−) transfers one electron further to butyryl-CoA dehydrogenase (Bcd); two such transfers enable Bcd to reduce crotonyl-CoA to butyryl-CoA. To get insight into the mechanism of these intricate reactions, we constructed an artificial reaction only with EtfAB containing α-FAD or α-FAD•− to monitor formation of α-FAD•− or α-FADH−, respectively, using stopped flow kinetic measurements. In the presence of α-FAD, we observed that NADH transferred a hydride to β-FAD at a rate of 920 s−1, yielding the charge–transfer complex NAD+:β-FADH− with an absorbance maximum at 650 nm. β-FADH− bifurcated one electron to α-FAD and the other electron to α-FAD of a second EtfAB molecule, forming two stable α-FAD•−. With α-FAD•−, the reduction of β-FAD with NADH was 1500 times slower. Reduction of β-FAD in the presence of α-FAD displayed a normal kinetic isotope effect (KIE) of 2.1, whereas the KIE was inverted in the presence of α-FAD•−. These data indicate that a nearby radical (14 Å apart) slows the rate of a hydride transfer and inverts the KIE. This unanticipated flavin chemistry is not restricted to Etf–Bcd but certainly occurs in other bifurcating Etfs found in anaerobic bacteria and archaea.
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Affiliation(s)
- Jeerus Sucharitakul
- Department of Biochemistry, Chulalongkorn University, Patumwan, Bangkok, Thailand; Skeletal Disorders Research Unit, Faculty of Dentistry, Chulalongkorn University, Patumwan, Bangkok, Thailand.
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie and Synmikro, Philipps-Universität, Marburg, Germany; Max-Plank-Institut für terrestrische Mikrobiologie, Marburg, Germany
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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3
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Savino S, Fraaije MW. The vast repertoire of carbohydrate oxidases: An overview. Biotechnol Adv 2020; 51:107634. [PMID: 32961251 DOI: 10.1016/j.biotechadv.2020.107634] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/06/2020] [Indexed: 01/01/2023]
Abstract
Carbohydrates are widely abundant molecules present in a variety of forms. For their biosynthesis and modification, nature has evolved a plethora of carbohydrate-acting enzymes. Many of these enzymes are of particular interest for biotechnological applications, where they can be used as biocatalysts or biosensors. Among the enzymes catalysing conversions of carbohydrates are the carbohydrate oxidases. These oxidative enzymes belong to different structural families and use different cofactors to perform the oxidation reaction of CH-OH bonds in carbohydrates. The variety of carbohydrate oxidases available in nature reflects their specificity towards different sugars and selectivity of the oxidation site. Thanks to their properties, carbohydrate oxidases have received a lot of attention in basic and applied research, such that nowadays their role in biotechnological processes is of paramount importance. In this review we provide an overview of the available knowledge concerning the known carbohydrate oxidases. The oxidases are first classified according to their structural features. After a description on their mechanism of action, substrate acceptance and characterisation, we report on the engineering of the different carbohydrate oxidases to enhance their employment in biocatalysis and biotechnology. In the last part of the review we highlight some practical applications for which such enzymes have been exploited.
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Affiliation(s)
- Simone Savino
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands.
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4
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Sriwaiyaphram K, Punthong P, Sucharitakul J, Wongnate T. Structure and function relationships of sugar oxidases and their potential use in biocatalysis. Enzymes 2020; 47:193-230. [PMID: 32951824 DOI: 10.1016/bs.enz.2020.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Several sugar oxidases that catalyze the oxidation of sugars have been isolated and characterized. These enzymes can be classified as flavoenzyme due to the presence of flavin adenine dinucleotide (FAD) as a cofactor. Sugar oxidases have been proposed to be the key biocatalyst in biotransformation of carbohydrates which can potentially convert sugars to provide a pool of intermediates for synthesis of rare sugars, fine chemicals and drugs. Moreover, sugar oxidases have been applied in biosensing of various biomolecules in food industries, diagnosis of diseases and environmental pollutant detection. This review provides the discussions on general properties, current mechanistic understanding, structural determination, biocatalytic application, and biosensor integration of representative sugar oxidase enzymes, namely pyranose 2-oxidase (P2O), glucose oxidase (GO), hexose oxidase (HO), and oligosaccharide oxidase. The information regarding the relationship between structure and function of these sugar oxidases points out the key properties of this particular group of enzymes that can be modified by engineering, which had resulted in a remarkable economic importance.
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Affiliation(s)
- Kanokkan Sriwaiyaphram
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Pangrum Punthong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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5
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Wongnate T, Surawatanawong P, Chuaboon L, Lawan N, Chaiyen P. The Mechanism of Sugar C−H Bond Oxidation by a Flavoprotein Oxidase Occurs by a Hydride Transfer Before Proton Abstraction. Chemistry 2019; 25:4460-4471. [DOI: 10.1002/chem.201806078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/16/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Thanyaporn Wongnate
- School of Biomolecular Science & EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley Rayong 21210 Thailand
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence, for Innovation in ChemistryMahidol University Bangkok 10400 Thailand
| | - Litavadee Chuaboon
- Department of Biochemistry and Center for Excellence, in Protein and Enzyme Technology, Faculty of ScienceMahidol University Bangkok 10400 Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science & EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley Rayong 21210 Thailand
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6
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Chuaboon L, Wongnate T, Punthong P, Kiattisewee C, Lawan N, Hsu C, Lin C, Bornscheuer UT, Chaiyen P. One‐Pot Bioconversion of
l
‐Arabinose to
l
‐Ribulose in an Enzymatic Cascade. Angew Chem Int Ed Engl 2019; 58:2428-2432. [DOI: 10.1002/anie.201814219] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Litavadee Chuaboon
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol University Bangkok 10400 Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science & EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pangrum Punthong
- School of Biomolecular Science & EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Cholpisit Kiattisewee
- School of Biomolecular Science & EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Narin Lawan
- Department of ChemistryFaculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Chia‐Yi Hsu
- Institute of Biological ChemistryAcademia Sinica Taipei 11529 Taiwan
| | - Chun‐Hung Lin
- Institute of Biological ChemistryAcademia Sinica Taipei 11529 Taiwan
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDepartment of Biotechnology and Enzyme CatalysisGreifswald University Felix-Hausdorff-Strasse 4 Greifswald Germany
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol University Bangkok 10400 Thailand
- School of Biomolecular Science & EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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7
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Chuaboon L, Wongnate T, Punthong P, Kiattisewee C, Lawan N, Hsu CY, Lin CH, Bornscheuer UT, Chaiyen P. One-Pot Bioconversion of l
-Arabinose to l
-Ribulose in an Enzymatic Cascade. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Litavadee Chuaboon
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology; Faculty of Science; Mahidol University; Bangkok 10400 Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science & Engineering; Vidyasirimedhi Institute of Science and Technology (VISTEC); Wangchan Valley Rayong 21210 Thailand
| | - Pangrum Punthong
- School of Biomolecular Science & Engineering; Vidyasirimedhi Institute of Science and Technology (VISTEC); Wangchan Valley Rayong 21210 Thailand
| | - Cholpisit Kiattisewee
- School of Biomolecular Science & Engineering; Vidyasirimedhi Institute of Science and Technology (VISTEC); Wangchan Valley Rayong 21210 Thailand
| | - Narin Lawan
- Department of Chemistry; Faculty of Science; Chiang Mai University; Chiang Mai 50200 Thailand
| | - Chia-Yi Hsu
- Institute of Biological Chemistry; Academia Sinica; Taipei 11529 Taiwan
| | - Chun-Hung Lin
- Institute of Biological Chemistry; Academia Sinica; Taipei 11529 Taiwan
| | - Uwe T. Bornscheuer
- Institute of Biochemistry; Department of Biotechnology and Enzyme Catalysis; Greifswald University; Felix-Hausdorff-Strasse 4 Greifswald Germany
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology; Faculty of Science; Mahidol University; Bangkok 10400 Thailand
- School of Biomolecular Science & Engineering; Vidyasirimedhi Institute of Science and Technology (VISTEC); Wangchan Valley Rayong 21210 Thailand
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8
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Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F, Taniguchi S, Chosrowjan H. Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation. Proteins 2017; 85:1913-1924. [DOI: 10.1002/prot.25345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/20/2017] [Accepted: 06/26/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Kiattisak Lugsanangarm
- Program of Chemistry, Faculty of Science and Technology; Bansomdejchaopraya Rajabhat University; Bangkok 10600 Thailand
| | - Arthit Nueangaudom
- Program of General Science, Faculty of Science and Technology; Thepsatri Rajabhat University; Lopburi 15000 Thailand
| | - Somsak Pianwanit
- Department of Chemistry, Faculty of Science; Chulalongkorn University; Bangkok 10330 Thailand
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science; Chulalongkorn University; Bangkok 10330 Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science; Mahasarakham University; Mahasarakham 44150 Thailand
| | - Fumio Tanaka
- Department of Chemistry, Faculty of Science; Chulalongkorn University; Bangkok 10330 Thailand
- Division of Laser Biochemistry; Institute for Laser Technology; Osaka 550-0004 Japan
| | - Seiji Taniguchi
- Division of Laser Biochemistry; Institute for Laser Technology; Osaka 550-0004 Japan
| | - Haik Chosrowjan
- Division of Laser Biochemistry; Institute for Laser Technology; Osaka 550-0004 Japan
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9
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10
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Cakir K, Erdem SS, Atalay VE. ONIOM calculations on serotonin degradation by monoamine oxidase B: insight into the oxidation mechanism and covalent reversible inhibition. Org Biomol Chem 2016; 14:9239-9252. [PMID: 27605388 DOI: 10.1039/c6ob01175f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Monoamine oxidase (MAO) is an enzyme which catalyzes the oxidation of neurotransmitter amines and regulates their level. There are two forms of the enzyme with 70% similarity, known as MAO-A and MAO-B. MAO inhibitors are used in the treatment of neurological disorders such as depression, Parkinson's and Alzheimer's diseases. Therefore, understanding the chemical steps of MAO catalyzed amine oxidation is crucial for rational drug design. However, despite many experimental studies and recent computational efforts in the literature, the amine oxidation mechanism by MAO enzymes is still controversial. The polar nucleophilic mechanism and hydride transfer mechanisms are under debate in recent QM/MM studies. In this study, the serotonin oxidation mechanism by MAO was explored via the ONIOM (QM : QM) methodology at the M06-2X/6-31+G(d,p):PM6 level. A modified MAO mechanism involving a covalent reversible inhibition step via formation of flavin N5 ylide was proposed. This mechanism can be used to modulate the potency and reversibility of novel mechanism-based covalent inhibitors by intelligent modifications of the structure of the inhibitors. NBO donor-acceptor analysis confirms that the rate-determining αC-H cleavage step is a hybrid of hydride and proton transfer where hydride transfer dominates over the proton transfer. The functional role of covalent FAD was also investigated by calculating the activation energy of noncovalent FAD models where a 22 fold decrease in the rate of catalysis was predicted. Geometrical features imply that the function of the covalent bond in FAD might be to maintain the correct geometry and conformation for a more efficient catalysis.
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Affiliation(s)
- Kubra Cakir
- Marmara University, Department of Chemistry, Faculty of Arts and Sciences, 34722 Göztepe, Istanbul, Turkey.
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11
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Lugsanangarm K, Nueangaudom A, Kokpol S, Pianwanit S, Nunthaboot N, Tanaka F, Taniguchi S, Chosrowjan H. Heterogeneous subunit structures in the pyranose 2-oxidase homotetramer revealed by theoretical analysis of the rates of photoinduced electron transfer from a tryptophan to the excited flavin. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2015.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Fitzpatrick PF. Combining solvent isotope effects with substrate isotope effects in mechanistic studies of alcohol and amine oxidation by enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1746-55. [PMID: 25448013 DOI: 10.1016/j.bbapap.2014.10.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
Abstract
Oxidation of alcohols and amines is catalyzed by multiple families of flavin- and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78212, USA.
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13
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Lugsanangarm K, Kokpol S, Nueangaudom A, Pianwanit S, Nunthaboot N, Tanaka F. Structural heterogeneity among four subunits in pyranose 2-oxidase: A molecular dynamics simulation study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614400100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The homotetramer pyranose 2-oxidase (P2O) from Tetrametes multicolor contains flavin adenine dinucleotide (FAD) as a cofactor, and displays two conformers with different transient fluorescence spectra and lifetimes (ca. 0.1 ps and 360 ps). The ultrashort lifetimes of isoalloxazine (Iso) are ascribed to the photoinduced electron transfer (ET) from Trp168 to the excited Iso. Here, the structural heterogeneity among the four subunits in solution was studied by means of molecular dynamics simulation (MDS). The ET donor–acceptor distances in crystal and solution were compared. The distribution of the H-bond distances between Iso and the surrounding amino acids revealed appreciable differences among the four subunits. The structural fluctuations in two distant places were examined for the Iso-P and Iso-Q distances (where P and Q are Trp or Tyr) with the correlation coefficients between Iso-P and Iso-Q distances, revealing cooperative motions even though P and Q were more than 1 nm apart and located in different subunits. Moreover, distributions of the distances between Iso and its closest ionic amino acids markedly differed among the four subunits. Electrostatic (ES) energies between the Iso anion and the ionic amino acids in the entire protein were obtained using a static dielectric constant of 1. The ES energy in each subunit was strongly influenced by the other subunits, whilst the distributions of the ES energies greatly differed among the four subunits. This heterogeneous distribution of the ES energy between subunits may contribute to the large differences in the experimentally detected ET rates.
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Affiliation(s)
- Kiattisak Lugsanangarm
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Arthit Nueangaudom
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somsak Pianwanit
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand
| | - Fumio Tanaka
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Laser BioScience, Institute for Laser Technology, Utsubo-Honmachi, 1-8-4, Nishiku, Osaka 550-0004, Japan
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14
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Frederick RE, Ojha S, Lamb A, Dubois JL. How pH modulates the reactivity and selectivity of a siderophore-associated flavin monooxygenase. Biochemistry 2014; 53:2007-16. [PMID: 24490904 PMCID: PMC3985866 DOI: 10.1021/bi401256b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Flavin-containing
monooxygenases (FMOs) catalyze the oxygenation
of diverse organic molecules using O2, NADPH, and the flavin
adenine dinucleotide (FAD) cofactor. The fungal FMO SidA initiates
peptidic siderophore biosynthesis via the highly selective hydroxylation
of l-ornithine, while the related amino acid l-lysine
is a potent effector of reaction uncoupling to generate H2O2. We hypothesized that protonation states could critically
influence both substrate-selective hydroxylation and H2O2 release, and therefore undertook a study of SidA’s
pH-dependent reaction kinetics. Consistent with other FMOs that stabilize
a C4a-OO(H) intermediate, SidA’s reductive half reaction is
pH independent. The rate constant for the formation of the reactive
C4a-OO(H) intermediate from reduced SidA and O2 is likewise
independent of pH. However, the rate constants for C4a-OO(H) reactions,
either to eliminate H2O2 or to hydroxylate l-Orn, were strongly pH-dependent and influenced by the nature
of the bound amino acid. Solvent kinetic isotope effects of 6.6 ±
0.3 and 1.9 ± 0.2 were measured for the C4a-OOH/H2O2 conversion in the presence and absence of l-Lys, respectively. A model is proposed in which l-Lys accelerates
H2O2 release via an acid–base mechanism
and where side-chain position determines whether H2O2 or the hydroxylation product is observed.
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Affiliation(s)
- Rosanne E Frederick
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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15
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Tan TC, Spadiut O, Gandini R, Haltrich D, Divne C. Structural basis for binding of fluorinated glucose and galactose to Trametes multicolor pyranose 2-oxidase variants with improved galactose conversion. PLoS One 2014; 9:e86736. [PMID: 24466218 PMCID: PMC3897772 DOI: 10.1371/journal.pone.0086736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/15/2013] [Indexed: 11/18/2022] Open
Abstract
Each year, about six million tons of lactose are generated from liquid whey as industrial byproduct, and optimally this large carbohydrate waste should be used for the production of value-added products. Trametes multicolor pyranose 2-oxidase (TmP2O) catalyzes the oxidation of various monosaccharides to the corresponding 2-keto sugars. Thus, a potential use of TmP2O is to convert the products from lactose hydrolysis, D-glucose and D-galactose, to more valuable products such as tagatose. Oxidation of glucose is however strongly favored over galactose, and oxidation of both substrates at more equal rates is desirable. Characterization of TmP2O variants (H450G, V546C, H450G/V546C) with improved D-galactose conversion has been given earlier, of which H450G displayed the best relative conversion between the substrates. To rationalize the changes in conversion rates, we have analyzed high-resolution crystal structures of the aforementioned mutants with bound 2- and 3-fluorinated glucose and galactose. Binding of glucose and galactose in the productive 2-oxidation binding mode is nearly identical in all mutants, suggesting that this binding mode is essentially unaffected by the mutations. For the competing glucose binding mode, enzyme variants carrying the H450G replacement stabilize glucose as the α-anomer in position for 3-oxidation. The backbone relaxation at position 450 allows the substrate-binding loop to fold tightly around the ligand. V546C however stabilize glucose as the β-anomer using an open loop conformation. Improved binding of galactose is enabled by subtle relaxation effects at key active-site backbone positions. The competing binding mode for galactose 2-oxidation by V546C stabilizes the β-anomer for oxidation at C1, whereas H450G variants stabilize the 3-oxidation binding mode of the galactose α-anomer. The present study provides a detailed description of binding modes that rationalize changes in the relative conversion rates of D-glucose and D-galactose and can be used to refine future enzyme designs for more efficient use of lactose-hydrolysis byproducts.
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Affiliation(s)
- Tien Chye Tan
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Oliver Spadiut
- School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Rosaria Gandini
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Divne
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden ; School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
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16
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Wongnate T, Surawatanawong P, Visitsatthawong S, Sucharitakul J, Scrutton NS, Chaiyen P. Proton-Coupled Electron Transfer and Adduct Configuration Are Important for C4a-Hydroperoxyflavin Formation and Stabilization in a Flavoenzyme. J Am Chem Soc 2013; 136:241-53. [DOI: 10.1021/ja4088055] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Thanyaporn Wongnate
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
| | - Panida Surawatanawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry, Mahidol University, Bangkok 10400 Thailand
| | - Surawit Visitsatthawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry, Mahidol University, Bangkok 10400 Thailand
| | - Jeerus Sucharitakul
- Department
of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant
Road, Patumwan, Bangkok, 10300 Thailand
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN United Kingdom
| | - Pimchai Chaiyen
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
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17
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Martinoli C, Dudek HM, Orru R, Edmondson DE, Fraaije MW, Mattevi A. Beyond the Protein Matrix: Probing Cofactor Variants in a Baeyer-Villiger Oxygenation Reaction. ACS Catal 2013; 3:3058-3062. [PMID: 24443704 DOI: 10.1021/cs400837z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A general question in biochemistry is the interplay between the chemical properties of cofactors and the surrounding protein matrix. Here, the functions of NADP+ and FAD are explored by investigation of a representative monooxygenase reconstituted with chemically-modified cofactor analogues. Like pieces of a jigsaw puzzle, the enzyme active site juxtaposes the flavin and nicotinamide rings, harnessing their H-bonding and steric properties to finely construct an oxygen-reacting center that restrains the flavin-peroxide intermediate in a catalytically-competent orientation. Strikingly, the regio- and stereoselectivities of the reaction are essentially unaffected by cofactor modifications. These observations indicate a remarkable robustness of this complex multi-cofactor active site, which has implications for enzyme design based on cofactor engineering approaches.
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Affiliation(s)
- Christian Martinoli
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
9, 27100 Pavia, Italy
| | - Hanna M. Dudek
- Molecular
Enzymology Group, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Roberto Orru
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
9, 27100 Pavia, Italy
| | - Dale E. Edmondson
- Departments
of Biochemistry and Chemistry, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, United States
| | - Marco W. Fraaije
- Molecular
Enzymology Group, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department
of Biology and Biotechnology, University of Pavia, Via Ferrata
9, 27100 Pavia, Italy
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18
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Hassan N, Tan TC, Spadiut O, Pisanelli I, Fusco L, Haltrich D, Peterbauer CK, Divne C. Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly. FEBS Open Bio 2013; 3:496-504. [PMID: 24282677 PMCID: PMC3839853 DOI: 10.1016/j.fob.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/17/2022] Open
Abstract
The flavin-dependent homotetrameric enzyme pyranose 2-oxidase (P2O) is found mostly, but not exclusively, in lignocellulose-degrading fungi where it catalyzes the oxidation of β-d-glucose to the corresponding 2-keto sugar concomitantly with hydrogen peroxide formation during lignin solubilization. Here, we present crystal structures of P2O from the efficient lignocellulolytic basidiomycete Phanerochaete chrysosporium. Structures were determined of wild-type PcP2O from the natural fungal source, and two variants of recombinant full-length PcP2O, both in complex with the slow substrate 3-deoxy-3-fluoro-β-d-glucose. The active sites in PcP2O and P2O from Trametes multicolor (TmP2O) are highly conserved with identical substrate binding. Our structural analysis suggests that the 17 °C higher melting temperature of PcP2O compared to TmP2O is due to an increased number of intersubunit salt bridges. The structure of recombinant PcP2O expressed with its natural N-terminal sequence, including a proposed propeptide segment, reveals that the first five residues of the propeptide intercalate at the interface between A and B subunits to form stabilizing, mainly hydrophobic, interactions. In the structure of mature PcP2O purified from the natural source, the propeptide segment in subunit A has been replaced by a nearby loop in the B subunit. We propose that the propeptide in subunit A stabilizes the A/B interface of essential dimers in the homotetramer and that, upon maturation, it is replaced by the loop in the B subunit to form the mature subunit interface. This would imply that the propeptide segment of PcP2O acts as an intramolecular chaperone for oligomerization at the A/B interface of the essential dimer. Structures of pyranose 2-oxidase from Phanerochaete chrysosporium were determined. The N-terminus may act as a propeptide with a role in homotetramer assembly. A large number of salt bridges between subunits provides thermostability. The substrate is bound in the productive binding mode for oxidation at C2.
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Key Words
- 2FGlc, 2-deoxy-2-fluoro-d-glucose
- 3FGlc, 3-deoxy-3-fluoro-d-glucose
- Crystal structure
- DTT, dithiothreitol
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- IMAC, by immobilized metal ion affinity chromatography
- IPTG, β-d-1-thiogalactopyranoside
- Lignin degradation
- MES, 2-(N-morpholino) ethanesulfonic acid
- MWCO, molecular weight cut off
- Oligomerization
- P2O, pyranose oxidase
- PBS, phosphate buffered saline
- PDB, Protein Data Bank
- PEG, polyethylene glycol
- Propeptide
- Pyranose 2-oxidase
- TEV, Tobacco Etch Virus
- Thermostability
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Affiliation(s)
- Noor Hassan
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
| | - Tien-Chye Tan
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Scheelelaboratoriet, Scheeles väg 2, S-17177 StockholmSweden
| | - Oliver Spadiut
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
| | - Ines Pisanelli
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Laura Fusco
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Dietmar Haltrich
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Clemens K. Peterbauer
- BOKU University of Natural Resources and Life Sciences, Food Biotechnology Laboratory, A-1190 ViennaAustria
| | - Christina Divne
- KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 StockholmSweden
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Scheelelaboratoriet, Scheeles väg 2, S-17177 StockholmSweden
- Corresponding author at: KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691StockholmSweden. Tel.: +46 8 55378296; fax: +46 8 55378468.
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19
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Wongnate T, Chaiyen P. The substrate oxidation mechanism of pyranose 2-oxidase and other related enzymes in the glucose-methanol-choline superfamily. FEBS J 2013; 280:3009-27. [DOI: 10.1111/febs.12280] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/01/2013] [Accepted: 04/04/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science; Mahidol University; Bangkok; Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science; Mahidol University; Bangkok; Thailand
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20
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Prongjit M, Sucharitakul J, Palfey BA, Chaiyen P. Oxidation mode of pyranose 2-oxidase is controlled by pH. Biochemistry 2013; 52:1437-45. [PMID: 23356577 DOI: 10.1021/bi301442x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoenzyme that catalyzes the oxidation of d-glucose and other aldopyranose sugars at the C2 position by using O₂ as an electron acceptor to form the corresponding 2-keto-sugars and H₂O₂. In this study, the effects of pH on the oxidative half-reaction of P2O were investigated using stopped-flow spectrophotometry. The results showed that flavin oxidation occurred via different pathways depending on the pH of the environment. At pH values lower than 8.0, reduced P2O reacts with O₂ to form a C4a-hydroperoxyflavin intermediate, leading to elimination of H₂O₂. At pH 8.0 and higher, the majority of the reduced P2O reacts with O₂ via a pathway that does not allow detection of the C4a-hydroperoxyflavin, and flavin oxidation occurs with decreased rate constants upon the rise in pH. The switching between the two modes of P2O oxidation is controlled by protonation of a group which has a pK(a) of 7.6 ± 0.1. Oxidation reactions of reduced P2O under rapid pH change as performed by stopped-flow mixing were different from the same reactions performed with enzyme pre-equilibrated at the same specified pH values, implying that the protonation of the group which controls the mode of flavin oxidation cannot be rapidly equilibrated with outside solvent. Using a double-mixing stopped-flow experiment, a rate constant for proton dissociation from the reaction site was determined to be 21.0 ± 0.4 s⁻¹.
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Affiliation(s)
- Methinee Prongjit
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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21
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Tan TC, Spadiut O, Wongnate T, Sucharitakul J, Krondorfer I, Sygmund C, Haltrich D, Chaiyen P, Peterbauer CK, Divne C. The 1.6 Å crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate. PLoS One 2013; 8:e53567. [PMID: 23326459 PMCID: PMC3541233 DOI: 10.1371/journal.pone.0053567] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022] Open
Abstract
Pyranose dehydrogenases (PDHs) are extracellular flavin-dependent oxidoreductases secreted by litter-decomposing fungi with a role in natural recycling of plant matter. All major monosaccharides in lignocellulose are oxidized by PDH at comparable yields and efficiencies. Oxidation takes place as single-oxidation or sequential double-oxidation reactions of the carbohydrates, resulting in sugar derivatives oxidized primarily at C2, C3 or C2/3 with the concomitant reduction of the flavin. A suitable electron acceptor then reoxidizes the reduced flavin. Whereas oxygen is a poor electron acceptor for PDH, several alternative acceptors, e.g., quinone compounds, naturally present during lignocellulose degradation, can be used. We have determined the 1.6-Å crystal structure of PDH from Agaricus meleagris. Interestingly, the flavin ring in PDH is modified by a covalent mono- or di-atomic species at the C(4a) position. Under normal conditions, PDH is not oxidized by oxygen; however, the related enzyme pyranose 2-oxidase (P2O) activates oxygen by a mechanism that proceeds via a covalent flavin C(4a)-hydroperoxide intermediate. Although the flavin C(4a) adduct is common in monooxygenases, it is unusual for flavoprotein oxidases, and it has been proposed that formation of the intermediate would be unfavorable in these oxidases. Thus, the flavin adduct in PDH not only shows that the adduct can be favorably accommodated in the active site, but also provides important details regarding the structural, spatial and physicochemical requirements for formation of this flavin intermediate in related oxidases. Extensive in silico modeling of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity. To evaluate the regioselectivity of D-glucose oxidation, reduction experiments were performed using fluorinated glucose. PDH was rapidly reduced by 3-fluorinated glucose, which has the C2 position accessible for oxidation, whereas 2-fluorinated glucose performed poorly (C3 accessible), indicating that the glucose C2 position is the primary site of attack.
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Affiliation(s)
- Tien Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Spadiut
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Iris Krondorfer
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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22
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Taniguchi S, Chosrowjan H, Wongnate T, Sucharitakul J, Chaiyen P, Tanaka F. Ultrafast fluorescence dynamics of flavin adenine dinucleotide in pyranose 2-oxidases variants and their complexes with acetate: Conformational heterogeneity with different dielectric constants. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Chaiyen P, Fraaije MW, Mattevi A. The enigmatic reaction of flavins with oxygen. Trends Biochem Sci 2012; 37:373-80. [DOI: 10.1016/j.tibs.2012.06.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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24
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Chosrowjan H, Taniguchi S, Wongnate T, Sucharitakul J, Chaiyen P, Tanaka F. Conformational heterogeneity in pyranose 2-oxidase from Trametes multicolor revealed by ultrafast fluorescence dynamics. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2011.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Liu L, Michelsen K, Kitova EN, Schnier PD, Brown A, Klassen JS. Deuterium Kinetic Isotope Effects on the Dissociation of a Protein–Fatty Acid Complex in the Gas Phase. J Am Chem Soc 2012; 134:5931-7. [DOI: 10.1021/ja300092w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - Klaus Michelsen
- Molecular Structure, Amgen, Thousand Oaks, California 91320, United States
| | | | - Paul D. Schnier
- Molecular Structure, Amgen, Thousand Oaks, California 91320, United States
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26
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Hernández-Ortega A, Ferreira P, Merino P, Medina M, Guallar V, Martínez AT. Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily. Chembiochem 2012; 13:427-35. [PMID: 22271643 DOI: 10.1002/cbic.201100709] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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27
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Fungal aryl-alcohol oxidase: a peroxide-producing flavoenzyme involved in lignin degradation. Appl Microbiol Biotechnol 2012; 93:1395-410. [DOI: 10.1007/s00253-011-3836-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 11/30/2022]
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28
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Wongnate T, Sucharitakul J, Chaiyen P. Identification of a Catalytic Base for Sugar Oxidation in the Pyranose 2-Oxidase Reaction. Chembiochem 2011; 12:2577-86. [DOI: 10.1002/cbic.201100564] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Indexed: 11/10/2022]
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29
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Tan TC, Haltrich D, Divne C. Regioselective Control of β-d-Glucose Oxidation by Pyranose 2-Oxidase Is Intimately Coupled to Conformational Degeneracy. J Mol Biol 2011; 409:588-600. [DOI: 10.1016/j.jmb.2011.04.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/01/2011] [Accepted: 04/08/2011] [Indexed: 10/18/2022]
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30
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Sucharitakul J, Wongnate T, Chaiyen P. Hydrogen peroxide elimination from C4a-hydroperoxyflavin in a flavoprotein oxidase occurs through a single proton transfer from flavin N5 to a peroxide leaving group. J Biol Chem 2011; 286:16900-9. [PMID: 21454569 DOI: 10.1074/jbc.m111.222976] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C4a-hydroperoxyflavin is found commonly in the reactions of flavin-dependent monooxygenases, in which it plays a key role as an intermediate that incorporates an oxygen atom into substrates. Only recently has evidence for its involvement in the reactions of flavoprotein oxidases been reported. Previous studies of pyranose 2-oxidase (P2O), an enzyme catalyzing the oxidation of pyranoses using oxygen as an electron acceptor to generate oxidized sugars and hydrogen peroxide (H(2)O(2)), have shown that C4a-hydroperoxyflavin forms in P2O reactions before it eliminates H(2)O(2) as a product (Sucharitakul, J., Prongjit, M., Haltrich, D., and Chaiyen, P. (2008) Biochemistry 47, 8485-8490). In this report, the solvent kinetic isotope effects (SKIE) on the reaction of reduced P2O with oxygen were investigated using transient kinetics. Our results showed that D(2)O has a negligible effect on the formation of C4a-hydroperoxyflavin. The ensuing step of H(2)O(2) elimination from C4a-hydroperoxyflavin was shown to be modulated by an SKIE of 2.8 ± 0.2, and a proton inventory analysis of this step indicates a linear plot. These data suggest that a single-proton transfer process causes SKIE at the H(2)O(2) elimination step. Double and single mixing stopped-flow experiments performed in H(2)O buffer revealed that reduced flavin specifically labeled with deuterium at the flavin N5 position generated kinetic isotope effects similar to those found with experiments performed with the enzyme pre-equilibrated in D(2)O buffer. This suggests that the proton at the flavin N5 position is responsible for the SKIE and is the proton-in-flight that is transferred during the transition state. The mechanism of H(2)O(2) elimination from C4a-hydroperoxyflavin is consistent with a single proton transfer from the flavin N5 to the peroxide leaving group, possibly via the formation of an intramolecular hydrogen bridge.
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Affiliation(s)
- Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Patumwan, Bangkok 10300, Thailand
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31
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Yuan H, Fu G, Brooks PT, Weber I, Gadda G. Steady-State Kinetic Mechanism and Reductive Half-Reaction of d-Arginine Dehydrogenase from Pseudomonas aeruginosa. Biochemistry 2010; 49:9542-50. [DOI: 10.1021/bi101420w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Irene Weber
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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32
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Tan TC, Pitsawong W, Wongnate T, Spadiut O, Haltrich D, Chaiyen P, Divne C. H-bonding and positive charge at the N5/O4 locus are critical for covalent flavin attachment in trametes pyranose 2-oxidase. J Mol Biol 2010; 402:578-94. [PMID: 20708626 DOI: 10.1016/j.jmb.2010.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 08/03/2010] [Accepted: 08/06/2010] [Indexed: 10/19/2022]
Abstract
Flavoenzymes perform a wide range of redox reactions in nature, and a subclass of flavoenzymes carry covalently bound cofactor. The enzyme-flavin bond helps to increase the flavin's redox potential to facilitate substrate oxidation in several oxidases. The formation of the enzyme-flavin covalent bond--the flavinylation reaction--has been studied for the past 40 years. For the most advocated mechanism of autocatalytic flavinylation, the quinone methide mechanism, appropriate stabilization of developing negative charges at the flavin N(1) and N(5) loci is crucial. Whereas the structural basis for stabilization at N(1) is relatively well studied, the structural requisites for charge stabilization at N(5) remain less clear. Here, we show that flavinylation of histidine 167 of pyranose 2-oxidase from Trametes multicolor requires hydrogen bonding at the flavin N(5)/O(4) locus, which is offered by the side chain of Thr169 when the enzyme is in its closed, but not open, state. Moreover, our data show that additional stabilization at N(5) by histidine 548 is required to ensure high occupancy of the histidyl-flavin bond. The combination of structural and spectral data on pyranose 2-oxidase mutants supports the quinone methide mechanism. Our results demonstrate an elaborate structural fine-tuning of the active site to complete its own formation that couples efficient holoenzyme synthesis to conformational substates of the substrate-recognition loop and concerted movements of side chains near the flavinylation ligand.
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Affiliation(s)
- Tien-Chye Tan
- Division of Biochemistry, School of Biotechnology, Royal Institute of Technology, Albanova University Center, Roslagstullsbacken 21, Stockholm, Sweden
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