1
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Wang L, Tang H, Zhu H, Xue Y, Zheng Y. Enhancement of the substrate specificity of D-amino acid oxidase based on tunnel-pocket engineering. Biotechnol Bioeng 2023; 120:3557-3569. [PMID: 37650151 DOI: 10.1002/bit.28541] [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: 06/08/2023] [Revised: 08/11/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
D-Amino acid oxidase (DAAO) selectively catalyzes the oxidative deamination of D-amino acids, making it one of the most promising routes for synthesizing optically pure L-amino acids, including L-phosphinothricin ( L-PPT), a chiral herbicide with significant market potential. However, the native DAAOs that have been reported have low activity against unnatural acid substrate D-PPT. Herein, we designed and screened a DAAO from Rhodotorula taiwanensis (RtwDAAO), and improved its catalytic potential toward D-PPT through protein engineering. A semirational design approach was employed to create a mutation library based on the tunnel-pocket engineering. After three rounds of iterative saturation mutagenesis, the optimal variant M3rd -SHVG was obtained, exhibiting a >2000-fold increase in relative activity. The kinetic parameters showed that M3rd -SHVG improved the substrate binding affinity and turnover number. This is the optimal parameter reported so far. Further, molecular dynamics simulation revealed that the M3rd -SHVG reshapes the tunnel-pocket and corrects the direction of enzyme-substrate binding, allowing efficiently catalyze unnatural substrates. Our strategy demonstrates that the redesign of tunnel-pockets is effective in improving the activity and kinetic efficiency of DAAO, which provides a valuable reference for enzymatic catalysis. With the M3rd -SHVG as biocatalyst, 500 mM D, L-PPT was completely converted and the yield reached 98%. The results laid the foundation for further industrial production.
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Affiliation(s)
- Liuyu Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Heng Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Hongli Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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2
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D-Amino Acids and Cancer: Friends or Foes? Int J Mol Sci 2023; 24:ijms24043274. [PMID: 36834677 PMCID: PMC9962368 DOI: 10.3390/ijms24043274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
α-amino acids exist in two configurations, named D-(dextro) and L-(levo) enantiomers. L-amino acids are used in protein synthesis and play a central role in cell metabolism. The effects of the L-amino acid composition of foods and the dietary modifications of this composition on the efficacy of cancer therapies have been widely investigated in relation to the growth and reproduction of cancerous cells. However, less is known about the involvement of D-amino acids. In recent decades, D-amino acids have been identified as natural biomolecules that play interesting and specific roles as common components of the human diet. Here, we focus on recent investigations showing altered D-amino acid levels in specific cancer types and on the various roles proposed for these biomolecules related to cancer cell proliferation, cell protection during therapy, and as putative, innovative biomarkers. Notwithstanding recent progress, the relationship between the presence of D-amino acids, their nutritional value, and cancer cell proliferation and survival represents an underrated scientific issue. Few studies on human samples have been reported to date, suggesting a need for routine analysis of D-amino acid content and an evaluation of the enzymes involved in regulating their levels in clinical samples in the near future.
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3
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Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids. Commun Chem 2020; 3:181. [PMID: 36703379 PMCID: PMC9814856 DOI: 10.1038/s42004-020-00432-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
L-amino acid oxidases (LAAOs) can be applied to convert racemic amino acids to D-isomers, which are potential precursors of pharmaceuticals. However, this application is hampered by the lack of available stable and structure-determined LAAOs. In this study, we attempt to address this limitation by utilizing two ancestral LAAOs: AncLAAO-N4 and AncLAAO-N5. AncLAAO-N4 has the highest thermal and temporal stabilities among the designed LAAOs that can be used for deracemization and stereoinversion. AncLAAO-N5 can provide X-ray crystal structures, which are helpful to reveal substrate recognition and reaction mechanisms of LAAOs at the molecular level. Next, we attempted to improve activity of AncLAAO-N4 toward L-Val through a semi-rational protein engineering method. Three variants with enhanced activity toward L-Val were obtained. Taken together, we believe that the activity and substrate selectivity of AncLAAOs give them the potential to be key enzymes in various chemoenzymatic reactions.
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4
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Puggioni V, Savinelli A, Miceli M, Molla G, Pollegioni L, Sacchi S. Biochemical characterization of mouse d-aspartate oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140472. [PMID: 32553892 DOI: 10.1016/j.bbapap.2020.140472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/27/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
D-amino acids research field has recently gained an increased interest since these atypical molecules have been discovered to play a plethora of different roles. In the mammalian central nervous system, d-aspartate (D-Asp) is critically involved in the regulation of glutamatergic neurotransmission by acting as an agonist of NMDA receptor. Accordingly, alterations in its metabolism have been related to different pathologies. D-Asp shows a peculiar temporal pattern of emergence during ontogenesis and soon after birth its brain levels are strictly regulated by the catabolic enzyme d-aspartate oxidase (DASPO), a FAD-dependent oxidase. Rodents have been widely used as in vivo models for deciphering molecular mechanisms and for testing novel therapeutic targets and drugs, but human targets can significantly differ. Based on these considerations, here we investigated the structural and functional properties of the mouse DASPO, in particular kinetic properties, ligand and flavin binding, oligomerization state and protein stability. We compared the obtained findings with those of the human enzyme (80% sequence identity) highlighting a different oligomeric state and a lower activity for the mouse DASPO, which apoprotein species exists in solution in two forms differing in FAD affinity. The features that distinguish mouse and human DASPO suggest that this flavoenzyme might control in a distinct way the brain D-Asp levels in different organisms.
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Affiliation(s)
- Vincenzo Puggioni
- "The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Antonio Savinelli
- "The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Matteo Miceli
- "The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Gianluca Molla
- "The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Loredano Pollegioni
- "The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; International Research Center on D-amino acids DAAIR, via Lepetit 34, 21040, Gerenzano (VA), Italy
| | - Silvia Sacchi
- "The Protein Factory 2.0", Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; International Research Center on D-amino acids DAAIR, via Lepetit 34, 21040, Gerenzano (VA), Italy.
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5
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Properties of l-amino acid deaminase: En route to optimize bioconversion reactions. Biochimie 2019; 158:199-207. [DOI: 10.1016/j.biochi.2019.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/18/2019] [Indexed: 12/24/2022]
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6
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Bernetti M, Rosini E, Mollica L, Masetti M, Pollegioni L, Recanatini M, Cavalli A. Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors. J Chem Inf Model 2018; 58:2255-2265. [DOI: 10.1021/acs.jcim.8b00518] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - Luca Mollica
- Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi″, Via F. Sforza 35, Milan, 20122, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano 20129, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100, Varese, Italy
| | - Maurizio Recanatini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum − Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
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7
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Subramanian K, Góra A, Spruijt R, Mitusińska K, Suarez-Diez M, Martins dos Santos V, Schaap PJ. Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access. PLoS One 2018; 13:e0198990. [PMID: 29906280 PMCID: PMC6003678 DOI: 10.1371/journal.pone.0198990] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/30/2018] [Indexed: 11/28/2022] Open
Abstract
D-amino acid oxidase (DAAO) degrades D-amino acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated and engineered for industrial and clinical applications. We combined information from literature with a detailed analysis of the structure to engineer mammalian DAAOs. The structural analysis was complemented with molecular dynamics simulations to characterize solvent accessibility and product release mechanisms. We identified non-obvious residues located on the loops on the border between the active site and the secondary binding pocket essential for pig and human DAAO substrate specificity and activity. We engineered DAAOs by mutating such critical residues and characterised the biochemical activity of the resulting variants. The results highlight the importance of the selected residues in modulating substrate specificity, product egress and enzyme activity, suggesting further steps of DAAO re-engineering towards desired clinical and industrial applications.
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Affiliation(s)
- Kalyanasundaram Subramanian
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
| | - Ruud Spruijt
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego, Gliwice, Poland
- Department of Chemistry, Silesian University of Technology, ks. Marcina Strzody, Gliwice, Poland
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Vitor Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng WE, Wageningen, The Netherlands
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8
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Toplak M, Wiedemann G, Ulićević J, Daniel B, Hoernstein SNW, Kothe J, Niederhauser J, Reski R, Winkler A, Macheroux P. The single berberine bridge enzyme homolog of Physcomitrella patens is a cellobiose oxidase. FEBS J 2018; 285:1923-1943. [PMID: 29633551 PMCID: PMC6001459 DOI: 10.1111/febs.14458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/17/2018] [Accepted: 03/29/2018] [Indexed: 11/28/2022]
Abstract
The berberine bridge enzyme from the California poppy Eschscholzia californica (EcBBE) catalyzes the oxidative cyclization of (S)‐reticuline to (S)‐scoulerine, that is, the formation of the berberine bridge in the biosynthesis of benzylisoquinoline alkaloids. Interestingly, a large number of BBE‐like genes have been identified in plants that lack alkaloid biosynthesis. This finding raised the question of the primordial role of BBE in the plant kingdom, which prompted us to investigate the closest relative of EcBBE in Physcomitrella patens (PpBBE1), the most basal plant harboring a BBE‐like gene. Here, we report the biochemical, structural, and in vivo characterization of PpBBE1. Our studies revealed that PpBBE1 is structurally and biochemically very similar to EcBBE. In contrast to EcBBE, we found that PpBBE1 catalyzes the oxidation of the disaccharide cellobiose to the corresponding lactone, that is, PpBBE1 is a cellobiose oxidase. The enzymatic reaction mechanism was characterized by a structure‐guided mutagenesis approach that enabled us to assign a catalytic role to amino acid residues in the active site of PpBBE1. In vivo experiments revealed the highest level of PpBBE1 expression in chloronema, the earliest stage of the plant's life cycle, where carbon metabolism is strongly upregulated. It was also shown that the enzyme is secreted to the extracellular space, where it may be involved in later steps of cellulose degradation, thereby allowing the moss to make use of cellulose for energy production. Overall, our results suggest that the primordial role of BBE‐like enzymes in plants revolved around primary metabolic reactions in carbohydrate utilization. Database Structural data are available in the PDB under the accession numbers 6EO4 and 6EO5.
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Affiliation(s)
- Marina Toplak
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | - Jelena Ulićević
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Bastian Daniel
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Jennifer Kothe
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany
| | | | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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9
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Nirasawa S, Nakahara K, Takahashi S. Cloning and characterization of the novel d-aspartyl endopeptidase, paenidase, from Paenibacillus sp. B38. J Biochem 2018; 164:103-112. [DOI: 10.1093/jb/mvy033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/26/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Satoru Nirasawa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Kazuhiko Nakahara
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Saori Takahashi
- Akita Research Institute of Food and Brewing, 4-26 Sanuki, Arayamachi, Akita 010-1623, Japan
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10
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Murtas G, Sacchi S, Valentino M, Pollegioni L. Biochemical Properties of Human D-Amino Acid Oxidase. Front Mol Biosci 2017; 4:88. [PMID: 29326945 PMCID: PMC5737116 DOI: 10.3389/fmolb.2017.00088] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/05/2017] [Indexed: 02/03/2023] Open
Abstract
D-amino acid oxidase catalyzes the oxidative deamination of D-amino acids. In the brain, the NMDA receptor coagonist D-serine has been proposed as its physiological substrate. In order to shed light on the mechanisms regulating D-serine concentration at the cellular level, we biochemically characterized human DAAO (hDAAO) in greater depth. In addition to clarify the physical-chemical properties of the enzyme, we demonstrated that divalent ions and nucleotides do not affect flavoenzyme function. Moreover, the definition of hDAAO substrate specificity demonstrated that D-cysteine is the best substrate, which made it possible to propose it as a putative physiological substrate in selected tissues. Indeed, the flavoenzyme shows a preference for hydrophobic amino acids, some of which are molecules relevant in neurotransmission, i.e., D-kynurenine, D-DOPA, and D-tryptophan. hDAAO shows a very low affinity for the flavin cofactor. The apoprotein form exists in solution in equilibrium between two alternative conformations: the one at higher affinity for FAD is favored in the presence of an active site ligand. This may represent a mechanism to finely modulate hDAAO activity by substrate/inhibitor presence. Taken together, the peculiar properties of hDAAO seem to have evolved in order to use this flavoenzyme in different tissues to meet different physiological needs related to D-amino acids.
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Affiliation(s)
- Giulia Murtas
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Silvia Sacchi
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli Studi dell'Insubria, Milan, Italy
| | - Mattia Valentino
- The Protein Factory, Politecnico di Milano and Università degli Studi dell'Insubria, Milan, Italy.,Sezione Adolfo Quilico, Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy.,The Protein Factory, Politecnico di Milano and Università degli Studi dell'Insubria, Milan, Italy
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11
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Rosini E, Melis R, Molla G, Tessaro D, Pollegioni L. Deracemization and Stereoinversion of α-Amino Acids byl-Amino Acid Deaminase. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700806] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
| | - Roberta Melis
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
| | - Gianluca Molla
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
| | - Davide Tessaro
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; p.zza Leonardo da Vinci 32 20133 Milano Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences; Università degli Studi dell'Insubria; via J.H. Dunant 3 21100 Varese Italy
- The Protein Factory; Politecnico di Milano and Università degli Studi dell'Insubria; via Mancinelli 7 20131 Milano Italy
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12
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Nakano S, Yasukawa K, Tokiwa T, Ishikawa T, Ishitsubo E, Matsuo N, Ito S, Tokiwa H, Asano Y. Origin of Stereoselectivity and Substrate/Ligand Recognition in an FAD-Dependent R-Selective Amine Oxidase. J Phys Chem B 2016; 120:10736-10743. [DOI: 10.1021/acs.jpcb.6b09328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Nakano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuyuki Yasukawa
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takaki Tokiwa
- Department
of Chemistry, Graduate School of Science, Tohoku University, Aramaki,
Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeshi Ishikawa
- Department
of Molecular Microbiology and Immunology, Graduate School of Biomedical
Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Erika Ishitsubo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Naoya Matsuo
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Sohei Ito
- School
of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroaki Tokiwa
- Department
of Chemistry, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
- Research
Center of Smart Molecules, Rikkyo University, Nishi-ikebukuro, Toshimaku, Tokyo 171-8501, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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13
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Lederer F, Vignaud C, North P, Bodevin S. Trifluorosubstrates as mechanistic probes for an FMN-dependent l-2-hydroxy acid-oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1215-1221. [PMID: 27155230 DOI: 10.1016/j.bbapap.2016.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 11/29/2022]
Abstract
A controversy exists with respect to the mechanism of l-2-hydroxy acid oxidation by members of a family of FMN-dependent enzymes. A so-called carbanion mechanism was initially proposed, in which the active site histidine abstracts the substrate α-hydrogen as a proton, followed by electron transfer from the carbanion to the flavin. But an alternative mechanism was not incompatible with some results, a mechanism in which the active site histidine instead picks up the substrate hydroxyl proton and a hydride transfer occurs. Even though more recent experiments ruling out such a mechanism were published (Rao & Lederer (1999) Protein Science 7, 1531-1537), a few authors have subsequently interpreted their results with variant enzymes in terms of a hydride transfer. In the present work, we analyse the reactivity of trifluorolactate, a substrate analogue, with the flavocytochrome b2 (Fcb2) flavodehydrogenase domain, compared to its reactivity with an NAD-dependent lactate dehydrogenase (LDH), for which this compound is known to be an inhibitor (Pogolotti & Rupley (1973) Biochem. Biophys. Res. Commun, 55, 1214-1219). Indeed, electron attraction by the three fluorine atoms should make difficult the removal of the α-H as a hydride. We also analyse the reactivity of trifluoropyruvate with the FMN- and NAD-dependent enzymes. The results substantiate a different effect of the fluorine substituents on the two enzymes compared to their normal substrates. In the discussion we analyse the conclusions of recent papers advocating a hydride transfer mechanism for the family of l-2-hydroxy acid oxidizing FMN-dependent enzymes.
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Affiliation(s)
- Florence Lederer
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France; Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Caroline Vignaud
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Paul North
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Sabrina Bodevin
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
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14
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Motta P, Molla G, Pollegioni L, Nardini M. Structure-Function Relationships in l-Amino Acid Deaminase, a Flavoprotein Belonging to a Novel Class of Biotechnologically Relevant Enzymes. J Biol Chem 2016; 291:10457-75. [PMID: 27022028 DOI: 10.1074/jbc.m115.703819] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/11/2023] Open
Abstract
l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a membrane flavoenzyme that catalyzes the deamination of neutral and aromatic l-amino acids into α-keto acids and ammonia. PmaLAAD does not use dioxygen to re-oxidize reduced FADH2 and thus does not produce hydrogen peroxide; instead, it uses a cytochrome b-like protein as an electron acceptor. Although the overall fold of this enzyme resembles that of known amine or amino acid oxidases, it shows the following specific structural features: an additional novel α+β subdomain placed close to the putative transmembrane α-helix and to the active-site entrance; an FAD isoalloxazine ring exposed to solvent; and a large and accessible active site suitable to bind large hydrophobic substrates. In addition, PmaLAAD requires substrate-induced conformational changes of part of the active site, particularly in Arg-316 and Phe-318, to achieve the correct geometry for catalysis. These studies are expected to pave the way for rationally improving the versatility of this flavoenzyme, which is critical for biocatalysis of enantiomerically pure amino acids.
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Affiliation(s)
- Paolo Motta
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese
| | - Gianluca Molla
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and
| | - Loredano Pollegioni
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and
| | - Marco Nardini
- the Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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15
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Luks L, Sacchi S, Pollegioni L, Dietrich DR. Novel insights into renal D-amino acid oxidase accumulation: propiverine changes DAAO localization and peroxisomal size in vivo. Arch Toxicol 2016; 91:427-437. [PMID: 26961980 DOI: 10.1007/s00204-016-1685-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/22/2016] [Indexed: 11/29/2022]
Abstract
Chronic exposure to propiverine, a frequently prescribed pharmaceutical for treatment of overactive bladder and incontinence, provokes massive protein accumulation in the cytosol and nucleus of renal proximal tubule epithelial cells in rats. Previously, the accumulating protein was identified as D-amino acid oxidase (DAAO), a peroxisomal flavoenzyme expressed in kidney, liver and brain. The cellular mechanism of propiverine-induced DAAO accumulation, however, remains unexplained and poorly characterized. Therefore, to further increase the understanding of DAAO accumulation in rat kidney, this study aimed to characterize DAAO accumulations using differential immunofluorescent staining of rat kidney sections as well as in vitro binding analyses and proteasomal activity studies. We demonstrated that propiverine is neither a ligand of DAAO nor an inhibitor of the proteasome in vitro. However, propiverine treatment resulted in a significant decrease of peroxisomal size in rat proximal tubule epithelial cells. Moreover, peroxisomal catalase also accumulated in the cytosol and nuclei of propiverine-treated rats concurrently with DAAO. Taken together, our study indicates that propiverine treatment affects the trafficking and/or degradation of peroxisomal proteins such as DAAO and catalase by a so far unique and unknown mechanism.
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Affiliation(s)
- Lisanne Luks
- Human and Environmental Toxicology, University of Konstanz, Universitätsstrasse 10, 78457, Constance, Germany
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,The Protein Factory Research Center, Politecnico di Milano and University of Insubria, Milan, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,The Protein Factory Research Center, Politecnico di Milano and University of Insubria, Milan, Varese, Italy
| | - Daniel R Dietrich
- Human and Environmental Toxicology, University of Konstanz, Universitätsstrasse 10, 78457, Constance, Germany.
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16
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Cappelletti P, Piubelli L, Murtas G, Caldinelli L, Valentino M, Molla G, Pollegioni L, Sacchi S. Structure-function relationships in human d-amino acid oxidase variants corresponding to known SNPs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1150-9. [PMID: 25701391 DOI: 10.1016/j.bbapap.2015.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/05/2015] [Accepted: 02/07/2015] [Indexed: 12/11/2022]
Abstract
In the brain, d-amino acid oxidase plays a key role in modulating the N-methyl-d-aspartate receptor (NMDAR) activation state, catalyzing the stereospecific degradation of the coagonist d-serine. A relationship between d-serine signaling deregulation, NMDAR dysfunction, and CNS diseases is presumed. Notably, the R199W substitution in human DAAO (hDAAO) was associated with familial amyotrophic lateral sclerosis (ALS), and further coding substitutions, i.e., R199Q and W209R, were also deposited in the single nucleotide polymorphism database. Here, we investigated the biochemical properties of these different hDAAO variants. The W209R hDAAO variant shows an improved d-serine degradation ability (higher activity and affinity for the cofactor FAD) and produces a greater decrease in cellular d/(d+l) serine ratio than the wild-type counterpart when expressed in U87 cells. The production of H2O2 as result of excessive d-serine degradation by this hDAAO variant may represent the factor affecting cell viability after stable transfection. The R199W/Q substitution in hDAAO altered the protein conformation and enzymatic activity was lost under conditions resembling the cellular ones: this resulted in an abnormal increase in cellular d-serine levels. Altogether, these results indicate that substitutions that affect hDAAO functionality directly impact on d-serine cellular levels (at least in the model cell system used). The pathological effect of the expression of the R199W hDAAO, as observed in familial ALS, originates from both protein instability and a decrease in kinetic efficiency: the increase in synaptic d-serine may be mainly responsible for the neurotoxic effect. This information is expected to drive future targeted treatments.
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Affiliation(s)
- Pamela Cappelletti
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Giulia Murtas
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Laura Caldinelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Mattia Valentino
- The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy; CNR, Istituto di Chimica del Riconoscimento Molecolare, Sezione Adolfo Quilico, via M. Bianchi 9, 20131 Milano, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Silvia Sacchi
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, via J. H. Dunant 3, 21100 Varese, Italy; The Protein Factory, Politecnico di Milano, ICMR-CNR, Università degli Studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy.
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17
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Tessaro D, Pollegioni L, Piubelli L, D’Arrigo P, Servi S. Systems Biocatalysis: An Artificial Metabolism for Interconversion of Functional Groups. ACS Catal 2015. [DOI: 10.1021/cs502064s] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- D. Tessaro
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, p.za L. da Vinci 32, 20133 Milano, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - L. Pollegioni
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - L. Piubelli
- Dipartimento
di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - P. D’Arrigo
- Dipartimento
di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, p.za L. da Vinci 32, 20133 Milano, Italy
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - S. Servi
- The
Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano and Università degli Studi dell’Insubria, via Mancinelli 7, 20131 Milano, Italy
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18
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D'Arrigo P, Allegretti C, Fiorati A, Piubelli L, Rosini E, Tessaro D, Valentino M, Pollegioni L. Immobilization of l-aspartate oxidase from Sulfolobus tokodaii as a biocatalyst for resolution of aspartate solutions. Catal Sci Technol 2015. [DOI: 10.1039/c4cy00968a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
l-Aspartate oxidase from the thermophilic archaebacterium Sulfolobus tokodaii (StLASPO) catalyzes the stereoselective oxidative deamination of l-aspartate to yield oxaloacetate, ammonia and hydrogen peroxide.
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Affiliation(s)
- Paola D'Arrigo
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Chiara Allegretti
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Andrea Fiorati
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Luciano Piubelli
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
| | - Elena Rosini
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
| | - Davide Tessaro
- Dipartimento di Chimica
- Materiali e Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20133 Milano
- Italy
| | - Mattia Valentino
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
| | - Loredano Pollegioni
- The Protein Factory
- Politecnico di Milano
- ICRM CNR Milano
- and Università degli Studi dell'Insubria
- 20131 Milano
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19
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Molla G, Nardini M, Motta P, D'Arrigo P, Panzeri W, Pollegioni L. Aminoacetone oxidase from Streptococcus oligofermentans belongs to a new three-domain family of bacterial flavoproteins. Biochem J 2014; 464:387-99. [PMID: 25269103 DOI: 10.1042/bj20140972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The aaoSo gene from Streptococcus oligofermentans encodes a 43 kDa flavoprotein, aminoacetone oxidase (SoAAO), which was reported to possess a low catalytic activity against several different L-amino acids; accordingly, it was classified as an L-amino acid oxidase. Subsequently, SoAAO was demonstrated to oxidize aminoacetone (a pro-oxidant metabolite), with an activity ~25-fold higher than the activity displayed on L-lysine, thus lending support to the assumption of aminoacetone as the preferred substrate. In the present study, we have characterized the SoAAO structure-function relationship. SoAAO is an FAD-containing enzyme that does not possess the classical properties of the oxidase/dehydrogenase class of flavoproteins (i.e. no flavin semiquinone formation is observed during anaerobic photoreduction as well as no reaction with sulfite) and does not show a true L-amino acid oxidase activity. From a structural point of view, SoAAO belongs to a novel protein family composed of three domains: an α/β domain corresponding to the FAD-binding domain, a β-domain partially modulating accessibility to the coenzyme, and an additional α-domain. Analysis of the reaction products of SoAAO on aminoacetone showed 2,5-dimethylpyrazine as the main product; we propose that condensation of two aminoacetone molecules yields 3,6-dimethyl-2,5-dihydropyrazine that is subsequently oxidized to 2,5-dimethylpyrazine. The ability of SoAAO to bind two molecules of the substrate analogue O-methylglycine ligand is thought to facilitate the condensation reaction. A specialized role for SoAAO in the microbial defence mechanism related to aminoacetone catabolism through a pathway yielding dimethylpyrazine derivatives instead of methylglyoxal can be proposed.
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Affiliation(s)
- Gianluca Molla
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
| | - Marco Nardini
- ‡Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Paolo Motta
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
| | - Paola D'Arrigo
- †The Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano, ICRM CNR Milano, and Università degli Studi deII'Insubria, Varese, Italy
| | - Walter Panzeri
- ║CNR-Istituto di Chimica del Riconoscimento Molecolare, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
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20
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Hopkins SC, Heffernan MLR, Saraswat LD, Bowen CA, Melnick L, Hardy LW, Orsini MA, Allen MS, Koch P, Spear KL, Foglesong RJ, Soukri M, Chytil M, Fang QK, Jones SW, Varney MA, Panatier A, Oliet SHR, Pollegioni L, Piubelli L, Molla G, Nardini M, Large TH. Structural, Kinetic, and Pharmacodynamic Mechanisms of d-Amino Acid Oxidase Inhibition by Small Molecules. J Med Chem 2013; 56:3710-24. [DOI: 10.1021/jm4002583] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Seth C. Hopkins
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | | | - Lakshmi D. Saraswat
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Carrie A. Bowen
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Laurence Melnick
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Larry W. Hardy
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Michael A. Orsini
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | | | - Patrick Koch
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Kerry L. Spear
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | | | | | - Milan Chytil
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Q. Kevin Fang
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Steven W. Jones
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Mark A. Varney
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Aude Panatier
- Neurocentre Magendie, Inserm U862 and Université de Bordeaux, Bordeaux, F-33077, France
| | - Stephane H. R. Oliet
- Neurocentre Magendie, Inserm U862 and Université de Bordeaux, Bordeaux, F-33077, France
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie
e Scienze della Vita, Università degli Studi dell’Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
- The Protein Factory, Politecnico di Milano, ICRM-CNR and Università degli Studi dell’Insubria, Via Mancinelli 7,
20131 Milano, Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie
e Scienze della Vita, Università degli Studi dell’Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
- The Protein Factory, Politecnico di Milano, ICRM-CNR and Università degli Studi dell’Insubria, Via Mancinelli 7,
20131 Milano, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie
e Scienze della Vita, Università degli Studi dell’Insubria, Via J. H. Dunant 3, 21100 Varese, Italy
- The Protein Factory, Politecnico di Milano, ICRM-CNR and Università degli Studi dell’Insubria, Via Mancinelli 7,
20131 Milano, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milan, I-20133 Milano, Italy
| | - Thomas H. Large
- Sunovion Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
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21
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Bava A, Gornati R, Cappellini F, Caldinelli L, Pollegioni L, Bernardini G. D-amino acid oxidase-nanoparticle system: a potential novel approach for cancer enzymatic therapy. Nanomedicine (Lond) 2013; 8:1797-806. [PMID: 23384700 DOI: 10.2217/nnm.12.187] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM The authors propose a new magnetic nanoparticle-enzyme system for cancer therapy capable of targeting the enzyme and consequently decreasing the adverse effects, meanwhile improving the patient's life quality. MATERIALS & METHODS The authors have functionalized Fe3O4 nanoparticles with 3-amino-propyltriethoxysilane (APTES) and conjugated it to yeast D-amino acid oxidase (DAAO) by coupling this with glutaraldehyde. RESULTS & CONCLUSION The authors have tested the Fe3O4-APTES-DAAO system on three tumor cell lines. Exposed cells show, at the electron microscope level, nanoparticles on the surface of the plasma membrane and inside endocytic vesicles. Fe3O4-APTES-DAAO caused a substantial decrease of cell viability greatly augmented when D-alanine, a DAAO substrate, was added. Fe3O4-APTES-DAAO was demonstrated to be more effective than free DAAO, confirming the validity of the system in cancer therapy.
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Affiliation(s)
- Adriana Bava
- Dipartimento di Biotecnologie & Scienze della Vita, Università degli Studi dell'Insubria, Via Dunant 3, Varese, Italy
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22
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A thermostable L-aspartate oxidase: a new tool for biotechnological applications. Appl Microbiol Biotechnol 2013; 97:7285-95. [PMID: 23371294 DOI: 10.1007/s00253-013-4688-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 12/22/2012] [Accepted: 12/27/2012] [Indexed: 11/27/2022]
Abstract
L-Amino acid oxidases (LAAOs) are homodimeric flavin adenine dinucleotide (FAD)-containing flavoproteins that catalyze the stereospecific oxidative deamination of L-amino acids to α-keto acids, ammonia, and hydrogen peroxide. Unlike the D-selective counterpart, the biotechnological application of LAAOs has not been thoroughly advanced because of the difficulties in their expression as recombinant protein in prokaryotic hosts. In this work, L-aspartate oxidase from the thermophilic archea Sulfolobus tokodaii (StLASPO, specific for L-aspartate and L-asparagine only) was efficiently produced as recombinant protein in E. coli in the active form as holoenzyme. This recombinant flavoenzyme shows the classical properties of FAD-containing oxidases. Indeed, StLASPO shows distinctive features that makes it attractive for biotechnological applications: high thermal stability (it is fully stable up to 80 °C) and high temperature optimum, stable activity in a broad range of pH (7.0-10.0), weak inhibition by the product oxaloacetate and by D-aspartate, and tight binding of the FAD cofactor. This latter property significantly distinguishes StLASPO from the E. coli counterpart. StLASPO represents an appropriate novel biocatalyst for the production of D-aspartate and a well-suited protein scaffold to evolve a LAAO activity by protein engineering.
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23
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Structure–function relationships in human d-amino acid oxidase. Amino Acids 2012; 43:1833-50. [DOI: 10.1007/s00726-012-1345-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/16/2012] [Indexed: 01/01/2023]
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24
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Frattini LF, Piubelli L, Sacchi S, Molla G, Pollegioni L. Is rat an appropriate animal model to study the involvement of D-serine catabolism in schizophrenia? Insights from characterization of D-amino acid oxidase. FEBS J 2011; 278:4362-73. [PMID: 21981077 DOI: 10.1111/j.1742-4658.2011.08354.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
D-Amino acid oxidase (DAAO; EC1.4.3.3) has been proposed to play a main role in the degradation of D-serine, an allosteric activator of the N-methyl-D-aspartate-type glutamate receptor in the human brain, and to be associated with the onset of schizophrenia. To prevent excessive D-serine degradation, novel drugs for schizophrenia treatment based on DAAO inhibition were designed and tested on rats. However, the properties of rat DAAO are unknown and various in vivo trials have demonstrated the effects of DAAO inhibitors on d-serine concentration in rats. In the present study, rat DAAO was efficiently expressed in Escherichia coli. The recombinant enzyme was purified as an active, 40 kDa monomeric flavoenzyme showing the basic properties of the dehydrogenase-oxidase class of flavoproteins. Rat DAAO differs significantly from the human counterpart because: (a) it possesses a different substrate specificity; (b) it shows a lower kinetic efficiency, mainly as a result of a low substrate affinity; (c) it differs in affinity for the binding of classical inhibitors; (d) it is a stable monomer in the absence of an active site ligand; and (e) it interacts with the mammalian protein modulator pLG72 yielding a ~100 kDa complex in addition to the ~200 kDa one, as formed by the human DAAO. Furthermore, the concentration of endogenous D-serine in U87 glioblastoma cells was not affected by transfection with rat DAAO, whereas it was significantly decreased when expressing the human homologue. These results raise doubt on the use of the rat as a model system for testing new drugs against schizophrenia and indicate a different physiological function of DAAO in rodents and humans.
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Affiliation(s)
- Luca F Frattini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, Varese, Italy
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25
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New biotech applications from evolved D-amino acid oxidases. Trends Biotechnol 2011; 29:276-83. [PMID: 21397351 DOI: 10.1016/j.tibtech.2011.01.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/24/2011] [Accepted: 01/27/2011] [Indexed: 11/20/2022]
Abstract
D-Amino acid oxidase (DAAO) is a well-known flavoenzyme that catalyzes the oxygen-dependent oxidative deamination of amino acid D-isomers with absolute stereospecificity, which results in α-keto acids, ammonia and hydrogen peroxide. Recently, the extraordinary functional plasticity of DAAO has become evident; in turn, boosting research on this flavoprotein. Protein engineering has allowed for a redesign of DAAO substrate specificity, oxygen affinity, cofactor binding, stability, and oligomeric state. We review recent developments in utilizing DAAO, including as a biocatalyst for resolving racemic amino acid mixtures, as a tool for biosensing, and as a new mechanism of herbicide resistance. Perspectives for future biotechnological applications of this oxidative biocatalyst are also outlined.
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High Soluble Expression of d-Amino Acid Oxidase in Escherichia coli Regulated by a Native Promoter. Appl Biochem Biotechnol 2008; 158:313-22. [DOI: 10.1007/s12010-008-8325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
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Boselli A, Piubelli L, Molla G, Pilone MS, Pollegioni L, Sacchi S. Investigating the role of active site residues of Rhodotorula gracilis d-amino acid oxidase on its substrate specificity. Biochimie 2007; 89:360-8. [PMID: 17145127 DOI: 10.1016/j.biochi.2006.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 10/27/2006] [Indexed: 11/21/2022]
Abstract
D-amino acid oxidase (DAAO) is a flavoprotein that catalyzes stereospecifically the oxidative deamination of D-amino acids. The wild-type DAAO is mainly active on neutral D-amino acids, while basic D-amino acids are poor substrates and the acidic ones are virtually not oxidized. To present a comprehensive picture of how the active site residues can modulate the substrate specificity a number of mutants at position M213, Y223, Y238, R285, S335, and Q339 were prepared in the enzyme from the yeast Rhodotorula gracilis. All DAAO mutants have spectral properties similar to those of the wild-type enzyme and are catalytically active, thus excluding an essential role in catalysis; a lower activity on neutral and basic amino acids was observed. Interestingly, an increase in activity and (k(cat)/K(m))(app) ratio on D-aspartate was observed for all the mutants containing an additional charged residue in the active site. The active site of yeast DAAO appears to be a highly evolved scaffold built up through evolution to optimize the oxidative deamination of neutral D-amino acids without limiting its substrate specificity. It is noteworthy, that introduction of a sole, additional, positively charged residue in the active site is sufficient to optimize the reactivity on acidic D-amino acids, giving rise to kinetic properties similar to those of D-aspartate oxidase.
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Affiliation(s)
- Angelo Boselli
- Department of Biotechnology and Molecular Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
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Geueke B, Weckbecker A, Hummel W. Overproduction and characterization of a recombinant D-amino acid oxidase from Arthrobacter protophormiae. Appl Microbiol Biotechnol 2007; 74:1240-7. [PMID: 17279391 DOI: 10.1007/s00253-006-0776-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 11/17/2006] [Accepted: 11/17/2006] [Indexed: 11/26/2022]
Abstract
A screening of soil samples for D-amino acid oxidase (D-AAO) activity led to the isolation and identification of the gram-positive bacterium Arthrobacter protophormiae. After purification of the wild-type D-AAO, the gene sequence was determined and designated dao. An alignment of the deduced primary structure with eukaryotic D-AAOs and D-aspartate oxidases showed that the D-AAO from A. protophormiae contains five of six conserved regions; the C-terminal type 1 peroxisomal targeting signal that is typical for D-AAOs from eukaryotic origin is missing. The dao gene was cloned and expressed in Escherichia coli. The purified recombinant D-AAO had a specific activity of 180 U mg protein(-1) for D-methionine and was slightly inhibited in the presence of L-methionine. Mainly, basic and hydrophobic D-amino acids were oxidized by the strictly enantioselective enzyme. After a high cell density fermentation, 2.29 x 10(6) U of D-AAO were obtained from 15 l of fermentation broth.
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Affiliation(s)
- Birgit Geueke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Research Centre Jülich, 52426 Jülich, Germany.
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29
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Katane M, Seida Y, Sekine M, Furuchi T, Homma H. Caenorhabditis eleganshas two genes encoding functionald-aspartate oxidases. FEBS J 2006; 274:137-49. [PMID: 17140416 DOI: 10.1111/j.1742-4658.2006.05571.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four cDNA clones that were annotated in the database as encoding d-amino acid oxidase (DAAO) or d-aspartate oxidase (DASPO) were isolated by RT-PCR from Caenorhabditis elegans RNA. The proteins (Y69Ap, C47Ap, F18Ep, and F20Hp) encoded by the cloned cDNAs were expressed in Escherichia coli as recombinant proteins with an N-terminal His-tag. All proteins except F20Hp were recovered in the soluble fractions. The recombinant Y69Ap has functional DAAO activity, as it can deaminate neutral and basic d-amino acids, whereas the recombinants C47Ap and F18Ep have functional DASPO activities, as they can deaminate acidic d-amino acids. Additional experiments using purified recombinant proteins revealed that Y69Ap deaminates d-Arg more efficiently than d-Ala and d-Met, and that C47Ap and F18Ep show distinct kinetic properties against d-Asp, d-Glu, and N-methyl-d-Asp. This is the first time that cDNA cloning of invertebrate DAAO and DASPO genes has been reported. In addition, our study reveals for the first time that C. elegans has at least two genes encoding functional DASPOs and one gene encoding DAAO, although it had previously been thought that organisms only bear one copy each of these genes. The two C. elegans DASPOs differ in their substrate specificities and possibly also in their subcellular localization.
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Affiliation(s)
- Masumi Katane
- Laboratory of Biomolecular Science, School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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Ferreira P, Ruiz-Dueñas FJ, Martínez MJ, van Berkel WJH, Martínez AT. Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme. FEBS J 2006; 273:4878-88. [PMID: 16999821 DOI: 10.1111/j.1742-4658.2006.05488.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Aryl-alcohol oxidase provides H(2)O(2) for lignin biodegradation, a key process for carbon recycling in land ecosystems that is also of great biotechnological interest. However, little is known of the structural determinants of the catalytic activity of this fungal flavoenzyme, which oxidizes a variety of polyunsaturated alcohols. Different alcohol substrates were docked on the aryl-alcohol oxidase molecular structure, and six amino acid residues surrounding the putative substrate-binding site were chosen for site-directed mutagenesis modification. Several Pleurotus eryngii aryl-alcohol oxidase variants were purified to homogeneity after heterologous expression in Emericella nidulans, and characterized in terms of their steady-state kinetic properties. Two histidine residues (His502 and His546) are strictly required for aryl-alcohol oxidase catalysis, as shown by the lack of activity of different variants. This fact, together with their location near the isoalloxazine ring of FAD, suggested a contribution to catalysis by alcohol activation, enabling its oxidation by flavin-adenine dinucleotide (FAD). The presence of two aromatic residues (at positions 92 and 501) is also required, as shown by the conserved activity of the Y92F and F501Y enzyme variants and the strongly impaired activity of Y92A and F501A. By contrast, a third aromatic residue (Tyr78) does not seem to be involved in catalysis. The kinetic and spectral properties of the Phe501 variants suggested that this residue could affect the FAD environment, modulating the catalytic rate of the enzyme. Finally, L315 affects the enzyme k(cat), although it is not located in the near vicinity of the cofactor. The present study provides the first evidence for the role of aryl-alcohol oxidase active site residues.
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Affiliation(s)
- Patricia Ferreira
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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31
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Errico F, Pirro MT, Affuso A, Spinelli P, De Felice M, D'Aniello A, Di Lauro R. A physiological mechanism to regulate d-aspartic acid and NMDA levels in mammals revealed by d-aspartate oxidase deficient mice. Gene 2006; 374:50-7. [PMID: 16516413 DOI: 10.1016/j.gene.2006.01.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Accepted: 01/13/2006] [Indexed: 11/18/2022]
Abstract
Free D-aspartic acid and NMDA are present in the mammalian central nervous system and endocrine glands at significant concentrations, but their physiological role is still matter of debate. The only enzyme known to metabolize in vitro selectively these D-amino acids is D-aspartate oxidase (DDO). To clarify the role in vivo of the enzyme, we generated mice with targeted deletion of Ddo gene by homologous recombination. Mutated animals showed increased amounts of both D-aspartic acid and NMDA in all tissues examined demonstrating a physiological role of DDO in the regulation of their endogenous levels.
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Affiliation(s)
- Francesco Errico
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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32
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Sacchi S, Boselli A, Job V, Pilone MS, Pollegioni L, Molla G. The role of tyrosines 223 and 238 in Rhodotorula gracilis d-amino acid oxidase catalysis: Interpretation of double mutations. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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33
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Sarower MG, Okada S, Abe H. Catalytic and structural characteristics of carp hepatopancreas D-amino acid oxidase expressed in Escherichia coli. Comp Biochem Physiol B Biochem Mol Biol 2005; 140:417-25. [PMID: 15694590 DOI: 10.1016/j.cbpc.2004.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 11/05/2004] [Accepted: 11/08/2004] [Indexed: 11/28/2022]
Abstract
D-amino acid oxidase of carp (Cyprinus carpio) hepatopancreas was overexpressed in Escherichia coli cells and purified to homogeneity for the first time in animal tissues other than pig kidney. The purified preparation had a specific activity of 293 units mg(-1) protein toward D-alanine as a substrate. It showed the highest activity toward D-alanine with a low Km of 0.23 mM and a high kcat of 190 s(-1) compared to 10 s(-1) of the pig kidney enzyme. Nonpolar and polar uncharged D-amino acids were preferable substrates to negatively or positively charged amino acids. The enzyme exhibited better thermal and pH stabilities than several yeast counterparts or the pig kidney enzyme. Secondary structure topology consisted of 11 alpha-helices and 17 beta-strands that differed slightly from pig kidney and Rhodotorula gracilis enzymes. A three-dimensional model of the carp enzyme constructed from a deduced amino acid sequence resembled that of pig kidney D-amino acid oxidase but with a shorter active site loop and a longer C-terminal loop. Judging from these characteristics, carp D-amino acid oxidase is close to the pig kidney enzyme structurally, but analogous to the R. gracilis enzyme enzymatically in turnover rate and pH and temperature stabilities.
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Affiliation(s)
- Mohammed Golam Sarower
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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34
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Pollegioni L, Caldinelli L, Molla G, Sacchi S, Pilone MS. Catalytic properties of D-amino acid oxidase in cephalosporin C bioconversion: a comparison between proteins from different sources. Biotechnol Prog 2004; 20:467-73. [PMID: 15058991 DOI: 10.1021/bp034206q] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lacking an efficient process to produce 7-aminocephalosporanic acid from cephalosporin C in a single step, d-amino acid oxidase (DAAO) is of foremost importance in the industrial, two-step process used for this purpose. We report a detailed study on the catalytic properties of the three available DAAOs, namely, a mammalian DAAO and two others from yeast (Rhodotorula gracilis and Trigonopsis variabilis). In comparing the kinetic parameters determined for the three DAAOs, with both cephalosporin C and d-alanine as substrate, the catalytic efficiency of the two enzymes from microorganism is at least 2 orders of magnitude higher than that of pig kidney DAAO. Furthermore, the mammalian enzyme is more sensitive to product inhibition (from hydrogen peroxide and glutaryl-7-aminocephalosporanic acid). Therefore, enzymes from microorganisms appear to be by far more suitable catalysts for bioconversion, although some different minor differences are present between them (e.g., a higher activity of the R. gracilis enzyme when the bioconversion is carried out at saturating oxygen concentration). The mammalian DAAO, even being a poor catalyst, is more stable with respect to temperature than the R. gracilis enzyme in the free form. In any case, for industrial purposes DAAO is used only in the immobilized form where a strong enzyme stabilization occurs.
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Affiliation(s)
- Loredano Pollegioni
- Department of Structural and Functional Biology, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
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35
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Fitzpatrick PF. Carbanion versus hydride transfer mechanisms in flavoprotein-catalyzed dehydrogenations. Bioorg Chem 2004; 32:125-39. [PMID: 15110192 DOI: 10.1016/j.bioorg.2003.02.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2003] [Indexed: 11/26/2022]
Abstract
The present understanding of the mechanisms by which flavoproteins oxidize amino acid or hydroxy acids to the respective imino or keto acids is reviewed. The observation that many of these enzymes catalyze the elimination of HBr or HCl from the appropriate beta-halogenated substrate was long considered evidence for a carbanion intermediate. Recent structural and mechanistic studies are not compatible with the intermediacy of carbanions in the reactions catalyzed by d-amino acid oxidase and flavocytochrome b(2). In contrast, the data are most consistent with mechanisms involving direct hydride transfer.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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36
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Boselli A, Piubelli L, Molla G, Sacchi S, Pilone MS, Ghisla S, Pollegioni L. On the mechanism of Rhodotorula gracilis d-amino acid oxidase: role of the active site serine 335. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1702:19-32. [PMID: 15450847 DOI: 10.1016/j.bbapap.2004.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 07/20/2004] [Indexed: 11/29/2022]
Abstract
Serine 335 at the active site of D-amino acid oxidase from the yeast Rhodotorula gracilis (RgDAAO) is not conserved in other DAAO sequences. To assess its role in catalysis, it was mutated to Gly, the residue present in mammalian DAAO, an enzyme with a 35-fold lower turnover number with D-alanine. The spectral and ligand binding properties of the S335G mutant are similar to those of wild-type enzyme, suggesting an active site with minimally altered electrostatic properties. The S335G mutant is catalytically active, excluding an essential role of S335 in catalysis. However, S335-OH contributes to the high efficiency of the mutant enzyme since the catalytic activity of the latter is lower due to a decreased rate of flavin reduction relative to wild-type RgDAAO. Catalytic rates are pH-dependent and appear to converge to very low, but finite and similar values at low pH for both wild-type and S335G RgDAAO. While this dependence exhibits two apparent pKs with wild-type RgDAAO, with the S335G mutant a single, apparent pK approximately 8 is observed, which is attributed to the ionization of the alphaNH2 group of the bound substrate. Removal of S335-OH thus suppresses an apparent pK approximately 6. Both wild-type RgDAAO and the S335G mutant exhibit a substantial deuterium solvent kinetic isotope effect (> or =4) at pH<7 that disappears with increasing pH and reflects a pKapp=6.9 +/- 0.4. Interestingly, the substitution suppresses the activity towards d-lactate, suggesting a role of the serine 335 in removal of the substrate alpha-OH hydrogen.
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Affiliation(s)
- Angelo Boselli
- Department of Structural and Functional Biology, University of Insubria, via JH Dunant 3, 21100 Varese, Italy
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Khang YH, Kim IW, Hah YR, Hwangbo JH, Kang KK. Fusion protein of Vitreoscilla hemoglobin with D-amino acid oxidase enhances activity and stability of biocatalyst in the bioconversion process of cephalosporin C. Biotechnol Bioeng 2003; 82:480-8. [PMID: 12632405 DOI: 10.1002/bit.10592] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this study we constructed an artificial flavohemoprotein by fusing Vitreoscilla hemoglobin (VHb) with D-amino acid oxidase (DAO) of Rhodotorula gracilis to determine whether bacterial hemoglobin can be used as an oxygen donor to immobilized flavoenzyme. This chimeric enzyme significantly enhanced DAO activity and stability in the bioconversion process of cephalosporin C. In a 200-mL bioreactor, the catalytic efficiency of immobilized VHb-DAO against cephalosporin C was 12.5-fold higher than that of immobilized DAO, and the operational stability of the immobilized VHb-DAO was approximately threefold better than that of the immobilized DAO. In the scaled-up bioprocess with a 5-L bioreactor, immobilized VHb-DAO (2500 U/L) resulted in 99% bioconversion of 120 mM cephalosporin C within 60 min at an oxygen flow rate of 0.2 (v/v) x min. Ninety percent of the initial activity of immobilized VHb-DAO could be maintained at up to 50 cycles of the enzymatic reaction without exogenous addition of H(2)O(2) and flavin adenine dinucleotide (FAD). The purity of the final product, glutaryl-7-aminocephalosporanic acid, was confirmed to be 99.77% by high-performance liquid chromatography (HPLC) analysis. Relative specificity of immobilized VHb-DAO on D-alpha-aminoadipic acid, a precursor in cephalosporin C biosynthesis, increased twofold, compared with that of immobilized DAO, suggesting that conformational modification of the VHb-DAO fusion protein may be altered in favor of cephalosporin C.
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Affiliation(s)
- Yong-Ho Khang
- Department of Applied Microbiology, Yeungnam University, Gyeongsan, 712-749, Republic of Korea.
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Pollegioni L, Diederichs K, Molla G, Umhau S, Welte W, Ghisla S, Pilone MS. Yeast D-amino acid oxidase: structural basis of its catalytic properties. J Mol Biol 2002; 324:535-46. [PMID: 12445787 DOI: 10.1016/s0022-2836(02)01062-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The 3D structure of the flavoprotein D-amino acid oxidase (DAAO) from the yeast Rhodotorula gracilis (RgDAAO) in complex with the competitive inhibitor anthranilate was solved (resolution 1.9A) and structural features relevant for the overall conformation and for catalytic activity are described. The FAD is bound in an elongated conformation in the core of the enzyme. Two anthranilate molecules are found within the active site cavity; one is located in a funnel forming the entrance, and the second is in contact with the flavin. The anchoring of the ligand carboxylate with Arg285 and Tyr223 is found for all complexes studied. However, while the active site group Tyr238-OH interacts with the carboxylate in the case of the substrate D-alanine, of D-CF(3)-alanine, or of L-lactate, in the anthranilate complex the phenol group rotates around the C2-C3 bond thus opening the entrance of the active site, and interacts there with the second bound anthranilate. This movement serves in channeling substrate to the bottom of the active site, the locus of chemical catalysis. The absence in RgDAAO of the "lid" covering the active site, as found in mammalian DAAO, is interpreted as being at the origin of the differences in kinetic mechanism between the two enzymes. This lid has been proposed to regulate product dissociation in the latter, while the side-chain of Tyr238 might exert a similar role in RgDAAO. The more open active site architecture of RgDAAO is the origin of its much broader substrate specificity. The RgDAAO enzyme forms a homodimer with C2 symmetry that is different from that reported for mammalian D-amino acid oxidase. This different mode of aggregation probably causes the differences in stability and tightness of FAD cofactor binding between the DAAOs from different sources.
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Affiliation(s)
- Loredano Pollegioni
- Department of Structural and Functional Biology, University of Insubria via J.H. Dunant, 3, 21100, Varese, Italy
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39
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Boselli A, Sacchi S, Job V, Pilone MS, Pollegioni L. Role of tyrosine 238 in the active site of Rhodotorula gracilis D-amino acid oxidase. A site-directed mutagenesis study. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:4762-71. [PMID: 12354107 DOI: 10.1046/j.1432-1033.2002.t01-1-03173.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Y238, one of the very few conserved residues in the active site of d-amino acid oxidases (DAAO), was mutated to phenylalanine and serine in the enzyme from the yeast Rhodotorula gracilis. The mutated proteins are catalytically competent thus eliminating Tyr238 as an active-site acid/base catalyst. Y238F and Y238S mutants exhibit a threefold slower turnover on d-alanine as substrate, which can be attributed to a slower rate of product release relative to the wild-type enzyme (a change of the rate constants for substrate binding was also evident). The Y238 DAAO mutants have spectral properties similar to those of the wild-type enzyme but the degree of stabilization of the flavin semiquinone and the redox properties in the free form of Y238S are different. The binding of the carboxylic acid competitive inhibitors and the substrate d-alanine are changed only slightly, suggesting that the overall substrate binding pocket remains intact. In agreement with data from the pH dependence of ligand binding and with the protein crystal structure, site-directed mutagenesis results emphasize the importance of residue Y238 in controlling access to the active site instead of a role in the substrate/ligand interaction.
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Affiliation(s)
- Angelo Boselli
- Department of Structural and Functional Biology, University of Insubria, Varese, Italy
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40
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Piubelli L, Caldinelli L, Molla G, Pilone MS, Pollegioni L. Conversion of the dimeric D-amino acid oxidase from Rhodotorula gracilis to a monomeric form. A rational mutagenesis approach. FEBS Lett 2002; 526:43-8. [PMID: 12208501 DOI: 10.1016/s0014-5793(02)03111-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The relevance of the dimeric state for the structure/function relationships of Rhodotorula gracilis D-amino acid oxidase (RgDAAO) holoenzyme has been investigated by rational mutagenesis. Deletion of 14 amino acids in a surface loop (connecting beta-strands 12 and 13) transforms RgDAAO from a dimeric protein into a stable monomer. The mutant enzyme is still catalytically competent and retains its binding with the FAD coenzyme. Dimerization has been used by this flavoenzyme in evolution to achieve maximal activity, a tighter interaction between the protein moiety and the coenzyme, and higher thermal stability.
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Affiliation(s)
- Luciano Piubelli
- Department of Structural and Functional Biology, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy.
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41
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Sacchi S, Lorenzi S, Molla G, Pilone MS, Rossetti C, Pollegioni L. Engineering the substrate specificity of D-amino-acid oxidase. J Biol Chem 2002; 277:27510-6. [PMID: 12021281 DOI: 10.1074/jbc.m203946200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The high resolution crystal structure of D-amino-acid oxidase (DAAO) from the yeast Rhodotorula gracilis provided us with the tool to engineer the substrate specificity of this flavo-oxidase. DAAO catalyzes the oxidative deamination of D-amino acids, with the exception of D-aspartate and D-glutamate (which are oxidized by D-aspartate oxidase, DASPO). Following sequence homology, molecular modeling, and simulated annealing docking analyses, the active site residue Met-213 was mutated to arginine. The mutant enzyme showed properties close to those of DASPO (e.g. the oxidation of D-aspartate and the binding of l-tartrate), and it was still active on D-alanine. The presence of an additional guanidinium group in the active site of the DAAO mutant allowed the binding (and thus the oxidation) of D-aspartate, but it was also responsible for a lower catalytic activity on D-alanine. Similar results were also obtained when two additional arginines were simultaneously introduced in the active site of DAAO (M213R/Y238R mutant, yielding an architecture of the active site more similar to that obtained for the DASPO model), but the double mutant showed very low stability in solution. The decrease in maximal activity observed with these DAAO mutants could be due to alterations in the precise orbital alignment required for efficient catalysis, although even the change in the redox properties (more evident in the DAAO-benzoate complex) could play a role. The rational design approach was successful in producing an enzymatic activity with a new, broader substrate specificity, and this approach could also be used to develop DAAO variants suitable for use in biotechnological applications.
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Affiliation(s)
- Silvia Sacchi
- Department of Structural and Functional Biology, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
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42
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Pollegioni L, Harris CM, Molla G, Pilone MS, Ghisla S. Identification and role of ionizing functional groups at the active center of Rhodotorula gracilis D-amino acid oxidase. FEBS Lett 2001; 507:323-6. [PMID: 11696364 DOI: 10.1016/s0014-5793(01)02983-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
D-Amino acid oxidase (DAAO) is a flavoprotein oxidase that catalyzes the oxidation of amino acids and produces ketoacids and H(2)O(2). The rate of product release from reduced DAAO from Rhodotorula gracilis is pH dependent and reflects a pK(a) of approximately 9.3. Binding of benzoate and 3,3,3-trifluoro-D-alanine to wild-type and Y238F-DAAO is also pH dependent (pK(a)=9.8+/-0.1 and 9.05+/-0.1, respectively for benzoate binding). However, binding of benzoate to Y223F-DAAO is pH independent, indicating the pK(a) is due to Y223-OH. This latter residue is thus involved in substrate binding, and probably is the group that governs product release. In contrast to this, the second active site tyrosine, Y238, has little influence on ligand binding.
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Affiliation(s)
- L Pollegioni
- Department of Structural and Functional Biology, University of Insubria, Varese, Italy.
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Harris CM, Pollegioni L, Ghisla S. pH and kinetic isotope effects in d-amino acid oxidase catalysis. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5504-20. [PMID: 11683874 DOI: 10.1046/j.1432-1033.2001.02462.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The effects of pH, solvent isotope, and primary isotope replacement on substrate dehydrogenation by Rhodotorula gracilis d-amino acid oxidase were investigated. The rate constant for enzyme-FAD reduction by d-alanine increases approximately fourfold with pH, reflecting apparent pKa values of approximately 6 and approximately 8, and reaches plateaus at high and low pH. Such profiles are observed in all presteady-state and steady-state kinetic experiments, using both d-alanine and d-asparagine as substrates, and are inconsistent with the operation of a base essential to catalysis. A solvent deuterium isotope effect of 3.1 +/- 1.1 is observed on the reaction with d-alanine at pH 6; it decreases to 1.2 +/- 0.2 at pH 10. The primary substrate isotope effect on the reduction rate with [2-D]d-alanine is 9.1 +/- 1.5 at low and 2.3 +/- 0.3 at high pH. At pH 6.0, the solvent isotope effect is 2.9 +/- 0.8 with [2-D]d-alanine, and the primary isotope effect is 8.4 +/- 2.4 in D2O. Thus, primary and solvent kinetic isotope effects (KIEs) are independent of the presence of the other isotope, i.e. the 'double' kinetic isotope effect is the product of the individual KIEs, consistent with a transition state in which rupture of the two bonds of the substrate to hydrogen is concerted. These results support a hydride transfer mechanism for the dehydrogenation reaction in d-amino acid oxidase and argue against the occurrence of any intermediates in the process. A pKa,app of approximately 8 is interpreted to arise from the microscopic ionization of the substrate amino acid alpha-amino group, but also includes contributions from kinetic parameters.
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Affiliation(s)
- C M Harris
- Department of Structural and Functional Biology, University of Insubria, Varese, Italy
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Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S. The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation. Proc Natl Acad Sci U S A 2000; 97:12463-8. [PMID: 11070076 PMCID: PMC18786 DOI: 10.1073/pnas.97.23.12463] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.
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Affiliation(s)
- S Umhau
- Section of Biology, University of Konstanz, P. O. Box 5560-M644, D-78434 Konstanz, Germany
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Pollegioni L, Porrini D, Molla G, Pilone MS. Redox potentials and their pH dependence of D-amino-acid oxidase of Rhodotorula gracilis and Trigonopsis variabilis. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6624-32. [PMID: 11054115 DOI: 10.1046/j.1432-1327.2000.01757.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The redox potentials and pH characteristics of D-amino-acid oxidase (EC 1.4.3.3; DAAO) from the yeast Rhodotorula gracilis and Trigonopsis variabilis were measured in the pH range 6.5-8.5 at 15 degrees C. In the free enzyme form, the anionic red semiquinone is quantitatively formed in both DAAOs, indicating that a two single-electron transfer mechanism is active. The semiquinone species is also thermodynamically stable, as indicated by the large separation of the single-electron transfer potentials. The first electron potential is pH-independent, while the second electron transfer is pH-dependent exhibiting a approximately -60 mV/pH unit slope, consistent with a one-electron/one-proton transfer. In the presence of the substrate analogue benzoate, the two-electron transfer is the thermodynamically favoured process for both DAAOs, with only a quantitative difference in the stabilization of the anionic semiquinone. Clearly binding of the substrate (or substrate analogue) modulates the redox properties of the two enzymes. In both cases, in the presence and absence of benzoate, the slope of Em vs. pH (-30 mV/pH unit) corresponds to an overall two-electron/one-proton transfer in the reduction to yield the anionic reduced flavin. This behaviour is similar to that reported for DAAO from pig kidney. The differences in potentials and the stability of the semiquinone intermediate measured for the three DAAOs probably stem from different isoalloxazine environments. In the case of R. gracilis DAAO, the low stability of the semiquinone form in the DAAO-benzoate complex can be explained by the shift in position of the side chain of Arg285 following substrate analogue binding.
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Affiliation(s)
- L Pollegioni
- Department of Structural and Functional Biology, University of Insubria, Varese, Italy
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Molla G, Porrini D, Job V, Motteran L, Vegezzi C, Campaner S, Pilone MS, Pollegioni L. Role of arginine 285 in the active site of Rhodotorula gracilis D-amino acid oxidase. A site-directed mutagenesis study. J Biol Chem 2000; 275:24715-21. [PMID: 10821840 DOI: 10.1074/jbc.m908193199] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arg(285), one of the very few conserved residues in the active site of d-amino acid oxidases, has been mutated to lysine, glutamine, aspartate, and alanine in the enzyme from the yeast Rhodotorula gracilis (RgDAAO). The mutated proteins are all catalytically competent. Mutations of Arg(285) result in an increase ( approximately 300-fold) of K(m) for the d-amino acid and in a large decrease ( approximately 500-fold) of turnover number. Stopped-flow analysis shows that the decrease in turnover is paralleled by a similar decrease in the rate of flavin reduction (k(2)), the latter still being the rate-limiting step of the reaction. In agreement with data from the protein crystal structure, loss of the guanidinium group of Arg(285) in the mutated DAAOs drastically reduces the binding of several carboxylic acids (e.g. benzoate). These results highlight the importance of this active site residue in the precise substrate orientation, a main factor in this redox reaction. Furthermore, Arg(285) DAAO mutants have spectral properties similar to those of the wild-type enzyme, but show a low degree of stabilization of the flavin semiquinone and a change in the redox properties of the free enzyme. From this, we can unexpectedly conclude that Arg(285) in the free enzyme form is involved in the stabilization of the negative charge on the N(1)-C(2)=O locus of the isoalloxazine ring of the flavin. We also suggest that the residue undergoes a conformational change in order to bind the carboxylate portion of the substrate/ligand in the complexed enzyme.
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Affiliation(s)
- G Molla
- Department of Structural and Functional Biology, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
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