1
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Toyama F, Kimura H, Zhang Y, Nishiya Y. Chemical modification of Arthrobacter sarcosine oxidase by N-methylisothiazolinone reduces reactivity toward oxygen. Biosci Biotechnol Biochem 2024; 88:630-636. [PMID: 38553959 DOI: 10.1093/bbb/zbae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/25/2024] [Indexed: 05/23/2024]
Abstract
N-Methylisothiazolinone (MIT) is a thiol group modifier and antimicrobial agent. Arthrobacter sarcosine oxidase (SoxA), a diagnostic enzyme for assaying creatinine, loses its activity upon the addition of MIT, and its inactivation mechanism remains unclear. In this study, SoxA was chemically modified using MIT (mo-SoxA), and its structural and chemical properties were characterized. Spectral analysis data, oxygen consumption rates, and reactions were compared between intact SoxA and mo-SoxA. These demonstrate that the oxidative half-reaction toward oxygen is inhibited by MIT modification. The oxidase activity of mo-SoxA was approximately 2.1% of that of intact SoxA, and its dehydrogenase activity was approximately 4.2 times higher. The C-to-S mutants revealed that cooperative modification of 2 specific cysteine residues caused a drastic change in the enzyme reaction mode. Based on the modeled tertiary structures, the putative entrance for oxygen uptake is predicted to be blocked by the chemical modification of the 2 cysteine residues.
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Affiliation(s)
- Fuka Toyama
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
| | - Hironori Kimura
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
| | - Yuqi Zhang
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
| | - Yoshiaki Nishiya
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
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2
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Okella H, Okello E, Mtewa AG, Ikiriza H, Kaggwa B, Aber J, Ndekezi C, Nkamwesiga J, Ajayi CO, Mugeni IM, Ssentamu G, Ochwo S, Odongo S, Tolo CU, Kato CD, Engeu PO. ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus. Front Mol Biosci 2022; 9:1039286. [PMID: 36567944 PMCID: PMC9772024 DOI: 10.3389/fmolb.2022.1039286] [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: 09/09/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Amidst rising cases of antimicrobial resistance, antimicrobial peptides (AMPs) are regarded as a promising alternative to traditional antibiotics. Even so, poor pharmacokinetic profiles of certain AMPs impede their utility necessitating, a careful assessment of potential AMPs' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties during novel lead exploration. Accordingly, the present study utilized ADMET scores to profile seven previously isolated African catfish antimicrobial peptides (ACAPs). After profiling, the peptides were docked against approved bacterial protein targets to gain insight into their possible mode of action. Promising ACAPs were then chemically synthesized, and their antibacterial activity was validated in vitro utilizing the broth dilution method. All seven examined antimicrobial peptides passed the ADMET screening, with two (ACAP-IV and ACAP-V) exhibiting the best ADMET profile scores. The ACAP-V had a higher average binding energy (-8.47 kcal/mol) and average global energy (-70.78 kcal/mol) compared to ACAP-IV (-7.60 kcal/mol and -57.53 kcal/mol), with the potential to penetrate and disrupt bacterial cell membrane (PDB Id: 2w6d). Conversely, ACAP-IV peptide had higher antibacterial activity against E. coli and S. aureus (Minimum Inhibitory Concentration, 520.7 ± 104.3 μg/ml and 1666.7 ± 416.7 μg/ml, respectively) compared to ACAP-V. Collectively, the two antimicrobial peptides (ACAP-IV and ACAP-V) are potential novel leads for the food, cosmetic and pharmaceutical industries. Future research is recommended to optimize the expression of such peptides in biological systems for extended evaluation.
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Affiliation(s)
- Hedmon Okella
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States,Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda,*Correspondence: Hedmon Okella,
| | - Emmanuel Okello
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Andrew Glory Mtewa
- Chemistry Section, Malawi Institute of Technology, Malawi University of Science and Technology, Limbe, Malawi
| | - Hilda Ikiriza
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Bruhan Kaggwa
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda,Department of Pharmacy, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Jacqueline Aber
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda,Department of Pharmacy, Faculty of Medicine, Gulu University, Gulu, Uganda
| | | | - Joseph Nkamwesiga
- International Livestock Research Institute, Nairobi, Kenya,Institut für Virologie, Freie Universität, Berlin, Germany
| | - Clement Olusoji Ajayi
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ivan Mulongo Mugeni
- Medical Entomology Laboratory, Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Geofrey Ssentamu
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Sylvester Ochwo
- Center for Animal Health and Food Safety, University of Minnesota, St. Paul, MN, United States
| | - Steven Odongo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Casim Umba Tolo
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Charles Drago Kato
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Patrick Ogwang Engeu
- Pharm-Biotechnology and Traditional Medicine Centre, Mbarara University of Science and Technology, Mbarara, Uganda
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3
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Lahham M, Jha S, Goj D, Macheroux P, Wallner S. The family of sarcosine oxidases: Same reaction, different products. Arch Biochem Biophys 2021; 704:108868. [PMID: 33812916 DOI: 10.1016/j.abb.2021.108868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
The subfamily of sarcosine oxidase is a set of enzymes within the larger family of amine oxidases. It is ubiquitously distributed among different kingdoms of life. The member enzymes catalyze the oxidization of an N-methyl amine bond of amino acids to yield unstable imine species that undergo subsequent spontaneous non-enzymatic reactions, forming an array of different products. These products range from demethylated simple species to complex alkaloids. The enzymes belonging to the sarcosine oxidase family, namely, monomeric and heterotetrameric sarcosine oxidase, l-pipecolate oxidase, N-methyltryptophan oxidase, NikD, l-proline dehydrogenase, FsqB, fructosamine oxidase and saccharopine oxidase have unique features differentiating them from other amine oxidases. This review highlights the key attributes of the sarcosine oxidase family enzymes, in terms of their substrate binding motif, type of oxidation reaction mediated and FAD regeneration, to define the boundaries of this group and demarcate these enzymes from other amine oxidase families.
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Affiliation(s)
- Majd Lahham
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria; Department of Biochemistry and Microbiology, Aljazeera Private University, Ghabagheb, Syria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Dominic Goj
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria.
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4
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Iacovino LG, Manzella N, Resta J, Vanoni MA, Rotilio L, Pisani L, Edmondson DE, Parini A, Mattevi A, Mialet-Perez J, Binda C. Rational Redesign of Monoamine Oxidase A into a Dehydrogenase to Probe ROS in Cardiac Aging. ACS Chem Biol 2020; 15:1795-1800. [PMID: 32589395 PMCID: PMC8009472 DOI: 10.1021/acschembio.0c00366] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Cardiac senescence
is a typical chronic frailty condition in the
elderly population, and cellular aging is often associated with oxidative
stress. The mitochondrial-membrane flavoenzyme monoamine oxidase A
(MAO A) catalyzes the oxidative deamination of neurotransmitters,
and its expression increases in aged hearts. We produced recombinant
human MAO A variants at Lys305 that play a key role in O2 reactivity leading to H2O2 production. The
K305Q variant is as active as the wild-type enzyme, whereas K305M
and K305S have 200-fold and 100-fold lower kcat values and similar Km. Under
anaerobic conditions, K305M MAO A was normally reduced by substrate,
whereas reoxidation by O2 was much slower but could be
accomplished by quinone electron acceptors. When overexpressed in
cardiomyoblasts by adenoviral vectors, the K305M variant showed enzymatic
turnover similar to that of the wild-type but displayed decreased
ROS levels and senescence markers. These results might translate into
pharmacological treatments as MAO inhibitors may attenuate cardiomyocytes
aging.
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Affiliation(s)
| | - Nicola Manzella
- Institute of Metabolic and Cardiovascular Diseases (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Jessica Resta
- Institute of Metabolic and Cardiovascular Diseases (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | | | - Laura Rotilio
- Department of Biology and Biotechnology, University of Pavia, Milan, Italy
| | - Leonardo Pisani
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | - Angelo Parini
- Institute of Metabolic and Cardiovascular Diseases (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Milan, Italy
| | - Jeanne Mialet-Perez
- Institute of Metabolic and Cardiovascular Diseases (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse, Toulouse, France
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Milan, Italy
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5
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Alteration of Electron Acceptor Preferences in the Oxidative Half-Reaction of Flavin-Dependent Oxidases and Dehydrogenases. Int J Mol Sci 2020; 21:ijms21113797. [PMID: 32471202 PMCID: PMC7312611 DOI: 10.3390/ijms21113797] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 11/30/2022] Open
Abstract
In this review, recent progress in the engineering of the oxidative half-reaction of flavin-dependent oxidases and dehydrogenases is discussed, considering their current and future applications in bioelectrochemical studies, such as for the development of biosensors and biofuel cells. There have been two approaches in the studies of oxidative half-reaction: engineering of the oxidative half-reaction with oxygen, and engineering of the preference for artificial electron acceptors. The challenges for engineering oxidative half-reactions with oxygen are further categorized into the following approaches: (1) mutation to the putative residues that compose the cavity where oxygen may be located, (2) investigation of the vicinities where the reaction with oxygen may take place, and (3) investigation of possible oxygen access routes to the isoalloxazine ring. Among these approaches, introducing a mutation at the oxygen access route to the isoalloxazine ring represents the most versatile and effective strategy. Studies to engineer the preference of artificial electron acceptors are categorized into three different approaches: (1) engineering of the charge at the residues around the substrate entrance, (2) engineering of a cavity in the vicinity of flavin, and (3) decreasing the glycosylation degree of enzymes. Among these approaches, altering the charge in the vicinity where the electron acceptor may be accessed will be most relevant.
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6
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Kiss DJ, Ferenczy GG. A detailed mechanism of the oxidative half-reaction of d-amino acid oxidase: another route for flavin oxidation. Org Biomol Chem 2020; 17:7973-7984. [PMID: 31407761 DOI: 10.1039/c9ob00975b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
d-Amino acid oxidase (DAAO) is a flavoenzyme whose inhibition is expected to have therapeutic potential in schizophrenia. DAAO catalyses hydride transfer from the substrate to the flavin in the reductive half-reaction, and the flavin is reoxidized by O2 in the oxidative half-reaction. Quantum mechanical/molecular mechanical calculations were performed and their results together with available experimental information were used to elucidate the detailed mechanism of the oxidative half-reaction. The reaction starts with a single electron transfer from FAD to O2, followed by triplet-singlet transition. FAD oxidation is completed by a proton coupled electron transfer to the oxygen species and the reaction terminates with H2O2 formation by proton transfer from the oxidized substrate to the oxygen species via a chain of water molecules. The substrate plays a double role by facilitating the first electron transfer and by providing a proton in the last step. The mechanism differs from the oxidative half-reaction of other oxidases.
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Affiliation(s)
- Dóra Judit Kiss
- Doctoral School of Chemistry, Eötvös Loránd University, Pázmány s 1/A, H-1117, Budapest, Hungary. and Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt 2, H-1117, Budapest, Hungary.
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt 2, H-1117, Budapest, Hungary.
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7
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Mishra VK, Mishra S. Flipped regiospecificity in L434F mutant of 8-lipoxygenase. Phys Chem Chem Phys 2020; 22:16013-16022. [DOI: 10.1039/d0cp02351e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conformational change of Phe434 controls regio- and stereospecificity of L434F lipoxygenase catalysis.
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Affiliation(s)
- Vipin Kumar Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - Sabyashachi Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
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8
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Mishra VK, Mishra S. Origin of Regio- and Stereospecific Catalysis by 8-Lipoxygenase. J Phys Chem B 2019; 123:10605-10621. [PMID: 31775504 DOI: 10.1021/acs.jpcb.9b07917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Vipin Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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9
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Kang C, Jun SY, Bravo AG, Vargas EM, Liu H, Lewis KM, Xun L. Structural and biochemical characterization of iminodiacetate oxidase from Chelativorans sp. BNC1. Mol Microbiol 2019; 112:1863-1874. [PMID: 31580513 DOI: 10.1111/mmi.14399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2019] [Indexed: 11/29/2022]
Abstract
Ethylenediaminetetraacetate (EDTA) is the most abundant organic pollutant in surface water because of its extensive usage and the recalcitrance of stable metal-EDTA complexes. A few bacteria including Chelativorans sp. BNC1 can degrade EDTA with a monooxygenase to ethylenediaminediacetate (EDDA) and then use iminodiacetate oxidase (IdaA) to further degrade EDDA into ethylenediamine in a two-step oxidation. To alleviate EDTA pollution into the environment, deciphering the mechanisms of the metabolizing enzymes is an imperative prerequisite for informed EDTA bioremediation. Although IdaA cannot oxidize glycine, the crystal structure of IdaA shows its tertiary and quaternary structures similar to those of glycine oxidases. All confirmed substrates, EDDA, ethylenediaminemonoacetate, iminodiacetate and sarcosine are secondary amines with at least one N-acetyl group. Each substrate was bound at the re-side face of the isoalloxazine ring in a solvent-connected cavity. The carboxyl group of the substrate was bound by Arg265 and Arg307 . The catalytic residue, Tyr250 , is under the hydrogen bond network to facilitate its deprotonation acting as a general base, removing an acetate group of secondary amines as glyoxylate. Thus, IdaA is a secondary amine oxidase, and our findings improve understanding of molecular mechanism involved in the bioremediation of EDTA and the metabolism of secondary amines.
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Affiliation(s)
- ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA, 99164-4630, USA
| | - Se-Young Jun
- Department of Chemistry, Washington State University, Pullman, WA, 99164-4630, USA
| | - Abigail G Bravo
- Department of Chemistry, Washington State University, Pullman, WA, 99164-4630, USA
| | - Erick M Vargas
- Department of Chemistry, Washington State University, Pullman, WA, 99164-4630, USA
| | - Honglei Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, P.R. China
| | - Kevin M Lewis
- Department of Chemistry, Washington State University, Pullman, WA, 99164-4630, USA
| | - Luying Xun
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164-4660, USA
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10
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Luo Y, Liu YJ. Theoretical Insight into a Nonadiabatic Proton-Coupled Electron Transfer Mechanism of Reduced Flavin Oxygenation. J Phys Chem A 2019; 123:4354-4359. [PMID: 31058505 DOI: 10.1021/acs.jpca.9b02084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxygenation of reduced flavin has been a fascinating research hotspot in flavin-dependent proteins because it plays an indispensable role in cellular metabolism and has potential applications in biocatalysis. This spin-forbidden reaction of high efficiency is far from being fully understood. Although investigation on the flavin chemistry has been going on for more than 60 years, there are few mechanistic explanations for the reaction of the singlet-reduced flavin with triplet oxygen. In this paper, the reaction between oxygen and the model of free reduced flavin (reduced lumiflavin anion) was studied by density functional and multireference calculations in detail. The results reveal that the reaction proceeds by an electronically nonadiabatic proton-coupled electron transfer mechanism. The intersystem crossing point has been captured.
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Affiliation(s)
- Yanling Luo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China
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11
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Pimviriyakul P, Chaiyen P. A complete bioconversion cascade for dehalogenation and denitration by bacterial flavin-dependent enzymes. J Biol Chem 2018; 293:18525-18539. [PMID: 30282807 DOI: 10.1074/jbc.ra118.005538] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/29/2018] [Indexed: 12/17/2022] Open
Abstract
Halogenated phenol and nitrophenols are toxic compounds that are widely accumulated in the environment. Enzymes in the had operon from the bacterium Ralstonia pickettii DTP0602 have the potential for application as biocatalysts in the degradation of many of these toxic chemicals. HadA monooxygenase previously was identified as a two-component reduced FAD (FADH-)-utilizing monooxygenase with dual activities of dehalogenation and denitration. However, the partner enzymes of HadA, that is, the flavin reductase and quinone reductase that provide the FADH- for HadA and reduce quinone to hydroquinone, remain to be identified. In this report, we overexpressed and purified the flavin reductases, HadB and HadX, to investigate their functional and catalytic properties. Our results indicated that HadB is an FMN-dependent quinone reductase that converts the quinone products from HadA to hydroquinone compounds that are more stable and can be assimilated by downstream enzymes in the pathway. Transient kinetics indicated that HadB prefers NADH and menadione as the electron donor and acceptor, respectively. We found that HadX is an FAD-bound flavin reductase, which can generate FADH- for HadA to catalyze dehalogenation or denitration reactions. Thermodynamic and transient kinetic experiments revealed that HadX prefers to bind FAD over FADH- and that HadX can transfer FADH- from HadX to HadA via free diffusion. Moreover, HadX rapidly catalyzed NADH-mediated reduction of flavin and provided the FADH- for a monooxygenase of a different system. Combination of all three flavin-dependent enzymes, i.e. HadA/HadB/HadX, reconstituted an effective dehalogenation and denitration cascade, which may be useful for future bioremediation applications.
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Affiliation(s)
- Panu Pimviriyakul
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and.,the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 14000, Thailand
| | - Pimchai Chaiyen
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and
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12
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Lahham M, Pavkov-Keller T, Fuchs M, Niederhauser J, Chalhoub G, Daniel B, Kroutil W, Gruber K, Macheroux P. Oxidative cyclization of N-methyl-dopa by a fungal flavoenzyme of the amine oxidase family. J Biol Chem 2018; 293:17021-17032. [PMID: 30194285 PMCID: PMC6222107 DOI: 10.1074/jbc.ra118.004227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/06/2018] [Indexed: 11/19/2022] Open
Abstract
Flavin-dependent enzymes catalyze many oxidations, including formation of ring structures in natural products. The gene cluster for biosynthesis of fumisoquins, secondary metabolites structurally related to isoquinolines, in the filamentous fungus Aspergillus fumigatus harbors a gene that encodes a flavoprotein of the amine oxidase family, termed fsqB (fumisoquin biosynthesis gene B). This enzyme catalyzes an oxidative ring closure reaction that leads to the formation of isoquinoline products. This reaction is reminiscent of the oxidative cyclization reported for berberine bridge enzyme and tetrahydrocannabinol synthase. Despite these similarities, amine oxidases and berberine bridge enzyme–like enzymes possess distinct structural properties, prompting us to investigate the structure–function relationships of FsqB. Here, we report the recombinant production and purification of FsqB, elucidation of its crystal structure, and kinetic analysis employing five putative substrates. The crystal structure at 2.6 Å resolution revealed that FsqB is a member of the amine oxidase family with a covalently bound FAD cofactor. N-methyl-dopa was the best substrate for FsqB and was completely converted to the cyclic isoquinoline product. The absence of the meta-hydroxyl group, as e.g. in l-N-methyl-tyrosine, resulted in a 25-fold lower rate of reduction and the formation of the demethylated product l-tyrosine, instead of a cyclic product. Surprisingly, FsqB did not accept the d-stereoisomer of N-methyltyrosine, in contrast to N-methyl-dopa, for which both stereoisomers were oxidized with similar rates. On the basis of the crystal structure and docking calculations, we postulate a substrate-dependent population of distinct binding modes that rationalizes stereospecific oxidation in the FsqB active site.
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Affiliation(s)
- Majd Lahham
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Tea Pavkov-Keller
- the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, and
| | - Michael Fuchs
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Johannes Niederhauser
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Gabriel Chalhoub
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Bastian Daniel
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz
| | - Wolfgang Kroutil
- the Institute of Chemistry, University of Graz, Heinrichstrasse 28/2, 8010 Graz, Austria
| | - Karl Gruber
- the Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, and
| | - Peter Macheroux
- From the Institutes of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz,
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13
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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14
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Molecular Basis for Converting (2S)-Methylsuccinyl-CoA Dehydrogenase into an Oxidase. Molecules 2017; 23:molecules23010068. [PMID: 29283425 PMCID: PMC6017585 DOI: 10.3390/molecules23010068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 11/17/2022] Open
Abstract
Although flavoenzymes have been studied in detail, the molecular basis of their dioxygen reactivity is only partially understood. The members of the flavin adenosine dinucleotide (FAD)-dependent acyl-CoA dehydrogenase and acyl-CoA oxidase families catalyze similar reactions and share common structural features. However, both enzyme families feature opposing reaction specificities in respect to dioxygen. Dehydrogenases react with electron transfer flavoproteins as terminal electron acceptors and do not show a considerable reactivity with dioxygen, whereas dioxygen serves as a bona fide substrate for oxidases. We recently engineered (2S)-methylsuccinyl-CoA dehydrogenase towards oxidase activity by rational mutagenesis. Here we characterized the (2S)-methylsuccinyl-CoA dehydrogenase wild-type, as well as the engineered (2S)-methylsuccinyl-CoA oxidase, in detail. Using stopped-flow UV-spectroscopy and liquid chromatography-mass spectrometry (LC-MS) based assays, we explain the molecular base for dioxygen reactivity in the engineered oxidase and show that the increased oxidase function of the engineered enzyme comes at a decreased dehydrogenase activity. Our findings add to the common notion that an increased activity for a specific substrate is achieved at the expense of reaction promiscuity and provide guidelines for rational engineering efforts of acyl-CoA dehydrogenases and oxidases.
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15
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X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction. Sci Rep 2017; 7:2790. [PMID: 28584265 PMCID: PMC5459902 DOI: 10.1038/s41598-017-02657-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 04/18/2017] [Indexed: 01/07/2023] Open
Abstract
Current enzymatic systems for quantifying glycated hemoglobin are based on the FAD-containing enzyme fructosyl peptide oxidase (FPOX). FPOX has substrate specificity for fructosyl-α N-valyl-histidine derived from proteolytic digestion of the N-terminus of the HbA1c β-chain. This study reports the X-ray structures of the wild-type and Asn56Ala (N56A) mutant of Phaeosphaeria nodorum fructosyl peptide oxidase (PnFPOX) to elucidate the residues responsible for the oxidative half-reaction. N56A showed decreased oxidase activity compared to the wild -type, while its dye-mediated dehydrogenase activity was higher than that of wild type. In wild-type PnFPOX, Asn56 forms a hydrogen bond with Lys274, thereby preventing it from forming a salt bridge with Asp54. By contrast, Lys274 of PnFPOX N56A moves toward Asp54, and they approach each other to form a salt bridge at a distance of 2.92-3.35 Å. Site-directed mutagenesis studies and protein channel analysis suggest that Asp54 assists in accepting oxygen properly at the position of the bound water molecule in the main oxygen channel. These results reveal that Asn56 in PnFPOX is essential for maintaining an effective oxygen accession path, and support the role of Asp54 as a gate keeper that cooperates with Lys274 to enable oxygen to reach the active site properly.
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16
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Abe Y, Shoji M, Nishiya Y, Aiba H, Kishimoto T, Kitaura K. The reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods. Phys Chem Chem Phys 2017; 19:9811-9822. [DOI: 10.1039/c6cp08172j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monomeric sarcosine oxidase (MSOX) is a flavoprotein that oxidizes sarcosine to the corresponding imine product and is widely used in clinical diagnostics to test renal function.
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Affiliation(s)
| | - Mitsuo Shoji
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Yoshiaki Nishiya
- Department of Life Science
- Faculty of Science and Engineering
- Setsunan University
- Neyagawa
- Japan
| | - Hiroshi Aiba
- Tsuruga Institute of Biotechnology
- TOYOBO Co., Ltd
- Tsuruga
- Japan
| | | | - Kazuo Kitaura
- Fukui Institute for Fundamental Chemistry
- Kyoto University
- Sakyou-ku
- Japan
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17
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Xin Y, Zheng M, Wang Q, Lu L, Zhang L, Tong Y, Wang W. Structural and catalytic alteration of sarcosine oxidase through reconstruction with coenzyme-like ligands. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Bucci A, Yu TQ, Vanden-Eijnden E, Abrams CF. Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics. J Chem Theory Comput 2016; 12:2964-72. [PMID: 27168219 DOI: 10.1021/acs.jctc.6b00071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The flavoenzyme monomeric sarcosine oxidase (MSOX) catalyzes a complex set of reactions currently lacking a consensus mechanism. A key question that arises in weighing competing mechanistic models of MSOX function is to what extent ingress of O2 from the solvent (and its egress after an unsuccessful oxidation attempt) limits the overall catalytic rate. To address this question, we have applied to the MSOX/O2 system the relatively new simulation method of Markovian milestoning molecular dynamics simulations, which, as we recently showed [ Yu et al. J. Am. Chem. Soc. 2015 , 137 , 3041 ], accurately predicted the entry and exit kinetics of CO in myoglobin. We show that the mechanism of O2 entry and exit, in terms of which possible solvent-to-active-site channels contribute to the flow of O2, is sensitive to the presence of the substrate-mimicking competitive inhibitor 2-furoate in the substrate site. The second-order O2 entry rate constants were computed to be 8.1 × 10(6) and 3.1 × 10(6) M(-1) s(-1) for bound and apo MSOX, respectively, both of which moderately exceed the experimentally determined second-order rate constant of (2.83 ± 0.07) × 10(5) M(-1) s(-1) for flavin oxidation by O2 in MSOX. This suggests that the rate of flavin oxidation by O2 is likely not strongly limited by diffusion from the solvent to the active site. The first-order exit rate constants were computed to be 10(7) s(-1) and 7.2 × 10(6) s(-1) for the apo and bound states, respectively. The predicted faster entry and slower exit of O2 for the bound state indicate a longer residence time within MSOX, increasing the likelihood of collisions with the flavin isoalloxazine ring, a step required for reduction of molecular O2 and subsequent reoxidation of the flavin. This is also indirectly supported by previous experimental evidence favoring the so-called modified ping-pong mechanism, the distinguishing feature of which is an intermediate complex involving O2, the flavin, and the oxidized substrate simultaneously in the cavity. These findings demonstrate the utility of the Markovian milestoning approach in contributing new understanding of complicated enyzmatic function.
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Affiliation(s)
- Anthony Bucci
- Department of Chemical and Biological Engineering, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Tang-Qing Yu
- Courant Institute of Mathematical Sciences, New York University , New York, New York 10012, United States
| | - Eric Vanden-Eijnden
- Courant Institute of Mathematical Sciences, New York University , New York, New York 10012, United States
| | - Cameron F Abrams
- Department of Chemical and Biological Engineering, Drexel University , Philadelphia, Pennsylvania 19104, United States
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19
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Visitsatthawong S, Chenprakhon P, Chaiyen P, Surawatanawong P. Mechanism of Oxygen Activation in a Flavin-Dependent Monooxygenase: A Nearly Barrierless Formation of C4a-Hydroperoxyflavin via Proton-Coupled Electron Transfer. J Am Chem Soc 2015; 137:9363-74. [DOI: 10.1021/jacs.5b04328] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Surawit Visitsatthawong
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pirom Chenprakhon
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pimchai Chaiyen
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Panida Surawatanawong
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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20
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Hernández-Ortega A, Quesne MG, Bui S, Heyes DJ, Steiner RA, Scrutton NS, de Visser SP. Catalytic Mechanism of Cofactor-Free Dioxygenases and How They Circumvent Spin-Forbidden Oxygenation of Their Substrates. J Am Chem Soc 2015; 137:7474-87. [DOI: 10.1021/jacs.5b03836] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Aitor Hernández-Ortega
- Manchester
Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Matthew G. Quesne
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Soi Bui
- Randall
Division of Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Roberto A. Steiner
- Randall
Division of Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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21
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Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P. Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. FEBS J 2015; 282:3060-74. [PMID: 25619330 DOI: 10.1111/febs.13212] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
UNLABELLED The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes. We have identified an alternative gatekeeper residue that similarly controls dioxygen reactivity in the grass pollen allergen Phl p 4, a member of this superfamily that has glucose dehydrogenase activity and the highest redox potential measured in a flavoenzyme. A substitution at the alternative gatekeeper site (I153V) transformed the enzyme into an efficient oxidase by increasing dioxygen reactivity by a factor of 60,000. An inverse exchange (V169I) in the structurally related berberine bridge enzyme (BBE) decreased its dioxygen reactivity by a factor of 500. Structural and biochemical characterization of these and additional variants showed that our model enzymes possess a cavity that binds an anion and resembles the 'oxyanion hole' in the proximity of the flavin ring. We showed also that steric control of access to this site is the most important parameter affecting dioxygen reactivity in BBE-like enzymes. Analysis of flavin-dependent oxidases from other superfamilies revealed similar structural features, suggesting that dioxygen reactivity may be governed by a common mechanistic principle. DATABASE Structural data are available in PDB database under the accession numbers 4PVE, 4PVH, 4PVJ, 4PVK, 4PWB, 4PWC and 4PZF.
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Affiliation(s)
- Domen Zafred
- Institute of Biochemistry, Graz University of Technology, Austria.,Institute of Molecular Biosciences, University of Graz, Austria
| | - Barbara Steiner
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Altijana Hromic
- Institute of Molecular Biosciences, University of Graz, Austria
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | | | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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22
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Björnberg O, Viennet T, Skjoldager N, Ćurović A, Nielsen KF, Svensson B, Hägglund P. Lactococcus lactis thioredoxin reductase is sensitive to light inactivation. Biochemistry 2015; 54:1628-37. [PMID: 25675241 DOI: 10.1021/bi5013639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Thioredoxin, involved in numerous redox pathways, is maintained in the dithiol state by the nicotinamide adenine dinucleotide phosphate-dependent flavoprotein thioredoxin reductase (TrxR). Here, TrxR from Lactococcus lactis is compared with the well-characterized TrxR from Escherichia coli. The two enzymes belong to the same class of low-molecular weight thioredoxin reductases and display similar kcat values (∼25 s(-1)) with their cognate thioredoxin. Remarkably, however, the L. lactis enzyme is inactivated by visible light and furthermore reduces molecular oxygen 10 times faster than E. coli TrxR. The rate of light inactivation under standardized conditions (λmax=460 nm and 4 °C) was reduced at lowered oxygen concentrations and in the presence of iodide. Inactivation was accompanied by a distinct spectral shift of the flavin adenine dinucleotide (FAD) that remained firmly bound. High-resolution mass spectrometric analysis of heat-extracted FAD from light-damaged TrxR revealed a mass increment of 13.979 Da, relative to that of unmodified FAD, corresponding to the addition of one oxygen atom and the loss of two hydrogen atoms. Tandem mass spectrometry confined the increase in mass of the isoalloxazine ring, and the extracted modified cofactor reacted with dinitrophenyl hydrazine, indicating the presence of an aldehyde. We hypothesize that a methyl group of FAD is oxidized to a formyl group. The significance of this not previously reported oxidation and the exceptionally high rate of oxygen reduction are discussed in relation to other flavin modifications and the possible occurrence of enzymes with similar properties.
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Affiliation(s)
- Olof Björnberg
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark , Building 224, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark
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23
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Karasulu B, Thiel W. Amine Oxidation Mediated by N-Methyltryptophan Oxidase: Computational Insights into the Mechanism, Role of Active-Site Residues, and Covalent Flavin Binding. ACS Catal 2015. [DOI: 10.1021/cs501694q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim, Germany
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24
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Bucci A, Abrams CF. Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction. J Chem Theory Comput 2014; 10:2668-2676. [PMID: 25061440 PMCID: PMC4095932 DOI: 10.1021/ct500088z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 01/12/2023]
Abstract
Monomeric sarcosine oxidase (MSOX) is a flavoprotein D-amino acid oxidase with reported sarcosine and oxygen activation sites on the re and si faces of the flavin ring, respectively. O2 transport routes to the catalytic interior are not well understood and are difficult to ascertain solely from MSOX crystal structures. A composite free-energy method known as single-sweep is used to map and thermodynamically characterize oxygen sites and routes leading to the catalytically active Lys265 from the protein surface. The result is a network of pathways and free energies within MSOX illustrating that oxygen can access two free-energy minima on the re face of the reduced flavin from four separate solvent portals. No such minimum is observed on the si face. The pathways are geometrically similar for three major states of the enzyme: (1) apo with a closed flavin cleft, (2) apo with an open flavin cleft, and (3) inhibitor-bound with a closed flavin cleft. Interestingly, free energies along these transport pathways display significantly deeper minima when the substrate-mimicking inhibitor 2-furoic acid is bound at the sarcosine site, even at locations far from this site. This suggests a substrate-dependent allosteric modulation of the kinetics of O2 transport from the solvent to the active site.
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Affiliation(s)
- Anthony Bucci
- Dept. Chemical and Biological
Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Cameron F. Abrams
- Dept. Chemical and Biological
Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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25
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Krondorfer I, Lipp K, Brugger D, Staudigl P, Sygmund C, Haltrich D, Peterbauer CK. Engineering of pyranose dehydrogenase for increased oxygen reactivity. PLoS One 2014; 9:e91145. [PMID: 24614932 PMCID: PMC3948749 DOI: 10.1371/journal.pone.0091145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/07/2014] [Indexed: 11/22/2022] Open
Abstract
Pyranose dehydrogenase (PDH), a member of the GMC family of flavoproteins, shows a very broad sugar substrate specificity but is limited to a narrow range of electron acceptors and reacts extremely slowly with dioxygen as acceptor. The use of substituted quinones or (organo)metals as electron acceptors is undesirable for many production processes, especially of food ingredients. To improve the oxygen reactivity, site-saturation mutagenesis libraries of twelve amino acids around the active site of Agaricus meleagris PDH were expressed in Saccharomyces cerevisiae. We established high-throughput screening assays for oxygen reactivity and standard dehydrogenase activity using an indirect Amplex Red/horseradish peroxidase and a DCIP/D-glucose based approach. The low number of active clones confirmed the catalytic role of H512 and H556. Only one position was found to display increased oxygen reactivity. Histidine 103, carrying the covalently linked FAD cofactor in the wild-type, was substituted by tyrosine, phenylalanine, tryptophan and methionine. Variant H103Y was produced in Pichia pastoris and characterized and revealed a five-fold increase of the oxygen reactivity.
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Affiliation(s)
- Iris Krondorfer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Katharina Lipp
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
- University of Applied Sciences Wiener Neustadt – Campus Tulln, Tulln, Austria
| | - Dagmar Brugger
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Petra Staudigl
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
- * E-mail:
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26
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Wongnate T, Surawatanawong P, Visitsatthawong S, Sucharitakul J, Scrutton NS, Chaiyen P. Proton-Coupled Electron Transfer and Adduct Configuration Are Important for C4a-Hydroperoxyflavin Formation and Stabilization in a Flavoenzyme. J Am Chem Soc 2013; 136:241-53. [DOI: 10.1021/ja4088055] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Thanyaporn Wongnate
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
| | - Panida Surawatanawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry, Mahidol University, Bangkok 10400 Thailand
| | - Surawit Visitsatthawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry, Mahidol University, Bangkok 10400 Thailand
| | - Jeerus Sucharitakul
- Department
of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant
Road, Patumwan, Bangkok, 10300 Thailand
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN United Kingdom
| | - Pimchai Chaiyen
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
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27
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Bonaiuto E, Milelli A, Cozza G, Tumiatti V, Marchetti C, Agostinelli E, Fimognari C, Hrelia P, Minarini A, Di Paolo ML. Novel polyamine analogues: From substrates towards potential inhibitors of monoamine oxidases. Eur J Med Chem 2013; 70:88-101. [DOI: 10.1016/j.ejmech.2013.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/09/2013] [Accepted: 07/12/2013] [Indexed: 01/12/2023]
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28
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Prongjit M, Sucharitakul J, Palfey BA, Chaiyen P. Oxidation mode of pyranose 2-oxidase is controlled by pH. Biochemistry 2013; 52:1437-45. [PMID: 23356577 DOI: 10.1021/bi301442x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoenzyme that catalyzes the oxidation of d-glucose and other aldopyranose sugars at the C2 position by using O₂ as an electron acceptor to form the corresponding 2-keto-sugars and H₂O₂. In this study, the effects of pH on the oxidative half-reaction of P2O were investigated using stopped-flow spectrophotometry. The results showed that flavin oxidation occurred via different pathways depending on the pH of the environment. At pH values lower than 8.0, reduced P2O reacts with O₂ to form a C4a-hydroperoxyflavin intermediate, leading to elimination of H₂O₂. At pH 8.0 and higher, the majority of the reduced P2O reacts with O₂ via a pathway that does not allow detection of the C4a-hydroperoxyflavin, and flavin oxidation occurs with decreased rate constants upon the rise in pH. The switching between the two modes of P2O oxidation is controlled by protonation of a group which has a pK(a) of 7.6 ± 0.1. Oxidation reactions of reduced P2O under rapid pH change as performed by stopped-flow mixing were different from the same reactions performed with enzyme pre-equilibrated at the same specified pH values, implying that the protonation of the group which controls the mode of flavin oxidation cannot be rapidly equilibrated with outside solvent. Using a double-mixing stopped-flow experiment, a rate constant for proton dissociation from the reaction site was determined to be 21.0 ± 0.4 s⁻¹.
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Affiliation(s)
- Methinee Prongjit
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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29
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Gannavaram S, Gadda G. Relative Timing of Hydrogen and Proton Transfers in the Reaction of Flavin Oxidation Catalyzed by Choline Oxidase. Biochemistry 2013; 52:1221-6. [DOI: 10.1021/bi3016235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Swathi Gannavaram
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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30
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Adachi MS, Taylor AB, Hart PJ, Fitzpatrick PF. Mechanistic and structural analyses of the roles of active site residues in yeast polyamine oxidase Fms1: characterization of the N195A and D94N enzymes. Biochemistry 2012; 51:8690-7. [PMID: 23034052 PMCID: PMC3548949 DOI: 10.1021/bi3011434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Flavoprotein Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine in the biosynthetic pathway for pantothenic acid. The same reaction is catalyzed by the mammalian polyamine and spermine oxidases. The active site of Fms1 contains three amino acid residues positioned to interact with the polyamine substrate, His67, Asn195, and Asp94. These three residues form a hydrogen-bonding triad with Asn195 being the central residue. Previous studies of the effects of mutating His67 are consistent with that residue being important both for interacting with the substrate and for maintaining the hydrogen bonds in the triad [Adachi, M. S., Taylor, A. B., Hart, P. J., and Fitzpatrick, P. F. (2012) Biochemistry 51, 4888-4897]. The N195A and D94N enzymes have now been characterized to evaluate their roles in catalysis. Both mutations primarily affect the reductive half-reaction. With N(1)-acetylspermine as the substrate, the rate constant for flavin reduction decreases ~450-fold for both mutations; the effects with spermine as the substrate are smaller, 20-40-fold. The k(cat)/K(amine)- and k(cat)-pH profiles with N(1)-acetylspermine are only slightly changed from the profiles for the wild-type enzyme, consistent with the pK(a) values arising from the amine substrate or product and not from active site residues. The structure of the N195A enzyme was determined at a resolution of 2.0 Å. The structure shows a molecule of tetraethylene glycol in the active site and establishes that the mutation has no effect on the protein structure. Overall, the results are consistent with the role of Asn195 and Asp94 being to properly position the polyamine substrate for oxidation.
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Affiliation(s)
- Mariya S. Adachi
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Alexander B. Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - P. John Hart
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
- Department of Veterans Affairs, Audie Murphy Division, Geriatric Research, Education, and Clinical Center, South Texas Veterans Health Care System, San Antonio, TX 78229
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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31
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Chaiyen P, Fraaije MW, Mattevi A. The enigmatic reaction of flavins with oxygen. Trends Biochem Sci 2012; 37:373-80. [DOI: 10.1016/j.tibs.2012.06.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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32
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Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Role of Active Site Histidines in the Two Half-Reactions of the Aryl-Alcohol Oxidase Catalytic Cycle. Biochemistry 2012; 51:6595-608. [DOI: 10.1021/bi300505z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fátima Lucas
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Patricia Ferreira
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Victor Guallar
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040
Madrid, Spain
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33
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Adachi MS, Taylor AB, Hart PJ, Fitzpatrick PF. Mechanistic and structural analyses of the role of His67 in the yeast polyamine oxidase Fms1. Biochemistry 2012; 51:4888-97. [PMID: 22642831 DOI: 10.1021/bi300517s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The flavoprotein oxidase Fms1 from Saccharomyces cerevisiae catalyzes the oxidation of spermine and N(1)-acetylspermine to spermidine and 3-aminopropanal or N-acetyl-3-aminopropanal. Within the active site of Fms1, His67 is positioned to form hydrogen bonds with the polyamine substrate. This residue is also conserved in other polyamine oxidases. The catalytic properties of H67Q, H67N, and H67A Fms1 have been characterized to evaluate the role of this residue in catalysis. With both spermine and N(1)-acetylspermine as the amine substrate, the value of the first-order rate constant for flavin reduction decreases 2-3 orders of magnitude, with the H67Q mutation having the smallest effect and H67N the largest. The k(cat)/K(O2) value changes very little upon mutation with N(1)-acetylspermine as the amine substrate and decreases only an order of magnitude with spermine. The k(cat)/K(M)-pH profiles with N(1)-acetylspermine are bell-shaped for all the mutants; the similarity to the profile of the wild-type enzyme rules out His67 as being responsible for either of the pK(a) values. The pH profiles for the rate constant for flavin reduction for all the mutant enzymes similarly show the same pK(a) as wild-type Fms1, about ∼7.4; this pK(a) is assigned to the substrate N4. The k(cat)/K(O2)-pH profiles for wild-type Fms1 and the H67A enzyme both show a pK(a) of about ∼6.9; this suggests His67 is not responsible for this pH behavior. With the H67Q, H67N, and H67A enzymes the k(cat) value decreases when a single residue is protonated, as is the case with the wild-type enzyme. The structure of H67Q Fms1 has been determined at a resolution of 2.4 Å. The structure shows that the mutation disrupts a hydrogen bond network in the active site, suggesting that His67 is important both for direct interactions with the substrate and to maintain the overall active site structure.
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Affiliation(s)
- Mariya S Adachi
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229, USA
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34
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Gadda G. Oxygen Activation in Flavoprotein Oxidases: The Importance of Being Positive. Biochemistry 2012; 51:2662-9. [DOI: 10.1021/bi300227d] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia
30302-4098, United States
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35
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Daithankar VN, Wang W, Trujillo JR, Thorpe C. Flavin-linked Erv-family sulfhydryl oxidases release superoxide anion during catalytic turnover. Biochemistry 2011; 51:265-72. [PMID: 22148553 DOI: 10.1021/bi201672h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Typically, simple flavoprotein oxidases couple the oxidation of their substrates with the formation of hydrogen peroxide without release of significant levels of the superoxide ion. However, two evolutionarily related single-domain sulfhydryl oxidases (Erv2p; a yeast endoplasmic reticulum resident protein and augmenter of liver regeneration, ALR, an enzyme predominantly found in the mitochondrial intermembrane) release up to ~30% of the oxygen they reduce as the superoxide ion. Both enzymes oxidize dithiol substrates via a redox-active disulfide adjacent to the flavin cofactor within the helix-rich Erv domain. Subsequent reduction of the flavin is followed by transfer of reducing equivalents to molecular oxygen. Superoxide release was initially detected using tris(3-hydroxypropyl)phosphine (THP) as an alternative reducing substrate to dithiothreitol (DTT). THP, and other phosphines, showed anomalously high turnover numbers with Erv2p and ALR in the oxygen electrode, but oxygen consumption was drastically suppressed upon the addition of superoxide dismutase. The superoxide ion initiates a radical chain reaction promoting the aerobic oxidation of phosphines with the formation of hydrogen peroxide. Use of a known flux of superoxide generated by the xanthine/xanthine oxidase system showed that one superoxide ion stimulates the reduction of 27 and 4.5 molecules of oxygen using THP and tris(2-carboxyethyl)phosphine (TCEP), respectively. This superoxide-dependent amplification of oxygen consumption by phosphines provides a new kinetic method for the detection of superoxide. Superoxide release was also observed by a standard chemiluminescence method using a luciferin analogue (MCLA) when 2 mM DTT was employed as a substrate of Erv2p and ALR. The percentage of superoxide released from Erv2p increased to ~65% when monomeric mutants of the normally homodimeric enzyme were used. In contrast, monomeric multidomain quiescin sulfhydryl oxidase enzymes that also contain an Erv FAD-binding fold release only 1-5% of their total reduced oxygen species as the superoxide ion. Aspects of the mechanism and possible physiological significance of superoxide release from these Erv-domain flavoproteins are discussed.
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Affiliation(s)
- Vidyadhar N Daithankar
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716-2522, United States
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36
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McDonald CA, Fagan RL, Collard F, Monnier VM, Palfey BA. Oxygen reactivity in flavoenzymes: context matters. J Am Chem Soc 2011; 133:16809-11. [PMID: 21958058 DOI: 10.1021/ja2081873] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many flavoenzymes--oxidases and monooxygenases--react faster with oxygen than free flavins do. There are many ideas on how enzymes cause this. Recent work has focused on the importance of a positive charge near N5 of the reduced flavin. Fructosamine oxidase has a lysine near N5 of its flavin. We measured a rate constant of 1.6 × 10(5) M(-1) s(-1) for its reaction with oxygen. The Lys276Met mutant reacted with a rate constant of 291 M(-1) s(-1), suggesting an important role for this lysine in oxygen activation. The dihydroorotate dehydrogenases from E. coli and L. lactis also have a lysine near N5 of the flavin. They react with O(2) with rate constants of 6.2 × 10(4) and 3.0 × 10(3) M(-1) s(-1), respectively. The Lys66Met and Lys43Met mutant enzymes react with rate constants that are nearly the same as those for the wild-type enzymes, demonstrating that simply placing a positive charge near N5 of the flavin does not guarantee increased oxygen reactivity. Our results show that the lysine near N5 does not exert an effect without an appropriate context; evolution did not find only one mechanism for activating the reaction of flavins with O(2).
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Affiliation(s)
- Claudia A McDonald
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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37
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Gaweska H, Fitzpatrick PF. Structures and Mechanism of the Monoamine Oxidase Family. Biomol Concepts 2011; 2:365-377. [PMID: 22022344 DOI: 10.1515/bmc.2011.030] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Members of the monoamine oxidase family of flavoproteins catalyze the oxidation of primary and secondary amines, polyamines, amino acids, and methylated lysine side chains in proteins. The enzymes have similar overall structures, with conserved FAD-binding domains and varied substrate-binding sites. Multiple mechanisms have been proposed for the catalytic reactions of these enzymes. The present review compares the structures of different members of the family and the various mechanistic proposals.
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Affiliation(s)
- Helena Gaweska
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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38
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Baron R, Binda C, Tortorici M, McCammon JA, Mattevi A. Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex. Structure 2011; 19:212-20. [PMID: 21300290 DOI: 10.1016/j.str.2011.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/20/2010] [Accepted: 01/04/2011] [Indexed: 11/26/2022]
Abstract
Histone demethylases LSD1 and LSD2 (KDM1A/B) catalyze the oxidative demethylation of Lys4 of histone H3. We used molecular dynamics simulations to probe the diffusion of the oxygen substrate. Oxygen can reach the catalytic center independently from the presence of a bound histone peptide, implying that LSD1 can complete subsequent demethylation cycles without detaching from the nucleosomal particle. The simulations highlight the role of a strictly conserved active-site Lys residue providing general insight into the enzymatic mechanism of oxygen-reacting flavoenzymes. The crystal structure of LSD1-CoREST bound to a peptide of the transcription factor SNAIL1 unravels a fascinating example of molecular mimicry. The SNAIL1 N-terminal residues bind to the enzyme active-site cleft, effectively mimicking the H3 tail. This finding predicts that other members of the SNAIL/Scratch transcription factor family might associate to LSD1/2. The combination of selective histone-modifying activity with the distinct recognition mechanisms underlies the biological complexity of LSD1/2.
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Affiliation(s)
- Riccardo Baron
- Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, and Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.
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39
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Kommoju PR, Chen ZW, Bruckner RC, Mathews FS, Jorns MS. Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate. Biochemistry 2011; 50:5521-34. [PMID: 21568312 DOI: 10.1021/bi200388g] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A single basic residue above the si-face of the flavin ring is the site of oxygen activation in glucose oxidase (GOX) (His516) and monomeric sarcosine oxidase (MSOX) (Lys265). Crystal structures of both flavoenzymes exhibit a small pocket at the oxygen activation site that might provide a preorganized binding site for superoxide anion, an obligatory intermediate in the two-electron reduction of oxygen. Chloride binds at these polar oxygen activation sites, as judged by solution and structural studies. First, chloride forms spectrally detectable complexes with GOX and MSOX. The protonated form of His516 is required for tight binding of chloride to oxidized GOX and for rapid reaction of reduced GOX with oxygen. Formation of a binary MSOX·chloride complex requires Lys265 and is not observed with Lys265Met. Binding of chloride to MSOX does not affect the binding of a sarcosine analogue (MTA, methylthioactetate) above the re-face of the flavin ring. Definitive evidence is provided by crystal structures determined for a binary MSOX·chloride complex and a ternary MSOX·chloride·MTA complex. Chloride binds in the small pocket at a position otherwise occupied by a water molecule and forms hydrogen bonds to four ligands that are arranged in approximate tetrahedral geometry: Lys265:NZ, Arg49:NH1, and two water molecules, one of which is hydrogen bonded to FAD:N5. The results show that chloride (i) acts as an oxygen surrogate, (ii) is an effective probe of polar oxygen activation sites, and (iii) provides a valuable complementary tool to the xenon gas method that is used to map nonpolar oxygen-binding cavities.
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Affiliation(s)
- Phaneeswara-Rao Kommoju
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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40
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Bruckner RC, Winans J, Jorns MS. Pleiotropic impact of a single lysine mutation on biosynthesis of and catalysis by N-methyltryptophan oxidase. Biochemistry 2011; 50:4949-62. [PMID: 21526853 DOI: 10.1021/bi200349m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Methyltryptophan oxidase (MTOX) contains covalently bound FAD. N-Methyltryptophan binds in a cavity above the re face of the flavin ring. Lys259 is located above the opposite, si face. Replacement of Lys259 with Gln, Ala, or Met blocks (>95%) covalent flavin incorporation in vivo. The mutant apoproteins can be reconstituted with FAD. Apparent turnover rates (k(cat,app)) of the reconstituted enzymes are ~2500-fold slower than those of wild-type MTOX. Wild-type MTOX forms a charge-transfer E(ox)·S complex with the redox-active anionic form of NMT. The E(ox)·S complex formed with Lys259Gln does not exhibit a charge-transfer band and is converted to a reduced enzyme·imine complex (EH(2)·P) at a rate 60-fold slower than that of wild-type MTOX. The mutant EH(2)·P complex contains the imine zwitterion and exhibits a charge-transfer band, a feature not observed with the wild-type EH(2)·P complex. Reaction of reduced Lys259Gln with oxygen is 2500-fold slower than that of reduced wild-type MTOX. The latter reaction is unaffected by the presence of bound product. Dissociation of the wild-type EH(2)·P complex is 80-fold slower than k(cat). The mutant EH(2)·P complex dissociates 15-fold faster than k(cat,app). Consequently, EH(2)·P and free EH(2) are the species that react with oxygen during turnover of the wild-type and mutant enzyme, respectively. The results show that (i) Lys259 is the site of oxygen activation in MTOX and also plays a role in holoenzyme biosynthesis and N-methyltryptophan oxidation and (ii) MTOX contains separate active sites for N-methyltryptophan oxidation and oxygen reduction on opposite faces of the flavin ring.
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Affiliation(s)
- Robert C Bruckner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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41
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Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family. Proc Natl Acad Sci U S A 2011; 108:4800-5. [PMID: 21383134 DOI: 10.1073/pnas.1016684108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FAD-linked oxidases constitute a class of enzymes which catalyze dehydrogenation as a fundamental biochemical reaction, followed by reoxidation of reduced flavin. Here, we present high-resolution crystal structures showing the flavoenzyme 6-hydroxy-l-nicotine oxidase in action. This enzyme was trapped during catalytic degradation of the native substrate in a sequence of discrete reaction states corresponding to the substrate-reduced enzyme, a complex of the enzyme with the intermediate enamine product and formation of the final aminoketone product. The inactive d-stereoisomer binds in mirror symmetry with respect to the catalytic axis, revealing absolute stereospecificity of hydrogen transfer to the flavin. The structural data suggest deprotonation of the substrate when bound at the active site, an overall binary complex mechanism and oxidation by direct hydride transfer. The amine nitrogen has a critical role in the dehydrogenation step and may activate carbocation formation at the α-carbon via delocalization from the lone pair to σ* C(α)-H. Enzymatically assisted hydrolysis of the intermediate product occurs at a remote (P site) cavity. Substrate entry and product exit follow different paths. Structural and kinetic data suggest that substrate can also bind to the reduced enzyme, associated with slower reoxidation as compared to the rate of reoxidation of free enzyme. The results are of general relevance for the mechanisms of flavin amine oxidases.
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42
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Fiorillo A, Federico R, Polticelli F, Boffi A, Mazzei F, Di Fusco M, Ilari A, Tavladoraki P. The structure of maize polyamine oxidase K300M mutant in complex with the natural substrates provides a snapshot of the catalytic mechanism of polyamine oxidation. FEBS J 2011; 278:809-21. [PMID: 21205212 DOI: 10.1111/j.1742-4658.2010.08000.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyamine oxidases are FAD-dependent enzymes catalyzing the oxidation of polyamines at the secondary amino groups. Zea mays PAO (ZmPAO) oxidizes the carbon on the endo-side of the N5-nitrogen of spermidine (Spd) and spermine (Spm). The structure of ZmPAO revealed that the active site is formed by a catalytic tunnel in which the N5 atom of FAD lies in close proximity to the K300 side chain, the only active-site residue conserved in all PAOs. A water molecule, (HOH309), is hydrogen-bound to the amino group of K300 and mutation of this residue results in a 1400-fold decrease in the rate of flavin reduction. The structural studies on the catalytically impaired ZmPAO-K300M mutant described here show that substrates are bound in an 'out-of-register' mode and the HOH309 water molecule is absent in the enzyme-substrate complexes. Moreover, K300 mutation brings about a 60 mV decrease in the FAD redox potential and a 30-fold decrease in the FAD reoxidation rate, within a virtually unaltered geometry of the catalytic pocket. Taken together, these results indicate that the HOH309-K300 couple plays a major role in multiple steps of ZmPAO catalytic mechanism, such as correct substrate binding geometry as well as FAD reduction and reoxidation kinetics.
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Affiliation(s)
- Annarita Fiorillo
- Department of Science and Biomedical Technology, University of L'Aquila, Italy
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43
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Yuan H, Fu G, Brooks PT, Weber I, Gadda G. Steady-State Kinetic Mechanism and Reductive Half-Reaction of d-Arginine Dehydrogenase from Pseudomonas aeruginosa. Biochemistry 2010; 49:9542-50. [DOI: 10.1021/bi101420w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Irene Weber
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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44
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Jorns MS, Chen ZW, Mathews FS. Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase . Biochemistry 2010; 49:3631-9. [PMID: 20353187 DOI: 10.1021/bi100160j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygen reduction and sarcosine oxidation in monomeric sarcosine oxidase (MSOX) occur at separate sites above the si- and re-faces, respectively, of the flavin ring. Mutagenesis studies implicate Lys265 as the oxygen activation site. Substitution of Lys265 with a neutral (Met, Gln, or Ala) or basic (Arg) residue results in an approximately 10(4)- or 250-fold decrease, respectively, in the reaction rate. The overall structure of MSOX and residue conformation in the sarcosine binding cavity are unaffected by replacement of Lys265 with Met or Arg. The side chain of Met265 exhibits the same configuration in each molecule of Lys265Met crystals and is nearly congruent with Lys265 in wild-type MSOX. The side chain of Arg265 is, however, dramatically shifted ( approximately 4-5 A) compared with Lys265, points in the opposite direction, and exhibits significant conformational variability between molecules of the same crystal. The major species in solutions of Lys265Arg is likely to contain a "flipped-out" Arg265 and exhibit negligible oxygen activation, similar to Lys265Met. The 400-fold higher oxygen reactivity observed with Lys265Arg is attributed to a minor (<1%) "flipped-in" Arg265 conformer whose oxygen reactivity is similar to that of wild-type MSOX. A structural water (WAT1), found above the si-face of the flavin ring in all previously determined MSOX structures, is part of an apparent proton relay system that extends from FAD N(5) to bulk solvent. WAT1 is strikingly absent in Lys265Met and Lys265Arg, a feature that may account for the apparent kinetic stabilization of a reductive half-reaction intermediate that is detectable with the mutants but not wild-type MSOX.
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Affiliation(s)
- Marilyn Schuman Jorns
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA.
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45
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Saam J, Rosini E, Molla G, Schulten K, Pollegioni L, Ghisla S. O2 reactivity of flavoproteins: dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase. J Biol Chem 2010; 285:24439-46. [PMID: 20498362 DOI: 10.1074/jbc.m110.131193] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular dynamics simulations and implicit ligand sampling methods have identified trajectories and sites of high affinity for O(2) in the protein framework of the flavoprotein D-amino-acid oxidase (DAAO). A specific dynamic channel for the diffusion of O(2) leads from solvent to the flavin Si-side (amino acid substrate and product bind on the Re-side). Based on this, amino acids that flank the putative O(2) high affinity sites have been exchanged with bulky residues to introduce steric constraints. In G52V DAAO, the valine side chain occupies the site that in wild-type DAAO has the highest O(2) affinity. In this variant, the reactivity of the reduced enzyme with O(2) is decreased >or=100-fold and the turnover number approximately 1000-fold thus verifying the concept. In addition, the simulations have identified a chain of three water molecules that might serve in relaying a H(+) from the product imino acid =NH(2)(+) group bound on the flavin Re-side to the developing peroxide on the Si-side. This function would be comparable with that of a similarly located histidine in the flavoprotein glucose oxidase.
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Affiliation(s)
- Jan Saam
- Beckman Institute, University of Illinois, Urbana, Illinois 61801, USA
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46
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Finnegan S, Agniswamy J, Weber IT, Gadda G. Role of Valine 464 in the Flavin Oxidation Reaction Catalyzed by Choline Oxidase,. Biochemistry 2010; 49:2952-61. [DOI: 10.1021/bi902048c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Irene T. Weber
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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47
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Rungsrisuriyachai K, Gadda G. Role of Asparagine 510 in the Relative Timing of Substrate Bond Cleavages in the Reaction Catalyzed by Choline Oxidase. Biochemistry 2010; 49:2483-90. [DOI: 10.1021/bi901796a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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48
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Kachalova GS, Bourenkov GP, Mengesdorf T, Schenk S, Maun HR, Burghammer M, Riekel C, Decker K, Bartunik HD. Crystal Structure Analysis of Free and Substrate-Bound 6-Hydroxy-l-Nicotine Oxidase from Arthrobacter nicotinovorans. J Mol Biol 2010; 396:785-99. [DOI: 10.1016/j.jmb.2009.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/04/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
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49
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Kommoju PR, Bruckner RC, Ferreira P, Carrell CJ, Mathews FS, Jorns MS. Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase. Biochemistry 2009; 48:9542-55. [PMID: 19702312 DOI: 10.1021/bi901056a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative two-electron oxidation of P2C, but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single two-electron oxidation step. Wild-type and mutant enzymes exhibit identical rate constants for oxidation of P2C to dihydropicolinate and isomerization of a reduced enzyme.dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Release of picolinate from Tyr258Phe is 100-fold faster than turnover. The presence of a bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10-75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate, or 1-cyclohexenoate, a 1-deaza-P2C analogue. The reduced Tyr258Phe x 1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD.
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Affiliation(s)
- Phaneeswara-Rao Kommoju
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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50
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Baron R, McCammon JA, Mattevi A. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation. Curr Opin Struct Biol 2009; 19:672-9. [DOI: 10.1016/j.sbi.2009.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 10/07/2009] [Indexed: 11/28/2022]
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