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Hassan FS, El-Fakharany EM, El-Maradny YA, Saleh AK, El-Sayed MH, Mazi W, Omer N, Abdelaziz MA, Jame R, Alatawi IS, El-Gendi H. Comprehensive insight into exploring the potential of microbial enzymes in cancer therapy: Progress, challenges, and opportunities: A review. Int J Biol Macromol 2024; 277:134535. [PMID: 39111467 DOI: 10.1016/j.ijbiomac.2024.134535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/03/2024] [Accepted: 08/04/2024] [Indexed: 09/03/2024]
Abstract
Microbial enzymes are crucial catalysts in various industries due to their versatility and efficiency. The microbial enzymes market has recently expanded due to increased demand for many reasons. Among them are eco-friendly solutions, developing novel microbial strains with enhanced enzymes that perform under harsh conditions, providing sustainability, and raising awareness about the benefits of enzyme-based products. By 2030, the global enzyme market is expected to account for $525 billion, with a growth rate of 6.7 %. L-asparaginase and L-glutaminase are among the leading applied microbial enzymes in antitumor therapy, with a growing market share of 16.5 % and 9.5 %, respectively. The use of microbial enzymes has opened new opportunities to fight various tumors, including leukemia, lymphosarcoma, and breast cancer, which has increased their demand in the pharmaceutical and medicine sectors. Despite their promising applications, commercial use of microbial enzymes faces challenges such as short half-life, immunogenicity, toxicity, and other side effects. Therefore, this review explores the industrial production, purification, formulation, and commercial utilization of microbial enzymes, along with an overview of the global enzyme market. With ongoing discoveries of novel enzymes and their applications, enzyme technology offers promising avenues for cancer treatment and other therapeutic interventions.
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Affiliation(s)
- Fareed Shawky Hassan
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Esmail M El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria 21934, Egypt; Pharmaceutical and Fermentation Industries Development Centre (PFIDC), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria, Egypt; Pharos University in Alexandria, Canal El Mahmoudia Street, Beside Green Plaza Complex, 21648, Alexandria, Egypt.
| | - Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Centre (PFIDC), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria, Egypt
| | - Ahmed K Saleh
- Cellulose and Paper Department, National Research Centre, El-Tahrir St., Dokki 12622, Giza, Egypt
| | - Mohamed H El-Sayed
- Department of Biology, College of Sciences and Arts-Rafha, Northern Border University, Arar, Saudi Arabia
| | - Wafa Mazi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Noha Omer
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Mahmoud A Abdelaziz
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Rasha Jame
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Ibrahim Saleem Alatawi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Hamada El-Gendi
- Bioprocess development department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, Alexandria 21934, Egypt
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2
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Koopmeiners S, Gilzer D, Widmann C, Berelsmann N, Sproß J, Niemann HH, Fischer von Mollard G. Crystal structure and enzyme engineering of the broad substrate spectrum l-amino acid oxidase 4 from the fungus Hebeloma cylindrosporum. FEBS Lett 2024; 598:2306-2320. [PMID: 39152524 DOI: 10.1002/1873-3468.15002] [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: 06/26/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/19/2024]
Abstract
l-Amino acid oxidases (LAAOs) catalyze the oxidative deamination of l-amino acids to α-keto acids. Recombinant production of LAAOs with broad substrate spectrum remains a formidable challenge. We previously achieved this for the highly active and thermostable LAAO4 of Hebeloma cylindrosporum (HcLAAO4). Here, we crystallized a proteolytically truncated surface entropy reduction variant of HcLAAO4 and solved its structure in substrate-free form and in complex with diverse substrates. The ability to support the aliphatic portion of a substrate's side chain by an overall hydrophobic active site is responsible for the broad substrate spectrum of HcLAAO4, including l-amino acids with big aromatic, acidic and basic side chains. Based on the structural findings, we generated an E288H variant with increased activity toward pharmaceutical building blocks of high interest.
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Affiliation(s)
- Simon Koopmeiners
- Biochemistry III, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Dominic Gilzer
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Christiane Widmann
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Nils Berelsmann
- Biochemistry III, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jens Sproß
- Industrial Organic Chemistry and Biotechnology, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
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3
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Yamamoto K, Masakari Y, Araki Y, Ichiyanagi A, Ito K. Modification of substrate specificity of L-arginine oxidase for detection of L-citrulline. AMB Express 2023; 13:137. [PMID: 38044351 PMCID: PMC10694123 DOI: 10.1186/s13568-023-01636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023] Open
Abstract
Enzymatic detection of citrulline, a potential biomarker for various diseases, is beneficial. However, determining citrulline levels requires expensive instrumental analyses and complicated colorimetric assays. Although L-amino acid oxidase/dehydrogenase is widely used to detect L-amino acids, an L-citrulline-specific oxidase/dehydrogenase has not been reported. Therefore, in this study, we aimed to develop an L-citrulline-specific enzyme by introducing a mutation into L-arginine oxidase (ArgOX) derived from Pseudomonas sp. TPU 7192 to provide a simple enzymatic L-citrulline detection system. The ratio of the oxidase activity against L-arginine to that against L-citrulline (Cit/Arg) was 1.2%, indicating that ArgOX could recognize L-citrulline as a substrate. In the dehydrogenase assay, the specific dehydrogenase activity towards L-arginine was considerably lower than the specific oxidase activity. However, the specific dehydrogenase activity towards L-citrulline was only slightly lower than the oxidase activity, resulting in improved substrate specificity with a Cit/Arg ratio of 49.5%. To enhance the substrate specificity of ArgOX, we performed site-directed mutagenesis using structure-based engineering. The 3D model structure indicated that E486 interacted with the L-arginine side chain. By introducing the E486 mutation, the specific dehydrogenase activity of ArgOX/E486Q for L-citrulline was 3.25 ± 0.50 U/mg, which was 3.8-fold higher than that of ArgOX. The Cit/Arg ratio of ArgOX/E486Q was 150%, which was higher than that of ArgOX. Using ArgOX/E486Q, linear relationships were observed within the range of 10-500 μM L-citrulline, demonstrating its suitability for detecting citrulline in human blood. Consequently, ArgOX/E486Q can be adapted as an enzymatic sensor in the dehydrogenase system.
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Affiliation(s)
- Kei Yamamoto
- Marketing and Planning Division, Kikkoman Biochemifa Company, 1600, Kaisuka, Kamogawa, Chiba, 296-0004, Japan.
| | - Yosuke Masakari
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Yasuko Araki
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Atsushi Ichiyanagi
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Kotaro Ito
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
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Mamounis KJ, Caldas Nogueira ML, Marchi Salvador DP, Andreo-Vidal A, Sanchez-Amat A, Davidson VL. Structural Determinants of the Specific Activities of an L-Amino Acid Oxidase from Pseudoalteromonas luteoviolacea CPMOR-1 with Broad Substrate Specificity. Molecules 2022; 27:molecules27154726. [PMID: 35897902 PMCID: PMC9331233 DOI: 10.3390/molecules27154726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
The Pseudoalteromonas luteoviolacea strain CPMOR-1 expresses a flavin adenine dinucleotide (FAD)-dependent L-amino acid oxidase (LAAO) with broad substrate specificity. Steady-state kinetic analysis of its reactivity towards the 20 proteinogenic amino acids showed some activity to all except proline. The relative specific activity for amino acid substrates was not correlated only with Km or kcat values, since the two parameters often varied independently of each other. Variation in Km was attributed to the differential binding affinity. Variation in kcat was attributed to differential positioning of the bound substrate relative to FAD that decreased the reaction rate. A structural model of this LAAO was compared with structures of other FAD-dependent LAAOs that have different substrate specificities: an LAAO from snake venom that prefers aromatic amino acid substrates and a fungal LAAO that is specific for lysine. While the amino acid sequences of these LAAOs are not very similar, their overall structures are comparable. The differential activity towards specific amino acids was correlated with specific residues in the active sites of these LAAOs. Residues in the active site that interact with the amino and carboxyl groups attached to the α-carbon of the substrate amino acid are conserved in all of the LAAOs. Residues that interact with the side chains of the amino acid substrates show variation. This provides insight into the structural determinants of the LAAOs that dictate their different substrate preferences. These results are of interest for harnessing these enzymes for possible applications in biotechnology, such as deracemization.
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Affiliation(s)
- Kyle J. Mamounis
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (K.J.M.); (M.L.C.N.)
| | - Maria Luiza Caldas Nogueira
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (K.J.M.); (M.L.C.N.)
| | - Daniela Priscila Marchi Salvador
- Department of Molecular Biology, Center of Exact and Natural Sciences, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil;
| | - Andres Andreo-Vidal
- Department of Genetics and Microbiology, University of Murcia, 30100 Murcia, Spain; (A.A.-V.); (A.S.-A.)
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, University of Murcia, 30100 Murcia, Spain; (A.A.-V.); (A.S.-A.)
| | - Victor L. Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA; (K.J.M.); (M.L.C.N.)
- Correspondence: ; Tel.: +1-407-266-7111; Fax: +1-407-266-7002
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5
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Lukasheva EV, Babayeva G, Karshieva SS, Zhdanov DD, Pokrovsky VS. L-Lysine α-Oxidase: Enzyme with Anticancer Properties. Pharmaceuticals (Basel) 2021; 14:1070. [PMID: 34832852 PMCID: PMC8618108 DOI: 10.3390/ph14111070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022] Open
Abstract
L-lysine α-oxidase (LO), one of L-amino acid oxidases, deaminates L-lysine with the yield of H2O2, ammonia, and α-keto-ε-aminocaproate. Multiple in vitro and in vivo studies have reported cytotoxic, antitumor, antimetastatic, and antitumor activity of LO. Unlike asparaginase, LO has a dual mechanism of action: depletion of L-lysine and formation of H2O2, both targeting tumor growth. Prominent results were obtained on murine and human tumor models, including human colon cancer xenografts HCT 116, LS174T, and T47D with maximum T/C 12, 37, and 36%, respectively. The data obtained from human cancer xenografts in immunodeficient mice confirm the potential of LO as an agent for colon cancer treatment. In this review, we discuss recently discovered molecular mechanisms of biological action and the potential of LO as anticancer enzyme.
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Affiliation(s)
- Elena V. Lukasheva
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho—Maklaya Street 6, 117198 Moscow, Russia; (E.V.L.); (G.B.)
| | - Gulalek Babayeva
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho—Maklaya Street 6, 117198 Moscow, Russia; (E.V.L.); (G.B.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia;
| | - Saida Sh. Karshieva
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia;
| | - Dmitry D. Zhdanov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10/8, 119121 Moscow, Russia;
| | - Vadim S. Pokrovsky
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho—Maklaya Street 6, 117198 Moscow, Russia; (E.V.L.); (G.B.)
- Laboratory of Combined Treatment, N.N. Blokhin Cancer Research Center, Kashirskoe Shosse 24, 115478 Moscow, Russia;
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Federal Territory Sirius, 1 Olimpiisky Prospect, 354340 Sochi, Russia
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Sugiura S, Nakano S, Niwa M, Hasebe F, Matsui D, Ito S. Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. J Biol Chem 2021; 297:101043. [PMID: 34358565 PMCID: PMC8405998 DOI: 10.1016/j.jbc.2021.101043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 11/23/2022] Open
Abstract
A large number of protein sequences are registered in public databases such as PubMed. Functionally uncharacterized enzymes are included in these databases, some of which likely have potential for industrial applications. However, assignment of the enzymes remained difficult tasks for now. In this study, we assigned a total of 28 original sequences to uncharacterized enzymes in the FAD-dependent oxidase family expressed in some species of bacteria including Chryseobacterium, Flavobacterium, and Pedobactor. Progenitor sequence of the assigned 28 sequences was generated by ancestral sequence reconstruction, and the generated sequence exhibited L-lysine oxidase activity; thus, we named the enzyme AncLLysO. Crystal structures of ligand-free and ligand-bound forms of AncLLysO were determined, indicating that the enzyme recognizes L-Lys by hydrogen bond formation with R76 and E383. The binding of L-Lys to AncLLysO induced dynamic structural change at a plug loop formed by residues 251 to 254. Biochemical assays of AncLLysO variants revealed the functional importance of these substrate recognition residues and the plug loop. R76A and E383D variants were also observed to lose their activity, and the kcat/Km value of G251P and Y253A mutations were approximately 800- to 1800-fold lower than that of AncLLysO, despite the indirect interaction of the substrates with the mutated residues. Taken together, our data demonstrate that combinational approaches to sequence classification from database and ancestral sequence reconstruction may be effective not only to find new enzymes using databases of unknown sequences but also to elucidate their functions.
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Affiliation(s)
- Sayaka Sugiura
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Shogo Nakano
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan; PREST, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Masazumi Niwa
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Fumihito Hasebe
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Daisuke Matsui
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
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7
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Yano Y, Matsuo S, Ito N, Tamura T, Kusakabe H, Inagaki K, Imada K. A new l-arginine oxidase engineered from l-glutamate oxidase. Protein Sci 2021; 30:1044-1055. [PMID: 33764624 DOI: 10.1002/pro.4070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 11/08/2022]
Abstract
The alternation of substrate specificity expands the application range of enzymes in industrial, medical, and pharmaceutical fields. l-Glutamate oxidase (LGOX) from Streptomyces sp. X-119-6 catalyzes the oxidative deamination of l-glutamate to produce 2-ketoglutarate with ammonia and hydrogen peroxide. LGOX shows strict substrate specificity for l-glutamate. Previous studies on LGOX revealed that Arg305 in its active site recognizes the side chain of l-glutamate, and replacement of Arg305 by other amino acids drastically changes the substrate specificity of LGOX. Here we demonstrate that the R305E mutant variant of LGOX exhibits strict specificity for l-arginine. The oxidative deamination activity of LGOX to l-arginine is higher than that of l-arginine oxidase form from Pseudomonas sp. TPU 7192. X-ray crystal structure analysis revealed that the guanidino group of l-arginine is recognized not only by Glu305 but also Asp433, Trp564, and Glu617, which interact with Arg305 in wild-type LGOX. Multiple interactions by these residues provide strict specificity and high activity of LGOX R305E toward l-arginine. LGOX R305E is a thermostable and pH stable enzyme. The amount of hydrogen peroxide, which is a byproduct of oxidative deamination of l-arginine by LGOX R305E, is proportional to the concentration of l-arginine in a range from 0 to 100 μM. The linear relationship is maintained around 1 μM of l-arginine. Thus, LGOX R305E is suitable for the determination of l-arginine.
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Affiliation(s)
- Yoshika Yano
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Shinsaku Matsuo
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Nanako Ito
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | | | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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Kitagawa M, Ito N, Matsumoto Y, Saito M, Tamura T, Kusakabe H, Inagaki K, Imada K. Structural basis of enzyme activity regulation by the propeptide of l-lysine α-oxidase precursor from Trichoderma viride. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100044. [PMID: 33554108 PMCID: PMC7844570 DOI: 10.1016/j.yjsbx.2021.100044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/17/2020] [Accepted: 01/07/2021] [Indexed: 11/04/2022]
Abstract
The suppression mechanism of activity by propeptide remains unclear for most LAAOs. The crystal structures of the LysOX precursor (prLysOX) have been determined. The propeptide indirectly changes the active site structure to suppress the activity. prLysOX can adopt another conformation similar to mature LysOX. prLysOX is able to be activated without proteolytic processing.
Harmuful proteins are usually synthesized as inactive precursors and are activated by proteolytic processing. l-Amino acid oxidase (LAAO) is a flavoenzyme that catalyzes the oxidative deamination of l-amino acid to produce a 2-oxo acid with ammonia and highly toxic hydrogen peroxide and, therefore, is expressed as a precursor. The LAAO precursor shows significant variation in size and the cleavage pattern for activation. However, the molecular mechanism of how the propeptide suppresses the enzyme activity remains unclear except for deaminating/decarboxylating Pseudomonasl-phenylalanine oxidase (PAO), which has a short N-terminal propeptide composed of 14 residues. Here we show the inactivation mechanism of the l-lysine oxidase (LysOX) precursor (prLysOX), which has a long N-terminal propeptide composed of 77 residues, based on the crystal structure at 1.97 Å resolution. The propeptide of prLysOX indirectly changes the active site structure to inhibit the enzyme activity. prLysOX retains weak enzymatic activity with strict specificity for l-lysine and shows raised activity in acidic conditions. The structures of prLysOX crystals that soaked in a solution with various concentrations of l-lysine have revealed that prLysOX can adopt two conformations; one is the inhibitory form, and the other is very similar to mature LysOX. The propeptide region of the latter form is disordered, and l-lysine is bound to the latter form. These results indicate that prLysOX uses a different strategy from PAO to suppress the enzyme activity and suggest that prLysOX can be activated quickly in response to the environmental change without proteolytic processing.
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Affiliation(s)
- Masaki Kitagawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Nanako Ito
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuya Matsumoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Masaya Saito
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | | | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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Kondo H, Kitagawa M, Matsumoto Y, Saito M, Amano M, Sugiyama S, Tamura T, Kusakabe H, Inagaki K, Imada K. Structural basis of strict substrate recognition of l-lysine α-oxidase from Trichoderma viride. Protein Sci 2020; 29:2213-2225. [PMID: 32894626 DOI: 10.1002/pro.3946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/07/2022]
Abstract
l-Lysine oxidase (LysOX) is a FAD-dependent homodimeric enzyme that catalyzes the oxidative deamination of l-lysine to produce α-keto-ε-aminocaproate with ammonia and hydrogen peroxide. LysOX shows strict substrate specificity for l-lysine, whereas most l-amino acid oxidases (LAAOs) exhibit broad substrate specificity for l-amino acids. Previous studies of LysOX showed that overall structural similarity to the well-studied snake venom LAAOs. However, the molecular mechanism of strict specificity for l-lysine was still unclear. We here determined the structure of LysOX in complex with l-lysine at 1.7 Å resolution. The structure revealed that the hydrogen bonding network formed by D212, D315, and A440 with two water molecules is responsible for the recognition of the side chain amino group. In addition, a narrow hole formed by five hydrophobic residues in the active site contributes to strict substrate specificity. Mutation studies demonstrated that D212 and D315 are essential for l-lysine recognition, and the D212A/D315A double mutant LysOX showed different substrate specificity from LysOX. Moreover, the structural basis of the substrate specificity change has also been revealed by the structural analysis of the mutant variant and its substrate complexes. These results clearly explain the molecular mechanism of the strict specificity of LysOX and suggest that LysOX is a potential candidate for a template to design LAAOs specific to other l-amino acids.
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Affiliation(s)
- Hiroki Kondo
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
| | - Masaki Kitagawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuya Matsumoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Masaya Saito
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Marie Amano
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Shigeru Sugiyama
- Faculty of Science and Technology, Kochi University, Kochi, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | | | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
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