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Bayer T, Palm GJ, Berndt L, Meinert H, Branson Y, Schmidt L, Cziegler C, Somvilla I, Zurr C, Graf LG, Janke U, Badenhorst CPS, König S, Delcea M, Garscha U, Wei R, Lammers M, Bornscheuer UT. Structural Elucidation of a Metagenomic Urethanase and Its Engineering Towards Enhanced Hydrolysis Profiles. Angew Chem Int Ed Engl 2024; 63:e202404492. [PMID: 38948941 DOI: 10.1002/anie.202404492] [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: 03/05/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/02/2024]
Abstract
While plastics like polyethylene terephthalate can already be degraded efficiently by the activity of hydrolases, other synthetic polymers like polyurethanes (PUs) and polyamides (PAs) largely resist biodegradation. In this study, we solved the first crystal structure of the metagenomic urethanase UMG-SP-1, identified highly flexible loop regions to comprise active site residues, and targeted a total of 20 potential hot spots by site-saturation mutagenesis. Engineering campaigns yielded variants with single mutations, exhibiting almost 3- and 8-fold improved activity against highly stable N-aryl urethane and amide bonds, respectively. Furthermore, we demonstrated the release of the corresponding monomers from a thermoplastic polyester-PU and a PA (nylon 6) by the activity of a single, metagenome-derived urethanase after short incubation times. Thereby, we expanded the hydrolysis profile of UMG-SP-1 beyond the reported low-molecular weight carbamates. Together, these findings promise advanced strategies for the bio-based degradation and recycling of plastic materials and waste, aiding efforts to establish a circular economy for synthetic polymers.
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Affiliation(s)
- Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Gottfried J Palm
- Department of Synthetic & Structural Biochemistry Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Leona Berndt
- Department of Synthetic & Structural Biochemistry Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Hannes Meinert
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Yannick Branson
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Louis Schmidt
- Department of Pharmaceutical & Medicinal Chemistry Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Clemens Cziegler
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Ina Somvilla
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Celine Zurr
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Leonie G Graf
- Department of Synthetic & Structural Biochemistry Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Una Janke
- Department of Biophysical Chemistry Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Christoffel P S Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Stefanie König
- Department of Pharmaceutical & Medicinal Chemistry Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Ulrike Garscha
- Department of Pharmaceutical & Medicinal Chemistry Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Ren Wei
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic & Structural Biochemistry Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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Ciuffreda P, Xynomilakis O, Casati S, Ottria R. Fluorescence-Based Enzyme Activity Assay: Ascertaining the Activity and Inhibition of Endocannabinoid Hydrolytic Enzymes. Int J Mol Sci 2024; 25:7693. [PMID: 39062935 PMCID: PMC11276806 DOI: 10.3390/ijms25147693] [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: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The endocannabinoid system, known for its regulatory role in various physiological processes, relies on the activities of several hydrolytic enzymes, such as fatty acid amide hydrolase (FAAH), N-acylethanolamine-hydrolyzing acid amidase (NAAA), monoacylglycerol lipase (MAGL), and α/β-hydrolase domains 6 (ABHD6) and 12 (ABHD12), to maintain homeostasis. Accurate measurement of these enzymes' activities is crucial for understanding their function and for the development of potential therapeutic agents. Fluorometric assays, which offer high sensitivity, specificity, and real-time monitoring capabilities, have become essential tools in enzymatic studies. This review provides a comprehensive overview of the principles behind these assays, the various substrates and fluorophores used, and advances in assay techniques used not only for the determination of the kinetic mechanisms of enzyme reactions but also for setting up kinetic assays for the high-throughput screening of each critical enzyme involved in endocannabinoid degradation. Through this comprehensive review, we aim to highlight the strengths and limitations of current fluorometric assays and suggest future directions for improving the measurement of enzyme activity in the endocannabinoid system.
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Affiliation(s)
| | | | | | - Roberta Ottria
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, 20157 Milan, Italy; (P.C.); (O.X.); (S.C.)
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Zhu Q, Pan K, Liu H, Hu J, Li Q, Bai X, Zhang M, Qiu J, Hong Q. Cloning and expression of the phenazine-1-carboxamide hydrolysis gene pzcH and the identification of the key amino acids necessary for its activity. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131924. [PMID: 37379601 DOI: 10.1016/j.jhazmat.2023.131924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023]
Abstract
Phenazine-1-carboxamide (PCN), a phenazine derivative, can cause toxicity risks to non target organisms. In this study, the Gram-positive bacteria Rhodococcus equi WH99 was found to have the ability to degrade PCN. PzcH, a novel amidase belonging to amidase signature (AS) family, responsible for hydrolyzing PCN to PCA was identified from strain WH99. PzcH shared no similarity with amidase PcnH which can also hydrolyze PCN and belong to the isochorismatase superfamily from Gram-negative bacteria Sphingomonas histidinilytica DS-9. PzcH also showed low similarity (˂ 39%) with other reported amidases. The optimal catalysis temperature and pH of PzcH was 30 °C and 9.0, respectively. The Km and kcat values of PzcH for PCN were 43.52 ± 4.82 μM and 17.028 ± 0.57 s-1, respectively. The molecular docking and point mutation experiment demonstrated that catalytic triad Lys80-Ser155-Ser179 are essential for PzcH to hydrolyze PCN. Strain WH99 can degrade PCN and PCA to reduce their toxicity against the sensitive organisms. This study enhances our understanding of the molecular mechanism of PCN degradation, presents the first report on the key amino acids in PzcH from the Gram-positive bacteria and provides an effective strain in the bioremediation PCN and PCA contaminated environments.
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Affiliation(s)
- Qian Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Kaihua Pan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Hongfei Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Junqiang Hu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qian Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Xuekun Bai
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mingliang Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiguo Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qing Hong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China.
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Zhang M, Bai X, Li Q, Zhang L, Zhu Q, Gao S, Ke Z, Jiang M, Hu J, Qiu J, Hong Q. Functional analysis, diversity, and distribution of carbendazim hydrolases MheI and CbmA, responsible for the initial step in carbendazim degradation. Environ Microbiol 2022; 24:4803-4817. [PMID: 35880585 DOI: 10.1111/1462-2920.16139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 11/29/2022]
Abstract
Strains Rhodococcus qingshengii djl-6 and Rhodococcus jialingiae djl-6-2 both harbor the typical carbendazim degradation pathway with the hydrolysis of carbendazim to 2-aminobenzimidazole (2-AB) as the initial step. However, the enzymes involved in this process are still unknown. In this study, the previous reported carbendazim hydrolase MheI was found in strain djl-6, but not in strain djl-6-2, then another carbendazim hydrolase CbmA was obtained by a four-step purification strategy from strain djl-6-2. CbmA was classified as a member of the amidase signature superfamily with conserved catalytic site residues Ser157, Ser181, and Lys82, while MheI was classified as a member of the Abhydrolase superfamily with conserved catalytic site residues Ser77 and His224. The catalytic efficiency (kcat /Km ) of MheI (24.0-27.9 μM-1 min-1 ) was 200 times more than that of CbmA (0.032-0.21 μM-1 min-1 ). The mheI gene (plasmid encoded) was highly conserved (> 99% identity) in the strains from different bacterial genera and its plasmid encoded flanked by mobile genetic elements. The cmbA gene was highly conserved only in strains of the genus Rhodococcus and it was chromosomally encoded. Overall, the function, diversity, and distribution of carbendazim hydrolases MheI and CbmA will provide insights into the microbial degradation of carbendazim.
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Affiliation(s)
- Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Xuekun Bai
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Qian Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Lu Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Qian Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Siyuan Gao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Mingli Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Junqiang Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
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Crooks BA, Mckenzie D, Cadd LC, McCoy CJ, McVeigh P, Marks NJ, Maule AG, Mousley A, Atkinson LE. Pan-phylum In Silico Analyses of Nematode Endocannabinoid Signalling Systems Highlight Novel Opportunities for Parasite Drug Target Discovery. Front Endocrinol (Lausanne) 2022; 13:892758. [PMID: 35846343 PMCID: PMC9283691 DOI: 10.3389/fendo.2022.892758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The endocannabinoid signalling (ECS) system is a complex lipid signalling pathway that modulates diverse physiological processes in both vertebrate and invertebrate systems. In nematodes, knowledge of endocannabinoid (EC) biology is derived primarily from the free-living model species Caenorhabditis elegans, where ECS has been linked to key aspects of nematode biology. The conservation and complexity of nematode ECS beyond C. elegans is largely uncharacterised, undermining the understanding of ECS biology in nematodes including species with key importance to human, veterinary and plant health. In this study we exploited publicly available omics datasets, in silico bioinformatics and phylogenetic analyses to examine the presence, conservation and life stage expression profiles of EC-effectors across phylum Nematoda. Our data demonstrate that: (i) ECS is broadly conserved across phylum Nematoda, including in therapeutically and agriculturally relevant species; (ii) EC-effectors appear to display clade and lifestyle-specific conservation patterns; (iii) filarial species possess a reduced EC-effector complement; (iv) there are key differences between nematode and vertebrate EC-effectors; (v) life stage-, tissue- and sex-specific EC-effector expression profiles suggest a role for ECS in therapeutically relevant parasitic nematodes. To our knowledge, this study represents the most comprehensive characterisation of ECS pathways in phylum Nematoda and inform our understanding of nematode ECS complexity. Fundamental knowledge of nematode ECS systems will seed follow-on functional studies in key nematode parasites to underpin novel drug target discovery efforts.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Louise E. Atkinson
- Microbes & Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
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6
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Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
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Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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7
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Shimamura K, Akiyama T, Yokoyama K, Takenoya M, Ito S, Sasaki Y, Yajima S. Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans. Biochem Biophys Res Commun 2020; 525:720-725. [PMID: 32143826 DOI: 10.1016/j.bbrc.2020.02.146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
Microbacterium hydrocarbonoxydans was isolated, using hydrazide compounds as its sole carbon source. The key enzyme that metabolizes these compounds was identified as hydrazidase, and the operon containing the gene coding for the enzyme, was revealed by genome sequencing. The operon also contained genes coding for an ATP-binding cassette transporter (ABC transporter), which was expected to transport the hydrazide compounds. Substrate binding protein (SBP), a component subunit of the transporter, plays an important role in recognizing the correct substrates for transport. Therefore, to elucidate the mechanism of recognition of the unnatural hydrazide compounds, we determined the crystal structures of the SBP, obtained from M. hydrocarbonoxydans (Mh-SBP), complexed with and without the hydrazide compound, at 2.2 Å and 1.75 Å resolutions, respectively. The overall structures of Mh-SBP were similar to those of the SBP in oligopeptide transporters such as OppA. On comparison, the liganded and unliganded structures of Mh-SBP showed an open - close conformation change. Interestingly, the binding mode of the compound to Mh-SBP was almost identical to that of the compound to hydrazidase, suggesting that the ABC transporter served transporting these compounds. Furthermore, based on the hydrazide complex structure, paraben, the other putative substrate of the protein, was successfully used with Mh-SBP to obtain the paraben complex structure.
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Affiliation(s)
- Kaho Shimamura
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Tomonori Akiyama
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Kazuhiro Yokoyama
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Mihoko Takenoya
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Shinsaku Ito
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.
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Aziz M, Chapman KD. Fatty Acid Amide Hydrolases: An Expanded Capacity for Chemical Communication? TRENDS IN PLANT SCIENCE 2020; 25:236-249. [PMID: 31919033 DOI: 10.1016/j.tplants.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 05/25/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is an enzyme that belongs to the amidase signature (AS) superfamily and is widely distributed in multicellular eukaryotes. FAAH hydrolyzes lipid signaling molecules - namely, N-acylethanolamines (NAEs) - which terminates their actions. Recently, the crystal structure of Arabidopsis thaliana FAAH was solved and key residues were identified for substrate-specific interactions. Here, focusing on residues surrounding the substrate-binding pocket, a comprehensive analysis of FAAH sequences from angiosperms reveals a distinctly different family of FAAH-like enzymes. We hypothesize that FAAH, in addition to its role in seedling development, also acts in an N-acyl amide communication axis to facilitate plant-microbe interactions and that structural diversity provides for the flexible use of a wide range of small lipophilic signaling molecules.
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Affiliation(s)
- Mina Aziz
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
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Gao S, Lu Y, Li Y, Huang R, Zheng G. Enhancement in the catalytic activity of Sulfolobus solfataricus P2 (+)-γ-lactamase by semi-rational design with the aid of a newly established high-throughput screening method. Appl Microbiol Biotechnol 2018; 103:251-263. [DOI: 10.1007/s00253-018-9428-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/26/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
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An Amidase Gene, ipaH, Is Responsible for the Initial Step in the Iprodione Degradation Pathway of Paenarthrobacter sp. Strain YJN-5. Appl Environ Microbiol 2018; 84:AEM.01150-18. [PMID: 30054359 DOI: 10.1128/aem.01150-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/20/2018] [Indexed: 11/20/2022] Open
Abstract
Iprodione [3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide] is a highly effective broad-spectrum dicarboxamide fungicide. Several bacteria with iprodione-degrading capabilities have been reported; however, the enzymes and genes involved in this process have not been characterized. In this study, an iprodione-degrading strain, Paenarthrobacter sp. strain YJN-5, was isolated and characterized. Strain YJN-5 degraded iprodione through the typical pathway, with hydrolysis of its N-1 amide bond to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine as the initial step. The ipaH gene, encoding a novel amidase responsible for this step, was cloned from strain YJN-5 by the shotgun method. IpaH shares the highest similarity (40%) with an indoleacetamide hydrolase (IAHH) from Bradyrhizobium diazoefficiens USDA 110. IpaH displayed maximal enzymatic activity at 35°C and pH 7.5, and it was not a metalloamidase. The kcat and Km of IpaH against iprodione were 22.42 s-1 and 7.33 μM, respectively, and the catalytic efficiency value (kcat/Km ) was 3.09 μM-1 s-1 IpaH has a Ser-Ser-Lys motif, which is conserved among members of the amidase signature family. The replacement of Lys82, Ser157, and Ser181 with alanine in IpaH led to the complete loss of enzymatic activity. Furthermore, strain YJN-5M lost the ability to degrade iprodione, suggesting that ipaH is the only gene responsible for the initial iprodione degradation step. The ipaH gene could also be amplified from another previously reported iprodione-degrading strain, Microbacterium sp. strain YJN-G. The sequence similarity between the two IpaHs at the amino acid level was 98%, indicating that conservation of IpaH exists in different strains.IMPORTANCE Iprodione is a widely used dicarboxamide fungicide, and its residue has been frequently detected in the environment. The U.S. Environmental Protection Agency has classified iprodione as moderately toxic to small animals and a probable carcinogen to humans. Bacterial degradation of iprodione has been widely investigated. Previous studies demonstrate that hydrolysis of its N-1 amide bond is the initial step in the typical bacterial degradation pathway of iprodione; however, enzymes or genes involved in iprodione degradation have yet to be reported. In this study, a novel ipaH gene encoding an amidase responsible for the initial degradation step of iprodione in Paenarthrobacter sp. strain YJN-5 was cloned. In addition, the characteristics and key amino acid sites of IpaH were investigated. These findings enhance our understanding of the microbial degradation mechanism of iprodione.
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Zheng RC, Jin JQ, Wu ZM, Tang XL, Jin LQ, Zheng YG. Biocatalytic hydrolysis of chlorinated nicotinamides by a superior AS family amidase and its application in enzymatic production of 2-chloronicotinic acid. Bioorg Chem 2018; 76:81-87. [DOI: 10.1016/j.bioorg.2017.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022]
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12
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Adediran SA, Wang PF, Shilabin AG, Baron CA, McLeish MJ, Pratt RF. Specificity and mechanism of mandelamide hydrolase catalysis. Arch Biochem Biophys 2017; 618:23-31. [PMID: 28129982 DOI: 10.1016/j.abb.2017.01.010] [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: 12/16/2016] [Revised: 01/15/2017] [Accepted: 01/23/2017] [Indexed: 11/16/2022]
Abstract
The best-studied amidase signature (AS) enzyme is probably fatty acid amide hydrolase (FAAH). Closely related to FAAH is mandelamide hydrolase (MAH), whose substrate specificity and mechanism of catalysis are described in this paper. First, we developed a convenient chromogenic substrate, 4-nitrophenylacetamide, for MAH. The lack of reactivity of MAH with the corresponding ethyl ester confirmed the very limited size of the MAH leaving group site. The reactivity of MAH with 4-nitrophenyl acetate and methyl 4-nitrophenyl carbonate, therefore, suggested formation of an "inverse" acyl-enzyme where the small acyl-group occupies the normal leaving group site. We have interpreted the specificity of MAH for phenylacetamide substrates and small leaving groups in terms of its active site structure, using a homology model based on a FAAH crystal structure. The relevant structural elements were compared with those of FAAH. Phenylmethylboronic acid is a potent inhibitor of MAH (Ki = 27 nM), presumably because it forms a transition state analogue structure with the enzyme. O-Acyl hydroxamates were not irreversible inactivators of MAH but some were found to be transient inhibitors.
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Affiliation(s)
- S A Adediran
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Pan-Fen Wang
- College of Pharmacy, University of Michigan, Ann Arbor, MI 48105, USA
| | - Abbas G Shilabin
- Department of Chemistry, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Charles A Baron
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Michael J McLeish
- College of Pharmacy, University of Michigan, Ann Arbor, MI 48105, USA; Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - R F Pratt
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA.
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13
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Ruan LT, Zheng RC, Zheng YG. Mining and characterization of two amidase signature family amidases from Brevibacterium epidermidis ZJB-07021 by an efficient genome mining approach. Protein Expr Purif 2016; 126:16-25. [DOI: 10.1016/j.pep.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
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14
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Ruan LT, Zheng RC, Zheng YG. A novel amidase from Brevibacterium epidermidis ZJB-07021: gene cloning, refolding and application in butyrylhydroxamic acid synthesis. ACTA ACUST UNITED AC 2016; 43:1071-83. [DOI: 10.1007/s10295-016-1786-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
Abstract
A novel amidase gene (bami) was cloned from Brevibacterium epidermidis ZJB-07021 by combination of degenerate PCR and high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). The deduced amino acid sequence showed low identity (≤55 %) with other reported amidases. The bami gene was overexpressed in Escherichia coli, and the resultant inclusion bodies were refolded and purified to homogeneity with a recovery of 22.6 %. Bami exhibited a broad substrate spectrum towards aliphatic, aromatic and heterocyclic amides, and showed the highest acyl transfer activity towards butyramide with specific activity of 1331.0 ± 24.0 U mg−1. Kinetic analysis demonstrated that purified Bami exhibited high catalytic efficiency (414.9 mM−1 s−1) for acyl transfer of butyramide, with turnover number (K cat) of 3569.0 s−1. Key parameters including pH, substrate/co-substrate concentration, reaction temperature and catalyst loading were investigated and the Bami showed maximum acyl transfer activity at 50 °C, pH 7.5. Enzymatic catalysis of 200 mM butyramide with 15 μg mL−1 purified Bami was completed in 15 min with a BHA yield of 88.1 % under optimized conditions. The results demonstrated the great potential of Bami for the production of a variety of hydroxamic acids.
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Affiliation(s)
- Li-Tao Ruan
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Ren-Chao Zheng
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Yu-Guo Zheng
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
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15
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Mishra P, Kaur S, Sharma AN, Jolly RS. Characterization of an Indole-3-Acetamide Hydrolase from Alcaligenes faecalis subsp. parafaecalis and Its Application in Efficient Preparation of Both Enantiomers of Chiral Building Block 2,3-Dihydro-1,4-Benzodioxin-2-Carboxylic Acid. PLoS One 2016; 11:e0159009. [PMID: 27391673 PMCID: PMC4938524 DOI: 10.1371/journal.pone.0159009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/25/2016] [Indexed: 11/19/2022] Open
Abstract
Both the enantiomers of 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid are valuable chiral synthons for enantiospecific synthesis of therapeutic agents such as (S)-doxazosin mesylate, WB 4101, MKC 242, 2,3-dihydro-2-hydroxymethyl-1,4-benzodioxin, and N-[2,4-oxo-1,3-thiazolidin-3-yl]-2,3-dihydro-1,4-benzodioxin-2-carboxamide. Pharmaceutical applications require these enantiomers in optically pure form. However, currently available methods suffer from one drawback or other, such as low efficiency, uncommon and not so easily accessible chiral resolving agent and less than optimal enantiomeric purity. Our interest in finding a biocatalyst for efficient production of enantiomerically pure 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid lead us to discover an amidase activity from Alcaligenes faecalis subsp. parafaecalis, which was able to kinetically resolve 2,3-dihydro-1,4-benzodioxin-2-carboxyamide with E value of >200. Thus, at about 50% conversion, (R)-2,3-dihydro-1,4-benzodioxin-2-carboxylic acid was produced in >99% e.e. The remaining amide had (S)-configuration and 99% e.e. The amide and acid were easily separated by aqueous (alkaline)-organic two phase extraction method. The same amidase was able to catalyse, albeit at much lower rate the hydrolysis of (S)-amide to (S)-acid without loss of e.e. The amidase activity was identified as indole-3-acetamide hydrolase (IaaH). IaaH is known to catalyse conversion of indole-3-acetamide (IAM) to indole-3-acetic acid (IAA), which is phytohormone of auxin class and is widespread among plants and bacteria that inhabit plant rhizosphere. IaaH exhibited high activity for 2,3-dihydro-1,4-benzodioxin-2-carboxamide, which was about 65% compared to its natural substrate, indole-3-acetamide. The natural substrate for IaaH indole-3-acetamide shared, at least in part a similar bicyclic structure with 2,3-dihydro-1,4-benzodioxin-2-carboxamide, which may account for high activity of enzyme towards this un-natural substrate. To the best of our knowledge this is the first application of IaaH in production of industrially important molecules.
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Affiliation(s)
- Pradeep Mishra
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
| | - Suneet Kaur
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
| | - Amar Nath Sharma
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
| | - Ravinder S. Jolly
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
- * E-mail:
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16
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Wu ZM, Zheng RC, Zheng YG. Exploitation and characterization of three versatile amidase super family members from Delftia tsuruhatensis ZJB-05174. Enzyme Microb Technol 2016; 86:93-102. [DOI: 10.1016/j.enzmictec.2016.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/01/2016] [Accepted: 02/09/2016] [Indexed: 10/22/2022]
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17
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Zhang Z, Zhang J, Zheng Q, Kong C, Li Z, Zhang H, Ma J. Theoretical investigation on binding process of allophanate to allophanate hydrolase. Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-5108-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Fuhshuku KI, Watanabe S, Nishii T, Ishii A, Asano Y. A novel S-enantioselective amidase acting on 3,3,3-trifluoro-2-hydroxy-2-methylpropanamide from Arthrobacter sp. S-2. Biosci Biotechnol Biochem 2015; 79:1587-96. [DOI: 10.1080/09168451.2015.1038216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
A novel S-enantioselective amidase acting on 3,3,3-trifluoro-2-hydroxy-2-methylpropanamide was purified from Arthrobacter sp. S-2. The enzyme acted S-enantioselectively on 3,3,3-trifluoro-2-hydroxy-2-methylpropanamide to yield (S)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoic acid. Based on the N-terminal amino acid sequence of this amidase, the gene coding S-amidase was cloned from the genomic DNA of Arthrobacter sp. S-2 and expressed in an Escherichia coli host. The recombinant S-amidase was purified and characterized. Furthermore, the purified recombinant S-amidase with the C-His6-tag, which was expressed in E. coli as the C-His6-tag fusion protein, was used in the kinetic resolution of (±)-3,3,3-trifluoro-2-hydroxy-2-methylpropanamide to obtain (S)-3,3,3-trifluoro-2-hydroxy-2-methylpropanoic acid and (R)-3,3,3-trifluoro-2-hydroxy-2-methylpropanamide.
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Affiliation(s)
- Ken-ichi Fuhshuku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
| | - Shunsuke Watanabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
| | - Tetsuro Nishii
- Chemical Research Center, Central Glass Co., Ltd., Kawagoe, Japan
| | - Akihiro Ishii
- Chemical Research Center, Central Glass Co., Ltd., Kawagoe, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
- Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan
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19
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Ramteke PW, Maurice NG, Joseph B, Wadher BJ. Nitrile-converting enzymes: an eco-friendly tool for industrial biocatalysis. Biotechnol Appl Biochem 2014; 60:459-81. [PMID: 23826937 DOI: 10.1002/bab.1139] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/21/2013] [Indexed: 11/10/2022]
Abstract
Nitriles are organic compounds bearing a − C ≡ N group; they are frequently known to occur naturally in both fauna and flora and are also synthesized chemically. They have wide applicability in the fields of medicine, industry, and environmental monitoring. However, the majority of nitrile compounds are considered to be lethal, mutagenic, and carcinogenic in nature and are known to cause potential health problems such as nausea, bronchial irritation, respiratory distress, convulsions, coma, and skeletal deformities in humans. Nitrile-converting enzymes, which are extracted from microorganisms, are commonly termed nitrilases and have drawn the attention of researchers all over the world to combat the toxicity of nitrile compounds. The present review focuses on the utility of nitrile-converting enzymes, sources, classification, structure, properties, and applications, as well as the future perspective on nitrilases.
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Affiliation(s)
- Pramod W Ramteke
- Department of Biological Sciences, Sam Higginbotom Institute of Agriculture, Technology and Sciences, Allahabad, India
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20
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Nitrilase superfamily aryl acylamidase from the halotolerant mangrove Streptomyces sp. 211726. Appl Microbiol Biotechnol 2014; 98:8583-90. [DOI: 10.1007/s00253-014-5762-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
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21
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Guo Y, Chen S, Su L, Wu J, Chen J. Cloning, expression, and characterization of polyamidase from Nocardia farcinica and its application to polyamide modification. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0189-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Abstract
Allophanate hydrolase converts allophanate to ammonium and carbon dioxide. It is conserved in many organisms and is essential for their utilization of urea as a nitrogen source. It also has important functions in a newly discovered eukaryotic pyrimidine nucleic acid precursor degradation pathway, the yeast-hypha transition that several pathogens utilize to escape the host defense, and an s-triazine herbicide degradation pathway recently emerged in many soil bacteria. We have determined the crystal structure of the Kluyveromyces lactis allophanate hydrolase. Together with structure-directed functional studies, we demonstrate that its N and C domains catalyze a two-step reaction and contribute to maintaining a dimeric form of the enzyme required for their optimal activities. Our studies also provide molecular insights into their catalytic mechanism. Interestingly, we found that the C domain probably catalyzes a novel form of decarboxylation reaction that might expand the knowledge of this common reaction in biological systems.
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Affiliation(s)
- Chen Fan
- From the Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi Li
- From the Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huiyong Yin
- From the Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Song Xiang
- From the Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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23
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Chudyk EI, Dyguda-Kazimierowicz E, Langner KM, Sokalski WA, Lodola A, Mor M, Sirirak J, Mulholland AJ. Nonempirical Energetic Analysis of Reactivity and Covalent Inhibition of Fatty Acid Amide Hydrolase. J Phys Chem B 2013; 117:6656-66. [DOI: 10.1021/jp401834v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ewa I. Chudyk
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | | | - Karol M. Langner
- Institute of Physical & Theoretical Chemistry, Wrocław University of Technology, 50-370 Wrocław, Poland
- Department of Molecular
Physiology
and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - W. Andrzej Sokalski
- Institute of Physical & Theoretical Chemistry, Wrocław University of Technology, 50-370 Wrocław, Poland
| | - Alessio Lodola
- Dipartimento Farmaceutico, Università degli Studi di Parma, 43100 Parma,
Italy
| | - Marco Mor
- Dipartimento Farmaceutico, Università degli Studi di Parma, 43100 Parma,
Italy
| | - Jitnapa Sirirak
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
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24
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Mehta PK, Bhatia SK, Bhatia RK, Bhalla TC. Purification and characterization of a novel thermo-active amidase from Geobacillus subterraneus RL-2a. Extremophiles 2013; 17:637-48. [DOI: 10.1007/s00792-013-0547-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/12/2013] [Indexed: 11/30/2022]
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25
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Lin Y, St. Maurice M. The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family. Biochemistry 2013; 52:690-700. [PMID: 23282241 PMCID: PMC3568674 DOI: 10.1021/bi301242m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Allophanate hydrolase (AH) catalyzes the hydrolysis of allophanate, an intermediate in atrazine degradation and urea catabolism pathways, to NH(3) and CO(2). AH belongs to the amidase signature family, which is characterized by a conserved block of 130 amino acids rich in Gly and Ser and a Ser-cis-Ser-Lys catalytic triad. In this study, the first structures of AH from Granulibacter bethesdensis were determined, with and without the substrate analogue malonate, to 2.2 and 2.8 Å, respectively. The structures confirm the identity of the catalytic triad residues and reveal an altered dimerization interface that is not conserved in the amidase signature family. The structures also provide insights into previously unrecognized substrate specificity determinants in AH. Two residues, Tyr(299) and Arg(307), are within hydrogen bonding distance of a carboxylate moiety of malonate. Both Tyr(299) and Arg(307) were mutated, and the resulting modified enzymes revealed >3 order of magnitude reductions in both catalytic efficiency and substrate stringency. It is proposed that Tyr(299) and Arg(307) serve to anchor and orient the substrate for attack by the catalytic nucleophile, Ser(172). The structure further suggests the presence of a unique C-terminal domain in AH. While this domain is conserved, it does not contribute to catalysis or to the structural integrity of the core domain, suggesting that it may play a role in mediating transient and specific interactions with the urea carboxylase component of urea amidolyase. Analysis of the AH active site architecture offers new insights into common determinants of catalysis and specificity among divergent members of the amidase signature family.
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Affiliation(s)
- Yi Lin
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Martin St. Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA,To whom correspondence should be addressed: Marquette University, Department of Biological Sciences, PO Box 1881, Milwaukee, WI 53201 Ph: 414 288 2087, Fax: 414 288 7357,
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26
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Neelamegan D, Schoenhofen IC, Richards JC, Cox AD. Identification and recombinant expression of anandamide hydrolyzing enzyme from Dictyostelium discoideum. BMC Microbiol 2012; 12:124. [PMID: 22730904 PMCID: PMC3412733 DOI: 10.1186/1471-2180-12-124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/25/2012] [Indexed: 11/20/2022] Open
Abstract
Background Anandamide (Arachidonoyl ethanolamide) is a potent bioactive lipid studied extensively in humans, which regulates several neurobehavioral processes including pain, feeding and memory. Bioactivity is terminated when hydrolyzed into free arachidonic acid and ethanolamine by the enzyme fatty acid amide hydrolase (FAAH). In this study we report the identification of a FAAH homolog from Dictyostelium discoideum and its function to hydrolyze anandamide. Results A putative FAAH DNA sequence coding for a conserved amidase signature motif was identified in the Dictyostelium genome database and the corresponding cDNA was isolated and expressed as an epitope tagged fusion protein in either E.coli or Dictyostelium. Wild type Dictyostelium cells express FAAH throughout their development life cycle and the protein was found to be predominantly membrane associated. Production of recombinant HIS tagged FAAH protein was not supported in E.coli host, but homologous Dictyostelium host was able to produce the same successfully. Recombinant FAAH protein isolated from Dictyostelium was shown to hydrolyze anandamide and related synthetic fatty acid amide substrates. Conclusions This study describes the first identification and characterisation of an anandamide hydrolyzing enzyme from Dictyostelium discoideum, suggesting the potential of Dictyostelium as a simple eukaryotic model system for studying mechanisms of action of any FAAH inhibitors as drug targets.
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Affiliation(s)
- Dhamodharan Neelamegan
- National Research Council, Institute for Biological Sciences, 100, Sussex Drive, Ottawa, ON K1A 0R6, Canada
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27
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Marron AO, Akam M, Walker G. Nitrile hydratase genes are present in multiple eukaryotic supergroups. PLoS One 2012; 7:e32867. [PMID: 22505998 PMCID: PMC3323583 DOI: 10.1371/journal.pone.0032867] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/01/2012] [Indexed: 11/18/2022] Open
Abstract
Background Nitrile hydratases are enzymes involved in the conversion of nitrile-containing compounds into ammonia and organic acids. Although they are widespread in prokaryotes, nitrile hydratases have only been reported in two eukaryotes: the choanoflagellate Monosiga brevicollis and the stramenopile Aureococcus anophagefferens. The nitrile hydratase gene in M. brevicollis was believed to have arisen by lateral gene transfer from a prokaryote, and is a fusion of beta and alpha nitrile hydratase subunits. Only the alpha subunit has been reported in A. anophagefferens. Methodology/Principal Findings Here we report the detection of nitrile hydratase genes in five eukaryotic supergroups: opisthokonts, amoebozoa, archaeplastids, CCTH and SAR. Beta-alpha subunit fusion genes are found in the choanoflagellates, ichthyosporeans, apusozoans, haptophytes, rhizarians and stramenopiles, and potentially also in the amoebozoans. An individual alpha subunit is found in a dinoflagellate and an individual beta subunit is found in a haptophyte. Phylogenetic analyses recover a clade of eukaryotic-type nitrile hydratases in the Opisthokonta, Amoebozoa, SAR and CCTH; this is supported by analyses of introns and gene architecture. Two nitrile hydratase sequences from an animal and a plant resolve in the prokaryotic nitrile hydratase clade. Conclusions/Significance The evidence presented here demonstrates that nitrile hydratase genes are present in multiple eukaryotic supergroups, suggesting that a subunit fusion gene was present in the last common ancestor of all eukaryotes. The absence of nitrile hydratase from several sequenced species indicates that subunits were lost in multiple eukaryotic taxa. The presence of nitrile hydratases in many other eukaryotic groups is unresolved due to insufficient data and taxon sampling. The retention and expression of the gene in distantly related eukaryotic species suggests that it plays an important metabolic role. The novel family of eukaryotic nitrile hydratases presented in this paper represents a promising candidate for research into their molecular biology and possible biotechnological applications.
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Affiliation(s)
- Alan O Marron
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
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28
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Teaster ND, Keereetaweep J, Kilaru A, Wang YS, Tang Y, Tran CNQ, Ayre BG, Chapman KD, Blancaflor EB. Overexpression of Fatty Acid Amide Hydrolase Induces Early Flowering in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:32. [PMID: 22645580 PMCID: PMC3355813 DOI: 10.3389/fpls.2012.00032] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 02/01/2012] [Indexed: 05/19/2023]
Abstract
N-acylethanolamines (NAEs) are bioactive lipids derived from the hydrolysis of the membrane phospholipid N-acylphosphatidylethanolamine (NAPE). In animal systems this reaction is part of the "endocannabinoid" signaling pathway, which regulates a variety of physiological processes. The signaling function of NAE is terminated by fatty acid amide hydrolase (FAAH), which hydrolyzes NAE to ethanolamine and free fatty acid. Our previous work in Arabidopsis thaliana showed that overexpression of AtFAAH (At5g64440) lowered endogenous levels of NAEs in seeds, consistent with its role in NAE signal termination. Reduced NAE levels were accompanied by an accelerated growth phenotype, increased sensitivity to abscisic acid (ABA), enhanced susceptibility to bacterial pathogens, and early flowering. Here we investigated the nature of the early flowering phenotype of AtFAAH overexpression. AtFAAH overexpressors flowered several days earlier than wild type and AtFAAH knockouts under both non-inductive short day (SD) and inductive long day (LD) conditions. Microarray analysis revealed that the FLOWERING LOCUS T (FT) gene, which plays a major role in regulating flowering time, and one target MADS box transcription factor, SEPATALLA3 (SEP3), were elevated in AtFAAH overexpressors. Furthermore, AtFAAH overexpressors, with the early flowering phenotype had lower endogenous NAE levels in leaves compared to wild type prior to flowering. Exogenous application of NAE 12:0, which was reduced by up to 30% in AtFAAH overexpressors, delayed the onset of flowering in wild type plants. We conclude that the early flowering phenotype of AtFAAH overexpressors is, in part, explained by elevated FT gene expression resulting from the enhanced NAE hydrolase activity of AtFAAH, suggesting that NAE metabolism may participate in floral signaling pathways.
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Affiliation(s)
- Neal D. Teaster
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Jantana Keereetaweep
- Department of Biological Sciences, Center for Plant Lipid Research, University of North TexasDenton, TX, USA
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State UniversityJohnson City, TN, USA
| | - Yuh-Shuh Wang
- Plant Signal Research Group, Institute of Technology, University of TartuTartu, Estonia
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Christopher N.-Q. Tran
- Department of Biological Sciences, Center for Plant Lipid Research, University of North TexasDenton, TX, USA
| | - Brian G. Ayre
- Department of Biological Sciences, Center for Plant Lipid Research, University of North TexasDenton, TX, USA
| | - Kent D. Chapman
- Department of Biological Sciences, Center for Plant Lipid Research, University of North TexasDenton, TX, USA
| | - Elison B. Blancaflor
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
- *Correspondence: Elison B. Blancaflor, Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, USA. e-mail:
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Shen W, Chen H, Jia K, Ni J, Yan X, Li S. Cloning and characterization of a novel amidase from Paracoccus sp. M-1, showing aryl acylamidase and acyl transferase activities. Appl Microbiol Biotechnol 2011; 94:1007-18. [PMID: 22101784 DOI: 10.1007/s00253-011-3704-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 10/04/2011] [Accepted: 11/02/2011] [Indexed: 11/29/2022]
Abstract
A novel amidase gene, designated pamh, was cloned from Paracoccus sp. M-1. Site-directed mutagenesis and bioinformatic analysis showed that the PamH protein belonged to the amidase signature enzyme family. PamH was expressed in Escherichia coli, purified, and characterized. The molecular mass of PamH was determined to be 52 kDa with an isoelectric point of 5.13. PamH displayed its highest enzymatic activity at 45°C and at pH 8.0 and was stable within a pH range of 5.0-10.0. The PamH enzyme exhibited amidase activity, aryl acylamidase activity, and acyl transferase activity, allowing it to function across a very broad substrate spectrum. PamH was highly active on aromatic and short-chain aliphatic amides (benzamide and propionamide), moderately active on amino acid amides, and possessed weak urease activity. Of the anilides examined, only propanil was a good substrate for PamH. For propanil, the k (cat) and K (m) were 2.8 s(-1) and 158 μM, respectively, and the catalytic efficiency value (k (cat)/K (m)) was 0.018 μM(-1) s(-1). In addition, PamH was able to catalyze the acyl transfer reaction to hydroxylamine for both amide and anilide substrates, including acetamide, propanil, and 4-nitroacetanilide; the highest reaction rate was shown with isobutyramide. These characteristics make PamH an excellent candidate for environmental remediation and an important enzyme for the biosynthesis of novel amides.
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Affiliation(s)
- Weiliang Shen
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, People's Republic of China
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Fatty acid amide hydrolase expression during retinal postnatal development in rats. Neuroscience 2011; 195:145-65. [PMID: 21867744 DOI: 10.1016/j.neuroscience.2011.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 07/12/2011] [Accepted: 08/03/2011] [Indexed: 01/01/2023]
Abstract
The endocannabinoid (eCB) system is thought to participate in developmental processes in the CNS. The rodent retina represents a valuable model to study CNS development because it contains well-identified cell types with established developmental timelines. The distribution of cannabinoid receptor type 1 (CB1R) was recently revealed in the developing retina; however, the expression patterns of other elements of this system remain unknown. In this study, we investigated the expression pattern of the degradative enzyme fatty acid amide hydrolase (FAAH), a key regulator of the eCB system, in the rat retina during postnatal development. To identify the cells expressing the enzyme, co-stainings were carried out for FAAH and retinal cell type markers. FAAH was expressed at postnatal day (P) 1 in ganglion and cholinergic amacrine cells. In the course of development, it appeared in cones, horizontal, and bipolar cells. For most cell types (horizontal, cholinergic amacrine cells, and cone bipolar cells), FAAH was transiently expressed, suggesting an important redistribution of the enzyme during postnatal development and thus a potential role of the eCB system in developmental processes. Our results also indicated that, in the adult retina, FAAH is expressed in cones, rod bipolar cells, and some retinal ganglion cells. The presence of FAAH in adult animals supports the hypothesis that the eCB system is involved in retinal functions. Overall these results indicate that, as shown in other structures of the brain, the eCB system could play an instrumental role in the development and function of the retina.
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Tian G, Paschetto KA, Gharahdaghi F, Gordon E, Wilkins DE, Luo X, Scott CW. Mechanism of inhibition of fatty acid amide hydrolase by sulfonamide-containing benzothiazoles: long residence time derived from increased kinetic barrier and not exclusively from thermodynamic potency. Biochemistry 2011; 50:6867-78. [PMID: 21728345 DOI: 10.1021/bi200552p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fatty acid amide hydrolase (FAAH) has emerged as a potential target for developing analgesic, anxiolytic, antidepressant, sleep-enhancing, and anti-inflammatory drugs, and tremendous efforts have been made to discover potent and selective inhibitors of FAAH. Most known potent FAAH inhibitors described to date employ covalent mechanisms, inhibiting the enzyme either reversibly or irreversibly. Recently, a benzothiazole-based analogue (1) has been described possessing a high potency against FAAH yet lacking a structural feature previously known to interact with FAAH covalently. However, covalent inhibition of FAAH by 1 has not been fully ruled out, and the issue of reversibility has not been addressed. Confirming previous reports, 1 inhibited recombinant human FAAH (rhFAAH) with high potency with IC(50) ~2 nM. It displayed an apparently noncompetitive and irreversible inhibition, titrating rhFAAH stoichiometrically within normal assay times. The inhibition appeared to be time dependent, but the time dependence only improved potency by a small degree (from ~8 to ~2 nM). However, mass spectrometric analyses of the reaction mixture failed to reveal any cleavage product or covalent adduct and showed full recovery of the parent compound, ruling out covalent, irreversible inhibition. Dialysis revealed recovery of enzyme activity from enzyme-inhibitor complex over a prolonged time (>10 h), demonstrating that 1 is indeed a reversible, albeit slowly dissociating inhibitor of FAAH. Molecular docking indicated that the sulfonamide group of 1 could form hydrogen bonds with several residues involved in catalysis, thereby mimicking the transition state. The long residence time displayed by 1 does not appear to derive exclusively from great thermodynamic potency and is consistent with an increased kinetic energy barrier that prevents dissociation from happening quickly.
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Affiliation(s)
- Gaochao Tian
- AstraZeneca Pharmaceuticals, Wilmington, Delaware 19850, United States.
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Salt-tolerant and thermostable glutaminases of cryptococcus species form a new glutaminase family. Biosci Biotechnol Biochem 2011; 75:1317-24. [PMID: 21737926 DOI: 10.1271/bbb.110092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genes encoding salt-tolerant and thermostable glutaminases were isolated from Cryptococcus species. The glutaminase gene, CngahA, from C. nodaensis NISL-3771 was 2,052 bp in length and encoded a 684-amino acid protein. The gene, CagahA, from C. albidus ATCC20293 was 2,100 bp in length and encoded a 700-amino acid protein. These glutaminases showed 44% identity. By searches on public databases, we found that these glutaminases are not similar to any other characterized glutaminases, but are similar to certain hypothetical proteins. On searching the conserved domain with the basic local alignment search tool (BLAST), it was found that they have the amidase domain and are members of the amidase signature superfamily. They were expressed in Saccharomyces cerevisiae, and their activity was detected on the cell surface. This study revealed that they are a new type of glutaminase with the amidase signature sequence, and that they form a new glutaminase family.
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Discovery and molecular basis of potent noncovalent inhibitors of fatty acid amide hydrolase (FAAH). Proc Natl Acad Sci U S A 2011; 108:7379-84. [PMID: 21502526 DOI: 10.1073/pnas.1016167108] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fatty acid amide hydrolase (FAAH), an amidase-signature family member, is an integral membrane enzyme that degrades lipid amides including the endogenous cannabinoid anandamide and the sleep-inducing molecule oleamide. Both genetic knock out and pharmacological administration of FAAH inhibitors in rodent models result in analgesic, anxiolytic, and antiinflammatory phenotypes. Targeting FAAH activity, therefore, presents a promising new therapeutic strategy for the treatment of pain and other neurological-related or inflammatory disorders. Nearly all FAAH inhibitors known to date attain their binding potency through a reversible or irreversible covalent modification of the nucleophile Ser241 in the unusual Ser-Ser-Lys catalytic triad. Here, we report the discovery and mechanism of action of a series of ketobenzimidazoles as unique and potent noncovalent FAAH inhibitors. Compound 2, a representative of these ketobenzimidazoles, was designed from a series of ureas that were identified from high-throughput screening. While urea compound 1 is characterized as an irreversible covalent inhibitor, the cocrystal structure of FAAH complexed with compound 2 reveals that these ketobenzimidazoles, though containing a carbonyl moiety, do not covalently modify Ser241. These inhibitors achieve potent inhibition of FAAH activity primarily from shape complementarity to the active site and through numerous hydrophobic interactions. These noncovalent compounds exhibit excellent selectivity and good pharmacokinetic properties. The discovery of this distinctive class of inhibitors opens a new avenue for modulating FAAH activity through nonmechanism-based inhibition.
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Unique aliphatic amidase from a psychrotrophic and haloalkaliphilic nesterenkonia isolate. Appl Environ Microbiol 2011; 77:3696-702. [PMID: 21498772 DOI: 10.1128/aem.02726-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nesterenkonia strain AN1 was isolated from a screening program for nitrile- and amide-hydrolyzing microorganisms in Antarctic desert soil samples. Strain AN1 showed significant 16S rRNA sequence identity to known members of the genus. Like known Nesterenkonia species, strain AN1 was obligately alkaliphilic (optimum environmental pH, 9 to 10) and halotolerant (optimum environmental Na(+) content, 0 to 15% [wt/vol]) but was also shown to be an obligate psychrophile with optimum growth at approximately 21°C. The partially sequenced genome of AN1 revealed an open reading frame (ORF) encoding a putative protein member of the nitrilase superfamily, referred to as NitN (264 amino acids). The protein crystallized readily as a dimer and the atomic structure of all but 10 amino acids of the protein was determined, confirming that the enzyme had an active site and a fold characteristic of the nitrilase superfamily. The protein was screened for activity against a variety of nitrile, carbamoyl, and amide substrates and was found to have only amidase activity. It had highest affinity for propionamide but demonstrated a low catalytic rate. NitN had maximal activity at 30°C and between pH 6.5 and 7.5, conditions which are outside the optimum growth range for the organism.
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Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 2010; 76:7029-35. [PMID: 20833789 DOI: 10.1128/aem.00464-10] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A reporter assay-based screening method for enzymes, which we named product-induced gene expression (PIGEX), was developed and used to screen a metagenomic library for amidases. A benzoate-responsive transcriptional activator, BenR, was placed upstream of the gene encoding green fluorescent protein and used as a sensor. Escherichia coli sensor cells carrying the benR-gfp gene cassette fluoresced in response to benzoate concentrations as low as 10 μM but were completely unresponsive to the substrate benzamide. An E. coli metagenomic library consisting of 96,000 clones was grown in 96-well format in LB medium containing benzamide. The library cells were then cocultivated with sensor cells. Eleven amidase genes were recovered from 143 fluorescent wells; eight of these genes were homologous to known bacterial amidase genes while three were novel genes. In addition to their activity toward benzamide, the enzymes were active toward various substrates, including d- and l-amino acid amides, and displayed enantioselectivity. Thus, we demonstrated that PIGEX is an effective approach for screening novel enzymes based on product detection.
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37
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Retraction. J Labelled Comp Radiopharm 2010. [DOI: 10.1002/jlcr.1781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Indole-3-acetamide-dependent auxin biosynthesis: a widely distributed way of indole-3-acetic acid production? Eur J Cell Biol 2010; 89:895-905. [PMID: 20701997 DOI: 10.1016/j.ejcb.2010.06.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
During the course of evolution plants have evolved a complex phytohormone-based network to regulate their growth and development. Herein auxins have a pivotal function, as they are involved in controlling virtually every aspect related to plant growth. Indole-3-acetic acid (IAA) is the major endogenous auxin of higher plants that is already known for more than 80 years. In spite of the long-standing interest in this topic, IAA biosynthesis is still only partially uncovered. Several pathways for the formation of IAA have been proposed over the past years, but none of these pathways are yet completely defined. The aim of this review is to summarize the current knowledge on the indole-3-acetamide (IAM)-dependent pathway of IAA production in plants and to discuss the properties of the involved proteins and genes, respectively. Their evolutionary relationship to known bacterial IAM hydrolases and other amidases from bacteria, algae, moss, and higher plants is discussed on the basis of phylogenetic analyses. Moreover, we report on the transcriptional regulation of the Arabidopsis AMI1 gene.
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Mileni M, Kamtekar S, Wood DC, Benson TE, Cravatt BF, Stevens RC. Crystal structure of fatty acid amide hydrolase bound to the carbamate inhibitor URB597: discovery of a deacylating water molecule and insight into enzyme inactivation. J Mol Biol 2010; 400:743-54. [PMID: 20493882 DOI: 10.1016/j.jmb.2010.05.034] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/13/2010] [Accepted: 05/14/2010] [Indexed: 12/22/2022]
Abstract
The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 A resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 A) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases.
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Affiliation(s)
- Mauro Mileni
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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40
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Ko HJ, Lee EW, Bang WG, Lee CK, Kim KH, Choi IG. Molecular characterization of a novel bacterial aryl acylamidase belonging to the amidase signature enzyme family. Mol Cells 2010; 29:485-92. [PMID: 20396964 DOI: 10.1007/s10059-010-0060-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 01/06/2010] [Accepted: 01/07/2010] [Indexed: 11/29/2022] Open
Abstract
In seeking aryl acylamidase (EC 3.5.1.13) acting on an amide bond in p-acetaminophenol (Tylenol), we identified a novel gene encoding 496 residues of a protein. The gene revealed a conserved amidase signature region with a canonical catalytic triad. The gene was expressed in E. coli and characterized for its biochemical properties. The optimum pH and temperature for the activity on p-acetaminophenol were 10 and 37 degrees C, respectively. The half-life of enzyme activity at 37 degrees C was 192 h and 90% of its activity remained after 3 h incubation at 40 degrees C. Divalent metals was found to inhibit the activity of enzyme. The K (m) values for various aryl acylamides such as 4-nitroacetanilide, p-acetaminophenol, phenacetin, 4-chloroacetanilide and acetanilide were 0.10, 0.32, 0.83, 1.9 and 19 mM, respectively. The reverse reaction activity (amide synthesis) was also examined using various chain lengths (C(1) approximately C(4) and C(10)) of carboxylic donors and aniline as substrates. These kinetic parameters and substrate specificity in forward and reverse reaction indicated that the aryl acylamidase in this study has a preference for aryl substrate having polar functional groups and hydrophobic carboxylic donors.
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Affiliation(s)
- Hyeok-Jin Ko
- Division of Biotechnology, Korea University, Seoul, 136-713, Korea
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41
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A new aryl acylamidase from Rhodococcus sp. strain Oct1 acting on ω-lactams: Its characterization and gene expression in Escherichia coli. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Ohtaki A, Murata K, Sato Y, Noguchi K, Miyatake H, Dohmae N, Yamada K, Yohda M, Odaka M. Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:184-92. [DOI: 10.1016/j.bbapap.2009.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/27/2009] [Accepted: 10/01/2009] [Indexed: 11/26/2022]
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43
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Zhao YS, Zheng QC, Zhang HX, Chu HY, Sun CC. Homology modelling and molecular dynamics study of human fatty acid amide hydrolase. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020903033133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kaczocha M, Glaser ST, Chae J, Brown DA, Deutsch DG. Lipid droplets are novel sites of N-acylethanolamine inactivation by fatty acid amide hydrolase-2. J Biol Chem 2009; 285:2796-806. [PMID: 19926788 DOI: 10.1074/jbc.m109.058461] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Anandamide (AEA) and other bioactive N-acylethanolamines (NAEs) are primarily inactivated by the enzyme fatty acid amide hydrolase (FAAH). Recently, FAAH-2 was discovered in humans, suggesting an additional enzyme can mediate NAE inactivation in higher mammals. Here, we performed a biochemical characterization of FAAH-2 and explored its capacity to hydrolyze NAEs in cells. In homogenate activity assays, FAAH-2 hydrolyzed AEA and palmitoylethanolamide (PEA) with activities approximately 6 and approximately 20% those of FAAH, respectively. In contrast, FAAH-2 hydrolyzed AEA and PEA in intact cells with rates approximately 30-40% those of FAAH, highlighting a potentially greater contribution toward NAE catabolism in vivo than previously appreciated. In contrast to endoplasmic reticulum-localized FAAH, immunofluorescence revealed FAAH-2 was localized on lipid droplets. Supporting this distribution pattern, the putative N-terminal hydrophobic region of FAAH-2 was identified as a functional lipid droplet localization sequence. Lipid droplet localization was essential for FAAH-2 activity as chimeras excluded from lipid droplets lacked activity and/or were poorly expressed. Lipid droplets represent novel sites of NAE inactivation. Therefore, we examined substrate delivery to these organelles. AEA was readily trafficked to lipid droplets, confirming that lipid droplets constitute functional sites of NAE inactivation. Collectively, these results establish FAAH-2 as a bone fide NAE-catabolizing enzyme and suggest that NAE inactivation is spatially separated in cells of higher mammals.
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Affiliation(s)
- Martin Kaczocha
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, USA.
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45
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Kim SC, Kang L, Nagaraj S, Blancaflor EB, Mysore KS, Chapman KD. Mutations in Arabidopsis fatty acid amide hydrolase reveal that catalytic activity influences growth but not sensitivity to abscisic acid or pathogens. J Biol Chem 2009; 284:34065-74. [PMID: 19801664 DOI: 10.1074/jbc.m109.059022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fatty acid amide hydrolase (FAAH) terminates the endocannabinoid signaling pathway that regulates numerous neurobehavioral processes in animals by hydrolyzing N-acylethanolamines (NAEs). Recently, an Arabidopsis FAAH homologue (AtFAAH) was identified, and several studies, especially those using AtFAAH overexpressing and knock-out lines, have suggested an in vivo role for FAAH in the catabolism of NAEs in plants. We previously reported that overexpression of AtFAAH in Arabidopsis resulted in accelerated seedling growth, and in seedlings that were insensitive to exogenous NAEs but hypersensitive to abscisic acid (ABA) and hypersusceptible to nonhost pathogens. Here we show that whereas the enhanced growth and NAE tolerance of the AtFAAH overexpressing seedlings depend on the catalytic activity of AtFAAH, hypersensitivity to ABA and hypersusceptibility to nonhost pathogens are independent of its enzymatic activity. Five amino acids known to be critical for rat FAAH activity are also conserved in AtFAAH (Lys-205, Ser-281, Ser-282, Ser-305, and Arg-307). Site-directed mutation of each of these conserved residues in AtFAAH abolished its hydrolytic activity when expressed in Escherichia coli, supporting a common catalytic mechanism in animal and plant FAAH enzymes. Overexpression of these inactive AtFAAH mutants in Arabidopsis showed no growth enhancement and no NAE tolerance, but still rendered the seedlings hypersensitive to ABA and hypersusceptible to nonhost pathogens to a degree similar to the overexpression of the native AtFAAH. Taken together, our findings suggest that the AtFAAH influences plant growth and interacts with ABA signaling and plant defense through distinctly different mechanisms.
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Affiliation(s)
- Sang-Chul Kim
- Department of Biological Sciences, Center for Plant Lipid Research, University of North Texas, Denton, Texas 76203, USA
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Wyffels L, Muccioli GG, De Bruyne S, Moerman L, Sambre J, Lambert DM, De Vos F. Synthesis, in vitro and in vivo evaluation, and radiolabeling of aryl anandamide analogues as candidate radioligands for in vivo imaging of fatty acid amide hydrolase in the brain. J Med Chem 2009; 52:4613-22. [PMID: 19719235 DOI: 10.1021/jm900324e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fatty acid amide hydrolyase (FAAH) is one of the main enzymes responsible for terminating the signaling of endocannabinoids in the brain. Imaging FAAH in vivo using PET or SPECT is important to deeper understanding of its role in neuropsychiatric disorders. However, at present, no radioligand is available for mapping the enzyme in vivo. Here, we synthesized 18 aryl analogues of anandamide, FAAH's endogenous substrate, and in vitro evaluated their potential as metabolic trapping tracers. Interaction studies with recombinant FAAH revealed good to very good interaction of the methoxy substituted aryl anandamide analogues 17, 18, 19, and 20 with FAAH and they were identified as competing substrates. Compounds 17 and 18 did not display significant binding to CB1 and CB2 cannabinoid receptors and stand out as potential candidate metabolic trapping tracers. They were successfully labeled with 11C in good yields and high radiochemical purity and displayed brain uptake in C57BL/6J mice. Radioligands [11C]-17 and [11C]-18 merit further investigation in vivo.
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Affiliation(s)
- Leonie Wyffels
- Department of Radiopharmacy, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium
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47
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Pacheco R, Karmali A, Matos-Lopes ML, Serralheiro ML. Amidase encapsulated in TTAB reversed micelles for the study of transamidation reactions. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500372419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ahn K, Johnson DS, Cravatt BF. Fatty acid amide hydrolase as a potential therapeutic target for the treatment of pain and CNS disorders. Expert Opin Drug Discov 2009; 4:763-784. [PMID: 20544003 DOI: 10.1517/17460440903018857] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND: Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme that hydrolyzes the endocannabinoid anandamide and related amidated signaling lipids. Genetic or pharmacological inactivation of FAAH produces analgesic, anti-inflammatory, anxiolytic, and antidepressant phenotypes without showing the undesirable side effects of direct cannabinoid receptor agonists, indicating that FAAH may be a promising therapeutic target. OBJECTIVES: This review highlights advances in the development of FAAH inhibitors of different mechanistic classes and their in vivo efficacy. Also highlighted are advances in technology for the in vitro and in vivo selectivity assessment of FAAH inhibitors employing activity-based protein profiling (ABPP) and click chemistry-ABPP, respectively. Recent reports on structure-based drug design for human FAAH generated by protein engineering using interspecies active site conversion are also discussed. METHODS: The literature searches of Medline and SciFinder databases were used. CONCLUSIONS: There has been tremendous progress in our understanding in FAAH and development of FAAH inhibitors with in vivo efficacy, selectivity, and drug like pharmacokinetic properties.
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Affiliation(s)
- Kay Ahn
- Pfizer Global Research and Development, Groton/New London Laboratories, Groton, CT 06340
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49
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Seierstad M, Breitenbucher JG. Discovery and development of fatty acid amide hydrolase (FAAH) inhibitors. J Med Chem 2009; 51:7327-43. [PMID: 18983142 DOI: 10.1021/jm800311k] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mark Seierstad
- Johnson & Johnson Pharmaceutical Research and Development, L.L.C., 3210 Merryfield Row, San Diego, California 92121, USA
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50
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pH-, temperature- and ion-dependent oligomerization of Sulfolobus solfataricus recombinant amidase: a study with site-specific mutants. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2009; 2:221-31. [PMID: 19478917 DOI: 10.1155/2009/280317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 12/22/2008] [Indexed: 11/17/2022]
Abstract
Recombinant amidase from Sulfolobus solfataricus occurred as a dimer of 110 kDa comprising identical subunits. Only dimers were present at pHs above 7.0, but with decreasing pH, dimers associated into octamers, with complete oligomerization occurring at pH 3.0. Oligomerization showed reversible temperature-dependence, with octamer formation increasing with temperature from 36 degrees C to between 70 and 80 degrees C. Increasing salt concentrations, favored dissociation of the octamers. Among the three investigated factors affecting the dimer-octamer equilibrium, the most important was pH. Among four mutants obtained by site-specific mutagenesis and selection for pH and temperature sensitivity, the T319I and D487N mutant amidases, like that of the native Sulfolobus solfataricus, responded to changes in pH and temperature with a conformational change affecting the dimer-octamer equilibrium. The Y41C and L34P mutant amidases were unaffected by pH and temperature, remaining always in the dimeric state. The differences among mutants in protein conformation must be related to the position of the introduced mutation. Although the L34P and Y41C mutations are located in the helical region 33-48 (LLKLQLESYERLDSLP), which is close to the amino-terminal segment of the protein, the T319I mutation is located in a strand on the surface of the protein, which is far from, and opposite to, the amino-terminal segment. The D487N mutation is located in the center of the protein, far distant from the 33-48 segment. These observations suggest that the segment of the protein closest to the amino-terminus plays a key role in the association of dimers into octamers.
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