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Ganjoo A, Babu V. Recombinant Amidases: Recent Insights and its Applications in the Production of Industrially Important Fine Chemicals. Mol Biotechnol 2024:10.1007/s12033-024-01123-8. [PMID: 38598092 DOI: 10.1007/s12033-024-01123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
The current research for the synthesis of industrially important fine chemicals is more inclined towards developing enzyme-based processes. The biotransformation reactions wherein microbial cells/enzymes are used, have become essential in making the process efficient, green, and economical. Amongst industrially important enzymes, amidase is one of the most versatile tools in biocatalysis and biotransformation reactions. It shows broad substrate specificity and sturdy functional characteristics because of its promiscuous nature. Further, advancement in the area led to the development of amidase recombinant systems, which are developed using biotechnology and enzyme engineering tools. Additionally, recombinant amidases may be instrumental in commercializing the synthesis of fine chemicals such as hydroxamic acids that have a significant pharmaceutical market. Hence, the present review focuses on highlighting and assimilating the tools and techniques used in developing recombinant systems followed by their applications.
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Affiliation(s)
- Ananta Ganjoo
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vikash Babu
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Jiang H, Yuan P, Ding J, Wu H, Wang L, Chen K, Jiang N, Dai Y. Novel biodegradation pathway of insecticide flonicamid mediated by an amidase and its unusual substrate spectrum. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129952. [PMID: 36116312 DOI: 10.1016/j.jhazmat.2022.129952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
The insecticide flonicamid (FLO) and its main degradation intermediate 4-trifluoromethylnicotinamide (TFNA-AM) are hazardous to the environment and animals. Microbial transformation of FLO has been well studied, but no study has yet reported on TFNA-AM degradation by a microorganism. Here, Pseudomonas stutzeri CGMCC 22915 effectively degraded TFNA-AM to 5-trifluoromethylnicotinic acid (TFNA). P. stutzeri CGMCC 22915 degraded 60.0% of TFNA-AM (1154.44 μmol/L) within 6 h with a half-life of just 4.5 h. Moreover, P. stutzeri CGMCC 22915 significantly promoted TFNA-AM decomposition in surface water. The reaction was catalyzed by an amidase, PsAmiA. PsAmiA is encoded in a novel nitrile-converting enzyme gene cluster. The enzyme shared only 20-44% identities with previously characterized signature amidases. PsAmiA was successfully expressed in Escherichia coli and its enzymatic properties were investigated using TFNA-AM as the substrate. PsAmiA was more active toward amides without hydrophilic groups, and did not hydrolyze another amide metabolite of FLO, N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM), which is structurally very similar to TFNA-AM. Molecular docking of PsAmiA and TFNA-AM indicated that hydrophobic residues Leu148, Ala150, Ala195, Ile225, Trp341, Leu460, and Ile463 may affect its substrate spectrum. This study provides new insights of the environmental fate of FLO at the molecular level and the structure-function relationships of amidases.
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Affiliation(s)
- Huoyong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Panpan Yuan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Jianjun Ding
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Hongkai Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Li Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Kexin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Nengdang Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
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3
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Rodrigues GL, Matteoli FP, Gazara RK, Rodrigues PSL, Dos Santos ST, Alves AF, Pedrosa-Silva F, Oliveira-Pinheiro I, Canedo-Alvarenga D, Olivares FL, Venancio TM. Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus. Microbiol Res 2021; 254:126896. [PMID: 34715447 DOI: 10.1016/j.micres.2021.126896] [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: 05/07/2021] [Revised: 08/11/2021] [Accepted: 10/14/2021] [Indexed: 11/19/2022]
Abstract
Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter by 13,8% and 88,6% respectively, as well as root dry matter by 61,4%, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.
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Affiliation(s)
- Gustavo L Rodrigues
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Rajesh K Gazara
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | | | - Samuel T Dos Santos
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil
| | - Alice F Alves
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Isabella Oliveira-Pinheiro
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Daniella Canedo-Alvarenga
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), UENF, Brazil; Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, UENF, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil.
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Carbamate C-N Hydrolase Gene ameH Responsible for the Detoxification Step of Methomyl Degradation in Aminobacter aminovorans Strain MDW-2. Appl Environ Microbiol 2020; 87:AEM.02005-20. [PMID: 33097501 DOI: 10.1128/aem.02005-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Methomyl {bis[1-methylthioacetaldehyde-O-(N-methylcarbamoyl)oximino]sulfide} is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain Aminobacter aminovorans MDW-2, and the encoding gene was termed ameH A comparative analysis between the mass fingerprints of AmeH and deduced proteins of the strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification step of methomyl degradation. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass of approximately 34 kDa and shared the highest identity (27%) with the putative formamidase from Schizosaccharomyces pombe ATCC 24843. AmeH displayed maximal enzymatic activity at 50°C and pH 8.5. Km and k cat of AmeH for methomyl were 87.5 μM and 345.2 s-1, respectively, and catalytic efficiency (k cat/Km ) was 3.9 μM-1 s-1 Phylogenetic analysis revealed AmeH to be a member of the FmdA_AmdA superfamily. Additionally, five key amino acid residues (162, 164, 191, 193, and 207) of AmeH were identified by amino acid variations.IMPORTANCE Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and N-methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond. Several genes, such as cehA, mcbA, cahA, and mcd, and their encoding enzymes have also been reported to be involved in the detoxification step. However, none of these enzymes can hydrolyze methomyl. In this study, a carbamate C-N hydrolase gene, ameH, responsible for the detoxification step of methomyl in strain MDW-2 was cloned and the key amino acid sites of AmeH were investigated. These findings provide insight into the microbial degradation mechanism of methomyl.
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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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Kulkarni NH, Muley AB, Bedade DK, Singhal RS. Cross-linked enzyme aggregates of arylamidase from Cupriavidus oxalaticus ICTDB921: process optimization, characterization, and application for mitigation of acrylamide in industrial wastewater. Bioprocess Biosyst Eng 2019; 43:457-471. [PMID: 31705314 DOI: 10.1007/s00449-019-02240-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Acrylamidase produced by Cupriavidus oxalaticus ICTDB921 was recovered directly from the fermentation broth by ammonium sulfate (40-50%) precipitation and then stabilized by cross-linking with glutaraldehyde. The optimum conditions for the preparation of cross-linked enzyme aggregates of acrylamidase (acrylamidase-CLEAs) were using 60 mM glutaraldehyde for 10 min at 35 °C and initial broth pH of 7.0. Acrylamidase-CLEAs were characterized by SDS-PAGE, FTIR, particle size analyzer and SEM. Cross-linking shifted the optimal temperature and pH from 70 to 50 °C and 5-7 to 6-8, respectively. It also altered the secondary structure fractions, pH and thermal stability along with the kinetic constants, Km and Vmax, respectively. A complete degradation of acrylamide ~ 1.75 g/L in industrial wastewater was achieved after 60 min in a batch process under optimum operating conditions, and the kinetics was best represented by Edward model (R2 = 0.70). Acrylamidase-CLEAs retained ~ 40% of its initial activity after three cycles for both pure acrylamide and industrial wastewater, and were stable for 15 days at 4 °C, retaining ~ 25% of its original activity.
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Affiliation(s)
- Nidhi H Kulkarni
- Food Engineering and Technology Department, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Abhijeet B Muley
- Food Engineering and Technology Department, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Dattatray K Bedade
- Food Engineering and Technology Department, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Rekha S Singhal
- Food Engineering and Technology Department, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
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Sun L, Gao X, Chen W, Huang K, Bai N, Lyu W, Liu H. Characterization of the Propham Biodegradation Pathway in Starkeya sp. Strain YW6 and Cloning of a Novel Amidase Gene mmH. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4193-4199. [PMID: 30864436 DOI: 10.1021/acs.jafc.8b06928] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We previously isolated a monocrotophos-degrading strain Starkeya sp. YW6, which could also degrade propham. Here, we show that strain YW6 metabolizes propham via a pathway in which propham is initially hydrolyzed to aniline and then converted to catechol, which is then oxidized via an ortho-cleavage pathway. The novel amidase gene mmH was cloned from strain YW6 and expressed in Escherichia coli BL21(DE3). MmH, which exhibits aryl acylamidase activity, was purified for enzymatic analysis. Bioinformatic analysis confirmed that MmH belongs to the amidase signature (AS) enzyme family and shares 26-50% identity with several AS family members. MmH (molecular mass of 53 kDa) was most active at 40 °C and pH 8.0 and showed high activity toward propham, with Kcat and Km values of 33.4 s-1 and 16.9 μM, respectively. These characteristics make MmH suitable for novel amide biosynthesis and environmental remediation.
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Affiliation(s)
- Lina Sun
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA) , Shanghai 201403 , People's Republic of China
| | - Xinhua Gao
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Environmental Protection Monitoring Station of Shanghai , Shanghai 201403 , People's Republic of China
| | - Wei Chen
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Key Laboratory of Horticultural Technology , Shanghai 201403 , People's Republic of China
| | - Kaihua Huang
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Environmental Protection Monitoring Station of Shanghai , Shanghai 201403 , People's Republic of China
| | - Naling Bai
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture , Shanghai 201403 , People's Republic of China
| | - Weiguang Lyu
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA) , Shanghai 201403 , People's Republic of China
- Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture , Shanghai 201403 , People's Republic of China
| | - Hongming Liu
- Institute of Molecular Biology and Biotechnology , Anhui Normal University , Wuhu , Anhui 241000 , People's Republic of China
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Dynamic kinetic resolution of Vince lactam catalyzed by γ-lactamases: a mini-review. ACTA ACUST UNITED AC 2018; 45:1017-1031. [DOI: 10.1007/s10295-018-2093-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 10/28/2022]
Abstract
Abstract
γ-Lactamases are versatile enzymes used for enzymatic kinetic resolution of racemic Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) in the industry. Optically pure enantiomers and their hydrolytic products are widely employed as key chemical intermediates for developing a wide range of carbocyclic nucleoside medicines, including US FDA-approved drugs peramivir and abacavir. Owing to the broad applications in the healthcare industry, the resolution process of Vince lactam has witnessed tremendous progress during the past decades. Some of the most important advances are the enzymatic strategies involving γ-lactamases. The strong industrial demand drives the progress in various strategies for discovering novel biocatalysts. In the past few years, several new scientific breakthroughs, including the genome-mining strategy and elucidation of several crystal structures, boosted the research on γ-lactamases. So far, several families of γ-lactamases for resolution of Vince lactam have been discovered, and their number is continuously increasing. The purpose of this mini-review is to describe the discovery strategy and classification of these intriguing enzymes and to cover our current knowledge on their potential biological functions. Moreover, structural properties are described in addition to their possible catalytic mechanisms. Additionally, recent advances in the newest approaches, such as immobilization to increase stability, and other engineering efforts are introduced.
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Scope, limitations and classification of lactamases. J Biotechnol 2016; 235:11-23. [DOI: 10.1016/j.jbiotec.2016.03.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
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T'Syen J, Tassoni R, Hansen L, Sorensen SJ, Leroy B, Sekhar A, Wattiez R, De Mot R, Springael D. Identification of the Amidase BbdA That Initiates Biodegradation of the Groundwater Micropollutant 2,6-dichlorobenzamide (BAM) in Aminobacter sp. MSH1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11703-13. [PMID: 26308673 DOI: 10.1021/acs.est.5b02309] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
2,6-dichlorobenzamide (BAM) is a recalcitrant groundwater micropollutant that poses a major problem for drinking water production in European countries. Aminobacter sp. MSH1 and related strains have the unique ability to mineralize BAM at micropollutant concentrations but no information exists on the genetics of BAM biodegradation. An amidase-BbdA-converting BAM to 2,6-dichlorobenzoic acid (DCBA) was purified from Aminobacter sp. MSH1. Heterologous expression of the corresponding bbdA gene and its absence in MSH1 mutants defective in BAM degradation, confirmed its BAM degrading function. BbdA shows low amino acid sequence identity with reported amidases and is encoded by an IncP1-β plasmid (pBAM1, 40.6 kb) that lacks several genes for conjugation. BbdA has a remarkably low KM for BAM (0.71 μM) and also shows activity against benzamide and ortho-chlorobenzamide (OBAM). Differential proteomics and transcriptional reporter analysis suggest the constitutive expression of bbdA in MSH1. Also in other BAM mineralizing Aminobacter sp. strains, bbdA and pBAM1 appear to be involved in BAM degradation. BbdA's high affinity for BAM and its constitutive expression are of interest for using strain MSH1 in treatment of groundwater containing micropollutant concentrations of BAM for drinking water production.
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Affiliation(s)
- Jeroen T'Syen
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Raffaella Tassoni
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Lars Hansen
- Department of Biology, University of Copenhagen , Universitetsparken 15, 2100 København, Denmark
| | - Søren J Sorensen
- Department of Biology, University of Copenhagen , Universitetsparken 15, 2100 København, Denmark
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons , Place du Parc 20, 7000 Mons, Belgium
| | - Aswini Sekhar
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons , Place du Parc 20, 7000 Mons, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven , Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, 3001 Leuven, Belgium
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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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12
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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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13
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Patten CL, Blakney AJC, Coulson TJD. Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria. Crit Rev Microbiol 2012; 39:395-415. [PMID: 22978761 DOI: 10.3109/1040841x.2012.716819] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The capacity to produce the phytohormone indole-3-acetic acid (IAA) is widespread among bacteria that inhabit diverse environments such as soils, fresh and marine waters, and plant and animal hosts. Three major pathways for bacterial IAA synthesis have been characterized that remove the amino and carboxyl groups from the α-carbon of tryptophan via the intermediates indolepyruvate, indoleacetamide, or indoleacetonitrile; the oxidized end product IAA is typically secreted. The enzymes in these pathways often catabolize a broad range of substrates including aromatic amino acids and in some cases the branched chain amino acids. Moreover, expression of some of the genes encoding key IAA biosynthetic enzymes is induced by all three aromatic amino acids. The broad distribution and substrate specificity of the enzymes suggests a role for these pathways beyond plant-microbe interactions in which bacterial IAA has been best studied.
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Affiliation(s)
- Cheryl L Patten
- Department of Biology, University of New Brunswick , Fredericton, New Brunswick , Canada
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14
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A novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by Variovorax sp. strain SRS16. Appl Environ Microbiol 2011; 77:8754-64. [PMID: 22003008 DOI: 10.1128/aem.06162-11] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The soil bacterial isolate Variovorax sp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatechol ortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ∼55 kDa with a K(m) and a V(max) for linuron of 5.8 μM and 0.16 nmol min⁻¹, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues of libA are present in all other tested linuron-degrading Variovorax strains with the exception of Variovorax strains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in different Variovorax strains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria.
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Wang J, Zhang X, Min C, Wu S, Zheng G. Single-step purification and immobilization of γ-lactamase and on-column transformation of 2-azabicyclo [2.2.1] hept-5-en-3-one. Process Biochem 2011. [DOI: 10.1016/j.procbio.2010.07.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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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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17
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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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Yue Y, Lian J, Tian P, Tan T. Cloning of amidase gene from Rhodococcus erythropolis and expression by distinct promoters in Bacillus subtilis. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wang PF, Yep A, Kenyon GL, McLeish MJ. Using directed evolution to probe the substrate specificity of mandelamide hydrolase. Protein Eng Des Sel 2008; 22:103-10. [DOI: 10.1093/protein/gzn073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Ewert C, Lutz-Wahl S, Fischer L. Enantioselective conversion of α-arylnitriles by Klebsiella oxytoca. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Sharma M, Sharma NN, Bhalla TC. A new thermophilic amidase of Bacillus sp. BTP-5x isolated from Tatapani thermal spring of Himachal Pradesh, India. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.1982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Pérez-Pantoja D, De la Iglesia R, Pieper DH, González B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134. FEMS Microbiol Rev 2008; 32:736-94. [DOI: 10.1111/j.1574-6976.2008.00122.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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23
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Pollock JA, Clark KM, Martynowicz BJ, Pridgeon MG, Rycenga MJ, Stolle KE, Taylor SK. A mild biosynthesis of lactones via enantioselective hydrolysis of hydroxynitriles. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Yun YS, Lee W, Shin S, Oh BH, Choi KY. Arg-158 Is Critical in Both Binding the Substrate and Stabilizing the Transition-state Oxyanion for the Enzymatic Reaction of Malonamidase E2. J Biol Chem 2006; 281:40057-64. [PMID: 17077089 DOI: 10.1074/jbc.m604515200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malonamidase E2 (MAE2) from Bradyrhizobium japonicum is an enzyme that hydrolyzes malonamate to malonate and has a Ser-cis-Ser-Lys catalytic triad at the active site. The crystal structures of wild type and mutant MAE2 exhibited that the guanido group of Arg-158 could be involved in the binding of malonamate in which the negative charge of the carboxyl group could destabilize a negatively charged transition-state oxyanion in the enzymatic reaction. In an attempt to elucidate the specific roles of Arg-158, site-directed mutants, R158Q, R158E, and R158K, were prepared (see Table 1). The crystal structure of R158Q determined at 2.2 Angstrom resolution showed that the guanido group of Arg-158 was important for the substrate binding with the marginal structural change upon the mutation. The k(cat) value of R158Q significantly decreased by over 1500-fold and the catalytic activity of R158E could not be detected. The k(cat) value of R158K was similar to that of the wild type with the K(m) value drastically increased by 100-fold, suggesting that Lys-158 of R158K can stabilize the negative charge of the carboxylate in the substrate to some extent and contribute to the stabilization of the transition-state oxyanion, but a single amine group of Lys-158 in R158K could not precisely anchor the carboxyl group of malonamate compared with the guanido group of Arg-158. Our kinetic and structural evidences demonstrate that Arg-158 in MAE2 should be critical to both binding the substrate and stabilizing the transition-state oxyanion for the catalytic reaction of MAE2.
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Affiliation(s)
- Young Sung Yun
- Department of Life Sciences, National CRI Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang 790-784, South Korea
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Hashimoto M, Mizutani A, Tago K, Ohnishi-Kameyama M, Shimojo T, Hayatsu M. Cloning and nucleotide sequence of carbaryl hydrolase gene (cahA) from Arthrobacter sp. RC100. J Biosci Bioeng 2006; 101:410-4. [PMID: 16781470 DOI: 10.1263/jbb.101.410] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 02/09/2006] [Indexed: 11/17/2022]
Abstract
A carbaryl hydrolase gene (cahA) encoded on the plasmid pRC1 in Arthrobacter sp. RC100 was cloned and sequenced. The entire region of the deduced amino acid sequence was found to be homologous to that of an amidase family. Parts of the consensus sequences of the amidase gene have been identified in CahA from strain RC100. CahA was overexpressed in Escherichia coli JM109, and the enzyme was purified to homogeneity by protamine sulfate treatment, ammonium sulfate precipitation, and hydrophobic and anion-exchange chromatographies. The purified enzyme showed hydrolase activity toward 1-naphthylacetamide and isobutyramide but showed no activity toward 1-naphthylacetate. This is the first report of an amidase that is able to hydrolyze N-methylcarbamate pesticides.
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Affiliation(s)
- Masayuki Hashimoto
- Division of Gene Research, Department of Life Science, Research Center for Human and Environmental Sciences, Shinshu University, Ueda City, Nagano, Japan
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26
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D’Abusco AS, Casadio R, Tasco G, Giangiacomo L, Giartosio A, Calamia V, Di Marco S, Chiaraluce R, Consalvi V, Scandurra R, Politi L. Oligomerization of Sulfolobus solfataricus signature amidase is promoted by acidic pH and high temperature. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2006; 1:411-23. [PMID: 16243781 PMCID: PMC2685583 DOI: 10.1155/2005/543789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The recombinant amidase from the hyperthermophylic archaeon Sulfolobus solfataricus (SSAM) a signature amidase, was cloned, purified and characterized. The enzyme is active on a large number of aliphatic and aromatic amides over the temperature range 60-95 degrees C and at pH values between 4.0 and 9.5, with an optimum at pH 5.0. The recombinant enzyme is in the form of a dimer of about 110 kD that reversibly associates into an octamer in a pH-dependent reaction. The pH dependence of the state of association was studied using gel permeation chromatography, analytical ultracentrifugation and dynamic light scattering techniques. At pH 7.0 all three techniques show the presence of two species, in about equal amounts, which is compatible with the existence of a dimeric and an octameric form. In decreasing pH, the dimers formed the octameric species and in increasing pH, the octameric species was converted to dimers. Above pH 8.0, only dimers were present, below pH 3.0 only octamers were present. The association of dimers into octamers decreased in non-polar solvents and increased with temperature. A mutant (Y41C) was obtained that did not show this behavior.
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Affiliation(s)
- Anna Scotto D’Abusco
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
| | - Rita Casadio
- CIRB Biocomputing Group, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Gianluca Tasco
- CIRB Biocomputing Group, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Laura Giangiacomo
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
| | - Anna Giartosio
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
| | - Valentina Calamia
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
| | | | - Roberta Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
| | - Valerio Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
| | - Roberto Scandurra
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
- Corresponding author ()
| | - Laura Politi
- Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli,” Università “La Sapienza,” P.le A. Moro 5, 00185 Roma, Italy
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Suzuki Y, Ohta H. Identification of a thermostable and enantioselective amidase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7. Protein Expr Purif 2006; 45:368-73. [PMID: 16125409 DOI: 10.1016/j.pep.2005.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 06/24/2005] [Accepted: 06/25/2005] [Indexed: 11/22/2022]
Abstract
We have characterized an amidase expressed from the putative amidase gene (ST0478) selected from the total genome analysis from the thermoacidophilic archaeon, Sulfolobus tokodaii strain 7. The ORF was cloned and expressed as an insoluble aggregated 6 x His-tagged fusion protein in Escherichia coli. The protein was purified with denaturing, refolding on affinity column chromatography, size exclusion filtration, and heat treatment. The enzyme exhibited high thermostability and the optimum activity for amide cleavage against benzamide was observed at around 75 degrees C and pH 7.0-8.0. It also showed enantioselectivity for (R,S)-2-phenylpropionamide and preferentially hydrolyzed the S-enantiomer. This novel enzyme is the second characterized archaeal amidase.
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Affiliation(s)
- Yoichi Suzuki
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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Pertsovich SI, Guranda DT, Podchernyaev DA, Yanenko AS, Svedas VK. Aliphatic Amidase from Rhodococcus rhodochrous M8 Is Related to the Nitrilase/Cyanide Hydratase Family. BIOCHEMISTRY (MOSCOW) 2005; 70:1280-7. [PMID: 16336190 DOI: 10.1007/s10541-005-0260-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A comparative study of amino acid sequence and physicochemical properties indicates the affiliation of an amidase from Rhodococcus rhodochrous M8 (EC 3.5.1.4) to the nitrilase/cyanide hydratase family. Cluster analysis and multiple alignments show that Cys166 is an active site nucleophile. The enzyme has been shown to be a typical aliphatic amidase, being the most active toward short-chain linear amides. Small polar molecules such as hydroxylamine and O-methyl hydroxylamine can serve as effective external nucleophiles in acyl transfer reactions. The kinetics of the industrially important amidase-catalyzed acrylamide hydrolysis has been studied over a wide range of substrate concentrations; inhibition during enzymatic hydrolysis by the substrate and product (acrylic acid) has been observed; an adequate kinetic scheme has been evaluated and the corresponding kinetic parameters have been determined.
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Affiliation(s)
- S I Pertsovich
- Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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Antranikian G, Vorgias CE, Bertoldo C. Extreme environments as a resource for microorganisms and novel biocatalysts. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 96:219-62. [PMID: 16566093 DOI: 10.1007/b135786] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The steady increase in the number of newly isolated extremophilic microorganisms and the discovery of their enzymes by academic and industrial institutions underlines the enormous potential of extremophiles for application in future biotechnological processes. Enzymes from extremophilic microorganisms offer versatile tools for sustainable developments in a variety of industrial application as they show important environmental benefits due to their biodegradability, specific stability under extreme conditions, improved use of raw materials and decreased amount of waste products. Although major advances have been made in the last decade, our knowledge of the physiology, metabolism, enzymology and genetics of this fascinating group of extremophilic microorganisms and their related enzymes is still limited. In-depth information on the molecular properties of the enzymes and their genes, however, has to be obtained to analyze the structure and function of proteins that are catalytically active around the boiling and freezing points of water and extremes of pH. New techniques, such as genomics, metanogenomics, DNA evolution and gene shuffling, will lead to the production of enzymes that are highly specific for countless industrial applications. Due to the unusual properties of enzymes from extremophiles, they are expected to optimize already existing processes or even develop new sustainable technologies.
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Affiliation(s)
- Garabed Antranikian
- Institute of Technical Microbiology, Technical University Hamburg-Harburg, Kasernenstrasse 12, 21073 Hamburg, Germany.
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Hongpattarakere T, Komeda H, Asano Y. Purification, characterization, gene cloning and nucleotide sequencing of D-stereospecific amino acid amidase from soil bacterium: Delftia acidovorans. J Ind Microbiol Biotechnol 2005; 32:567-76. [PMID: 15959727 DOI: 10.1007/s10295-005-0246-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Accepted: 05/03/2005] [Indexed: 10/25/2022]
Abstract
The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.
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Valiña ALB, Mazumder-Shivakumar D, Bruice TC. Probing the Ser-Ser-Lys Catalytic Triad Mechanism of Peptide Amidase: Computational Studies of the Ground State, Transition State, and Intermediate. Biochemistry 2004; 43:15657-72. [PMID: 15595822 DOI: 10.1021/bi049025r] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide amidase (Pam), a hydrolytic enzyme that belongs to the amidase signature (AS) family, selectively catalyzes the hydrolysis of the C-terminal amide bond (CO-NH(2)) of peptides. The recent availability of the X-ray structures of Pam, fatty acid amide hydrolase, and malonamidase E2 has led to the proposal of a novel Ser-Ser-Lys catalytic triad mechanism for the amide hydrolysis by the AS enzymes. The molecular dynamics (MD) simulations using the CHARMM force field were performed to explore the catalytic mechanism of Pam. The 1.8 A X-ray crystal structure of Pam in complex with the amide analogue of chymostatin was chosen for the initial coordinates for the MD simulations. The five systems that were investigated are as follows: (i) enzyme.substrate with Lys123-NH(2), (ii) enzyme.substrate with Lys123-NH(3)(+), (iii) enzyme.substrate with Lys123-NH(3)(+) and Ser226-O(-), (iv) enzyme.transition state, and (v) enzyme.tetrahedral intermediate. Our data support the presence of the hydrogen bonding network among the catalytic triad residues, Ser226, Ser202, and Lys123, where Ser226 acts as the nucleophile and Ser202 bridges Ser226 and Lys123. The MD simulation supports the catalytic role of the crystallographic waters, Wat1 and Wat2. In all the systems that have been studied, the backbone amide nitrogens of Asp224 and Thr223 create an oxyanion hole by hydrogen bonding to the terminal amide oxygen of the substrate, and stabilize the oxyanion tetrahedral intermediate. The results from both our computational investigation and previously published experimental pH profile support two mechanisms. In a mechanism that is relevant at lower pH, the Lys123-NH(3)(+)-Ser202 dyad provides structural support to the catalytic residue Ser226, which in turn carries out a nucleophilic attack at the substrate amide carbonyl in concert with Wat1-mediated deprotonation and stabilization of the tetrahedral transition state by the oxyanion hole. In the mechanism operating at higher pH, the Lys123-NH(2)-Ser202 catalytic dyad acts as a general base to assist addition of Ser226 to the substrate amide carbonyl. The results from the MD simulation of the tetrahedral intermediate state show that both Ser202 and Lys123 are possible candidates for protonation of the leaving group, NH(2), to form the acyl-enzyme intermediate.
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Affiliation(s)
- Anna Liza B Valiña
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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Krieg L, Slusarczyk H, Verseck S, Kula MR. Identification and characterization of a novel D-amidase gene from Variovorax paradoxus and its expression in Escherichia coli. Appl Microbiol Biotechnol 2004; 66:542-50. [PMID: 15480636 DOI: 10.1007/s00253-004-1716-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 07/08/2004] [Accepted: 07/09/2004] [Indexed: 10/26/2022]
Abstract
The gene for the newly described D-amidase from Variovorax paradoxus (Krieg et al. 2002) was cloned and functionally expressed in Escherichia coli. Since native enzyme was available in minute amounts only, we determined the N-terminal sequence of the enzyme and utilized the Universal GenomeWalker Approach to make use of the common internal sequence of the amidase signature family. The high GC content of the gene made it necessary to employ an appropriate DNA polymerase in the amplification reactions. Thus, the sequence of the complete gene and the flanking regions was established. In independent experiments, the gene was then amplified from genomic DNA of V. paradoxus, expressed in E. coli, and characterized. The recombinant enzyme has a specific activity of 1.7 units/mg with racemic tert-leucine amide as substrate and is a homodimer of 49.6-kDa monomers.
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Affiliation(s)
- L Krieg
- Institute of Enzyme Technology, Heinrich-Heine University Düsseldorf, 52426 Jülich, Germany
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Gopalakrishna KN, Stewart BH, Kneen MM, Andricopulo AD, Kenyon GL, McLeish MJ. Mandelamide hydrolase from Pseudomonas putida: characterization of a new member of the amidase signature family. Biochemistry 2004; 43:7725-35. [PMID: 15196015 DOI: 10.1021/bi049907q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently discovered enzyme in the mandelate pathway of Pseudomonas putida, mandelamide hydrolase (MAH), catalyzes the hydrolysis of mandelamide to mandelic acid and ammonia. Sequence analysis suggests that MAH is a member of the amidase signature family, which is widespread in nature and contains a novel Ser-cis-Ser-Lys catalytic triad. Here we report the expression in Escherichia coli, purification, and characterization of both wild-type and His(6)-tagged MAH. The recombinant enzyme was stable, exhibited a pH optimum of 7.8, and was able to hydrolyze both enantiomers of mandelamide with little enantiospecificity. The His-tagged variant showed no significant change in kinetic constants. Phenylacetamide was found to be the best substrate, with changes in chain length or replacement of the phenyl group producing greatly decreased values of k(cat)/K(m). As with another member of this family, fatty acid amide hydrolase, MAH has the uncommon ability to hydrolyze esters and amides at similar rates. MAH is even more unusual in that it will only hydrolyze esters and amides with little steric bulk. Ethyl and larger esters and N-ethyl and larger amides are not substrates, suggesting that the MAH active site is very sterically hindered. Mutation of each residue in the putative catalytic triad to alanine resulted in total loss of activity for S204A and K100A, while S180A exhibited a 1500-fold decrease in k(cat) and significant increases in K(m) values. Overall, the MAH data are similar to those of fatty acid amide hydrolase and support the suggestion that there are two distinct subgroups within the amidase signature family.
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Affiliation(s)
- Kota N Gopalakrishna
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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35
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Xudong S, Yue S, Huimin Y, Zhongyao S. Bioconversion of acrylnitrile to acrylamide using hollow-fiber membrane bioreactor system. Biochem Eng J 2004. [DOI: 10.1016/j.bej.2003.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Cowan DA, Cameron RA, Tsekoa TL. Comparative biology of mesophilic and thermophilic nitrile hydratases. ADVANCES IN APPLIED MICROBIOLOGY 2003; 52:123-58. [PMID: 12964242 DOI: 10.1016/s0065-2164(03)01005-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Don A Cowan
- Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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37
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Shin S, Yun YS, Koo HM, Kim YS, Choi KY, Oh BH. Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad. J Biol Chem 2003; 278:24937-43. [PMID: 12711609 DOI: 10.1074/jbc.m302156200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amidase signature family enzymes, which are widespread in nature, contain a newly identified Ser-cisSer-Lys catalytic triad in which the peptide bond between Ser131 and the preceding residue Gly130 is in a cis configuration. In order to characterize the property of the novel triad, we have determined the structures of five mutant malonamidase E2 enzymes that contain a Cys-cisSer-Lys, Ser-cisAla-Lys, or Ser-cisSer-Ala triad or a substitution of Gly130 with alanine. Cysteine cannot replace the role of Ser155 due to a hyper-reactivity of the residue, which results in the modification of the cysteine to cysteinyl sulfinic acid, most likely inside the expression host cells. The lysine residue plays a structural as well as a catalytic role, since the substitution of the residue with alanine disrupts the active site structure completely. The two observations are in sharp contrast with the consequences of the corresponding substitutions in the classical Ser-His-Asp triad. Structural data on the mutant containing the Ser-cisAla-Lys triad convincingly suggest that Ser131 plays an analogous catalytic role as the histidine of the Ser-His-Asp triad. The unusual cis configuration of Ser131 appears essential for the precise contacts of this residue with the other triad residues, as indicated by the near invariance of the preceding glycine residue (Gly130), structural data on the G130A mutant, and by a modeling experiment. The data provide a deep understanding of the role of each residue of the new triad at the atomic level and demonstrate that the new triad is a catalytic device distinctively different from the classical triad or its variants.
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Affiliation(s)
- Sejeong Shin
- Center for Biomolecular Recognition, Pohang, Kyungbuk, 790-784, Korea
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38
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Schnizer HG, Boehlein SK, Stewart JD, Richards NGJ, Schuster SM. gamma-Glutamyl thioester intermediate in glutaminase reaction catalyzed by Escherichia coli asparagine synthetase B. Methods Enzymol 2003; 354:260-71. [PMID: 12418233 DOI: 10.1016/s0076-6879(02)54022-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Holly G Schnizer
- Department of Biochemistry, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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39
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Baek DH, Song JJ, Lee SG, Kwon SJ, Asano Y, Sung MH. New thermostable d-methionine amidase from Brevibacillus borstelensis BCS-1 and its application for d-phenylalanine production. Enzyme Microb Technol 2003. [DOI: 10.1016/s0141-0229(02)00268-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Labahn J, Neumann S, Büldt G, Kula MR, Granzin J. An alternative mechanism for amidase signature enzymes. J Mol Biol 2002; 322:1053-64. [PMID: 12367528 DOI: 10.1016/s0022-2836(02)00886-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide amidase (Pam) interesting for different biotechnological applications. Pam belongs to the amidase signature (AS) family. It is the first protein within this family whose tertiary structure has been solved. The structure of the native Pam has been determined with a resolution of 1.4A and in complex with the competitive inhibitor chymostatin at a resolution of 1.8A. Chymostatin, which forms acyl adducts with many serine proteases, binds non-covalently to this enzyme.Pam folds as a very compact single-domain protein. The AS sequence represents a core domain that is covered by alpha-helices. This AS domain contains the catalytic residues. It is topologically homologous to the phosphoinositol phosphatase domain. The structural data do not support the recently proposed Ser-Lys catalytic dyad mechanism for AS enzymes. Our results are in agreement with the role of Ser226 as the primary nucleophile but differ concerning the roles of Ser202 and Lys123: Ser202, with direct contact both to the substrate molecule and to Ser226, presumably serves as an acid/bases catalyst. Lys123, with direct contact to Ser202 but no contact to Ser226 or the substrate molecule, most likely acts as an acid catalyst.
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Affiliation(s)
- Jörg Labahn
- Forschungszentrum Jülich Gmbh, Institut für Biologische Informationsverarbeitung, IBI-2, Structural Biology, D-52425 Jülich, Germany
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41
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Trott S, Bürger S, Calaminus C, Stolz A. Cloning and heterologous expression of an enantioselective amidase from Rhodococcus erythropolis strain MP50. Appl Environ Microbiol 2002; 68:3279-86. [PMID: 12089004 PMCID: PMC126760 DOI: 10.1128/aem.68.7.3279-3286.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene for an enantioselective amidase was cloned from Rhodococcus erythropolis MP50, which utilizes various aromatic nitriles via a nitrile hydratase/amidase system as nitrogen sources. The gene encoded a protein of 525 amino acids which corresponded to a protein with a molecular mass of 55.5 kDa. The deduced complete amino acid sequence showed homology to other enantioselective amidases from different bacterial genera. The nucleotide sequence approximately 2.5 kb upstream and downstream of the amidase gene was determined, but no indications for a structural coupling of the amidase gene with the genes for a nitrile hydratase were found. The amidase gene was carried by an approximately 40-kb circular plasmid in R. erythropolis MP50. The amidase was heterologously expressed in Escherichia coli and shown to hydrolyze 2-phenylpropionamide, alpha-chlorophenylacetamide, and alpha-methoxyphenylacetamide with high enantioselectivity; mandeloamide and 2-methyl-3-phenylpropionamide were also converted, but only with reduced enantioselectivity. The recombinant E. coli strain which synthesized the amidase gene was shown to grow with organic amides as nitrogen sources. A comparison of the amidase activities observed with whole cells or cell extracts of the recombinant E. coli strain suggested that the transport of the amides into the cells becomes the rate-limiting step for amide hydrolysis in recombinant E. coli strains.
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Affiliation(s)
- Sandra Trott
- Institut für Mikrobiologie, Universität Stuttgart, 70569 Stuttgart, Germany
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42
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Shin S, Lee TH, Ha NC, Koo HM, Kim SY, Lee HS, Kim YS, Oh BH. Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature. EMBO J 2002; 21:2509-16. [PMID: 12032064 PMCID: PMC126024 DOI: 10.1093/emboj/21.11.2509] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A large group of hydrolytic enzymes, which contain a conserved stretch of approximately 130 amino acids designated the amidase signature (AS) sequence, constitutes a super family that is distinct from any other known hydrolase family. AS family enzymes are widespread in nature, ranging from bacteria to humans, and exhibit a variety of biological functions. Here we report the first structure of an AS family enzyme provided by the crystal structure of malonamidase E2 from Bradyrhizobium japonicum. The structure, representing a new protein fold, reveals a previously unidentified Ser-cisSer-Lys catalytic machinery that is absolutely conserved throughout the family. This family of enzymes appears to be evolutionarily distinct but has diverged to acquire a wide spectrum of individual substrate specificities, while maintaining a core structure that supports the catalytic function of the unique triad. Based of the structures of the enzyme in two different inhibited states, an unusual action mechanism of the triad is proposed that accounts for the role of the cis conformation in the triad.
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Affiliation(s)
- Sejeong Shin
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - Tae-Hee Lee
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - Nam-Chul Ha
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - Hyun Min Koo
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - So-yeon Kim
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - Heung-Soo Lee
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - Yu Sam Kim
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
| | - Byung-Ha Oh
- National Creative Research Initiative Center for Biomolecular Recognition, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749 and Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea Corresponding author e-mail: or
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43
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Abstract
The fatty acid amide hydrolase (FAAH), is the enzyme responsible for the hydrolysis of anandamide, an endocannabinoid. The FAAH knockout, the assays for FAAH, the activity of its substrates, its reversibility and its cloning from rat, mouse, human, and pig are covered in this review. The conserved regions of FAAH are described in terms of sequence and function, including the domains that contains the serine catalytic nucleophile, the hydrophobic domain important for self-association, the proline rich domain region which may be important for subcellular localization and the fatty acid chain binding domain. The FAAH mouse promoter region was characterized in terms of its transcription start site and its activity in different cell types. The distribution of FAAH in the major organs in the body is described as well as regional distribution in the brain and its correlation with cannabinoid receptors. Since FAAH is recognized as a drug target, a large number of inhibitors have been synthesized and tested since 1994 and these are reviewed in terms of reversibility, potency, and specificity for FAAH.
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Affiliation(s)
- D G Deutsch
- Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, Stony Brook, NY 11794-5215, USA.
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44
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Martínková L, Kren V, Cvak L, Ovesná M, Prepechalová I. Hydrolysis of lysergamide to lysergic acid by Rhodococcus equi A4. J Biotechnol 2001; 84:63-6. [PMID: 11035188 DOI: 10.1016/s0168-1656(00)00332-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
From a mixture of lysergamide and its epimer isolysergamide, Rhodococcus equi A4 containing amidase preferentially hydrolyzed lysergamide into lysergic acid.
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Affiliation(s)
- L Martínková
- Laboratory of Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, CZ-142 20 4, Prague, Czech Republic.
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45
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Fournand D, Arnaud A. Aliphatic and enantioselective amidases: from hydrolysis to acyl transfer activity. J Appl Microbiol 2001; 91:381-93. [PMID: 11556902 DOI: 10.1046/j.1365-2672.2001.01378.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- D Fournand
- GER de Chimie Biologique, Institut National Agronomique Paris-Grignon, Thiverval-Grignon, France
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46
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Trott S, Bauer R, Knackmuss HJ, Stolz A. Genetic and biochemical characterization of an enantioselective amidase from Agrobacterium tumefaciens strain d3. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1815-24. [PMID: 11429459 DOI: 10.1099/00221287-147-7-1815] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An enantioselective amidase was purified to homogeneity from Agrobacterium tumefaciens d3. The enzyme has a molecular mass of about 490000 Da and is composed of identical subunits with a molecular mass of about 63000 Da. The purified enzyme converted racemic 2-phenylpropionamide to the corresponding S-acid with an enantiomeric excess (ee) value >95% at almost 50% conversion of the racemic amide. The purified enzyme was digested with trypsin and the amino acid sequences of the N terminus and different tryptic peptides determined. These amino acid sequences were used to clone the encoding gene. Finally, a 9330 bp DNA fragment was sequenced and the amidase gene identified. The deduced amino acid sequence showed homology to other enantioselective amidases from different bacterial genera. No indications of a structural coupling of the amidase gene with the genes for a nitrile hydratase could be found on the cloned DNA fragment. The amidase gene was encoded by an approximately 500 kb circular plasmid in A. tumefaciens d3. The amidase was heterologously expressed in Escherichia coli and, as well as 2-phenylpropionamide, was shown to hydrolyse alpha-chloro- and alpha-methoxyphenylacetamide and 2-methyl-3-phenylpropionamide highly enantioselectively. Some amino acids within a highly conserved region common amongst all known enantioselective amidases ('amidase signature') were changed by site-specific mutagenesis and significant changes in the relative activities with different amides observed.
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Affiliation(s)
- S Trott
- Institut für Mikrobiologie, Universität Stuttgart, 70569 Stuttgart, Germany
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47
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Abstract
The topic of this review is fatty acid amide hydrolase (FAAH), one of the best-characterized enzymes involved in the hydrolysis of bioactive lipids such as anandamide, 2-arachidonoylglycerol (2-AG), and oleamide. Herein, we discuss the nomenclature, the various assays that have been developed, the relative activity of the various substrates and the reversibility of the enzyme reactions catalyzed by FAAH. We also describe the cloning of the enzyme from rat and subsequent cDNA isolation from mouse, human, and pig. The proteins and the mRNAs from different species are compared. Cloning the enzyme permitted the purification and characterization of recombinant FAAH. The conserved regions of FAAH are described in terms of sequence and function, including the amidase domain which contains the serine catalytic nucleophile, the hydrophobic domain important for self association, and the proline rich domain region, which may be important for subcellular localization. The distribution of FAAH in the major organs of the body is described as well as regional distribution in the brain and its correlation with cannabinoid receptors. Since FAAH is recognized as a drug target, a large number of inhibitors have been synthesized and tested since 1994 and these are reviewed in terms of reversibility, potency, and specificity for FAAH and cannabinoid receptors.
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Affiliation(s)
- N Ueda
- Department of Biochemistry, School of Medicine, University of Tokushima, Kuramoto-cho, 770-8503, Tokushima, Japan
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48
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Marti T, Hu Z, Pohl NL, Shah AN, Khosla C. Cloning, nucleotide sequence, and heterologous expression of the biosynthetic gene cluster for R1128, a non-steroidal estrogen receptor antagonist. Insights into an unusual priming mechanism. J Biol Chem 2000; 275:33443-8. [PMID: 10931852 DOI: 10.1074/jbc.m006766200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
R1128 substances are anthraquinone natural products that were previously reported as non-steroidal estrogen receptor antagonists with in vitro and in vivo potency approaching that of tamoxifen. From a biosynthetic viewpoint, these polyketides possess structurally interesting features such as an unusual primer unit that are absent in the well studied anthracyclic and tetracyclic natural products. The entire R1128 gene cluster was cloned and expressed in Streptomyces lividans, a genetically well developed heterologous host. In addition to R1128C, a novel optically active natural product, designated HU235, was isolated. Nucleotide sequence analysis of the biosynthetic gene cluster revealed genes encoding two ketosynthases, a chain length factor, an acyl transferase, three acetyl-CoA carboxylase subunits, two cyclases, two oxygenases, an amidase, and remarkably, two acyl carrier proteins. Feeding studies indicate that the unusual 4-methylvaleryl side chain of R1128C is derived from valine. Together with the absence of a dedicated ketoreductase, dehydratase, or enoylreductase within the R1128 gene cluster, this suggests a functional link between fatty acid biosynthesis and R1128 biosynthesis in the engineered host. Specifically, we propose that the R1128 synthase recruits four subunits from the endogenous fatty acid synthase during the biosynthesis of this family of pharmacologically significant natural products.
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Affiliation(s)
- T Marti
- Departments of Chemical Engineering and Chemistry and Biochemistry, Stanford University, Stanford, California 94305-5025, USA
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49
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Cloning and expression of the nitrile hydratase and amidase genes from Bacillus sp. BR449 into Escherichia coli. Enzyme Microb Technol 2000; 27:492-501. [PMID: 10978771 DOI: 10.1016/s0141-0229(00)00248-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A moderate thermophile, Bacillus sp. BR449 was previously shown to exhibit a high level of nitrile hydratase (NHase) activity when growing on high levels of acrylonitrile at 55 degrees C. In this report, we describe the cloning of a 6.1 kb SalI DNA fragment encoding the NHase gene cluster of BR449 into Escherichia coli. Nucleotide sequencing revealed six ORFs encoding (in order), two unidentified putative proteins, amidase, NHase beta- and alpha-subunits and a small putative protein of 101 amino acids designated P12K. Spacings and orientation of the coding regions as well as their gene expression in E. coli suggest that the beta-subunit, alpha-subunit, and P12K genes are co-transcribed. Analysis of deduced amino acid sequences indicate that the amidase (348 aa, MW 38.6 kDa) belongs to the nitrilase-related aliphatic amidase family, and that the NHase beta- (229 aa, MW 26.5 kDa) and alpha- (214 aa, MW 24.5 kDa) subunits comprise a cobalt-containing member of the NHase family, which includes Rhodococcus rhodochrous J1 and Pseudomonas putida 5B NHases. The amidase/NHase gene cluster differs both in arrangement and composition from those described for other NHase-producing strains. When expressed in Escherichia coli DH5alpha, the subcloned NHase genes produced significant levels of active NHase enzyme when cobalt ion was added either to the culture medium or cell extracts. Presence of the P12K gene and addition of amide compounds as inducers were not required for this expression.
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50
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Soong CL, Ogawa J, Shimizu S. A novel amidase (half-amidase) for half-amide hydrolysis involved in the bacterial metabolism of cyclic imides. Appl Environ Microbiol 2000; 66:1947-52. [PMID: 10788365 PMCID: PMC101438 DOI: 10.1128/aem.66.5.1947-1952.2000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel amidase involved in bacterial cyclic imide metabolism was purified from Blastobacter sp. strain A17p-4. The enzyme physiologically functions in the second step of cyclic imide degradation, i.e., the hydrolysis of monoamidated dicarboxylates (half-amides) to dicarboxylates and ammonia. Enzyme production was enhanced by cyclic imides such as succinimide and glutarimide but not by amide compounds which are conventional substrates and inducers of known amidases. The purified amidase showed high catalytic efficiency toward half-amides such as succinamic acid (K(m) = 6.2 mM; k(cat) = 5.76 s(-1)) and glutaramic acid (K(m) = 2.8 mM; k(cat) = 2.23 s(-1)). However, the substrates of known amidases such as short-chain (C(2) to C(4)) aliphatic amides, long-chain (above C(16)) aliphatic amides, amino acid amides, aliphatic diamides, alpha-keto acid amides, N-carbamoyl amino acids, and aliphatic ureides were not substrates for the enzyme. Based on its high specificity toward half-amides, the enzyme was named half-amidase. This half-amidase exists as a monomer with an M(r) of 48,000 and was strongly inhibited by heavy metal ions and sulfhydryl reagents.
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Affiliation(s)
- C L Soong
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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