1
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Zhang F, Naeem M, Yu B, Liu F, Ju J. Improving the enzymatic activity and stability of N-carbamoyl hydrolase using deep learning approach. Microb Cell Fact 2024; 23:164. [PMID: 38834993 PMCID: PMC11151596 DOI: 10.1186/s12934-024-02439-5] [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: 02/14/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Optically active D-amino acids are widely used as intermediates in the synthesis of antibiotics, insecticides, and peptide hormones. Currently, the two-enzyme cascade reaction is the most efficient way to produce D-amino acids using enzymes DHdt and DCase, but DCase is susceptible to heat inactivation. Here, to enhance the enzymatic activity and thermal stability of DCase, a rational design software "Feitian" was developed based on kcat prediction using the deep learning approach. RESULTS According to empirical design and prediction of "Feitian" software, six single-point mutants with high kcat value were selected and successfully constructed by site-directed mutagenesis. Out of six, three mutants (Q4C, T212S, and A302C) showed higher enzymatic activity than the wild-type. Furthermore, the combined triple-point mutant DCase-M3 (Q4C/T212S/A302C) exhibited a 4.25-fold increase in activity (29.77 ± 4.52 U) and a 2.25-fold increase in thermal stability as compared to the wild-type, respectively. Through the whole-cell reaction, the high titer of D-HPG (2.57 ± 0.43 mM) was produced by the mutant Q4C/T212S/A302C, which was about 2.04-fold of the wild-type. Molecular dynamics simulation results showed that DCase-M3 significantly enhances the rigidity of the catalytic site and thus increases the activity of DCase-M3. CONCLUSIONS In this study, an efficient rational design software "Feitian" was successfully developed with a prediction accuracy of about 50% in enzymatic activity. A triple-point mutant DCase-M3 (Q4C/T212S/A302C) with enhanced enzymatic activity and thermostability was successfully obtained, which could be applied to the development of a fully enzymatic process for the industrial production of D-HPG.
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Affiliation(s)
- Fa Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Bo Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feixia Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
- Hebei Collaborative Innovation Center for Eco-Environment, Shijiazhuang, 050024, China.
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2
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Wang F, Qi H, Li H, Ma X, Gao X, Li C, Lu F, Mao S, Qin HM. State-of-the-art strategies and research advances for the biosynthesis of D-amino acids. Crit Rev Biotechnol 2024; 44:495-513. [PMID: 37160372 DOI: 10.1080/07388551.2023.2193861] [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: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 05/11/2023]
Abstract
D-amino acids (D-AAs) are the enantiomeric counterparts of L-amino acids (L-AAs) and important functional factors with a wide variety of physiological activities and applications in the food manufacture industry. Some D-AAs, such as D-Ala, D-Leu, and D-Phe, have been favored by consumers as sweeteners and fragrances because of their unique flavor. The biosynthesis of D-AAs has attracted much attention in recent years due to their unique advantages. In this review, we comprehensively analyze the structure-function relationships, biosynthesis pathways, multi-enzyme cascade and whole-cell catalysis for the production of D-AAs. The state-of-the-art strategies, including immobilization, protein engineering, and high-throughput screening, are summarized. Future challenges and perspectives of strategies-driven by bioinformatics technologies and smart computing technologies, as well as enzyme immobilization, are also discussed. These new approaches will promote the commercial production and application of D-AAs in the food industry by optimizing the key enzymes for industrial biocatalysts.
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Affiliation(s)
- Fenghua Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Hongbin Qi
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Huimin Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Xuanzhen Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Xin Gao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Chao Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Shuhong Mao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Hui-Min Qin
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
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3
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Aguirre-Sampieri S, Casañal A, Emsley P, Garza-Ramos G. Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis. J Struct Biol 2024; 216:108093. [PMID: 38615726 PMCID: PMC7616060 DOI: 10.1016/j.jsb.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Many enzymes can self-assemble into higher-order structures with helical symmetry. A particularly noteworthy example is that of nitrilases, enzymes in which oligomerization of dimers into spiral homo-oligomers is a requirement for their enzymatic function. Nitrilases are widespread in nature where they catalyze the hydrolysis of nitriles into the corresponding carboxylic acid and ammonia. Here, we present the Cryo-EM structure, at 3 Å resolution, of a C-terminal truncate nitrilase from Rhodococcus sp. V51B that assembles in helical filaments. The model comprises a complete turn of the helical arrangement with a substrate-intermediate bound to the catalytic cysteine. The structure was solved having added the substrate to the protein. The length and stability of filaments was made more substantial in the presence of the aromatic substrate, benzonitrile, but not for aliphatic nitriles or dinitriles. The overall structure maintains the topology of the nitrilase family, and the filament is formed by the association of dimers in a chain-like mechanism that stabilizes the spiral. The active site is completely buried inside each monomer, while the substrate binding pocket was observed within the oligomerization interfaces. The present structure is in a closed configuration, judging by the position of the lid, suggesting that the intermediate is one of the covalent adducts. The proximity of the active site to the dimerization and oligomerization interfaces, allows the dimer to sense structural changes once the benzonitrile was bound, and translated to the rest of the filament, stabilizing the helical structure.
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Affiliation(s)
- Sergio Aguirre-Sampieri
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico
| | - Ana Casañal
- Human Technopole, Palazzo Italia, Viale Rita Levi‑Montalcini, 1, 20157 Milan, Italy
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Structural Studies Division, Francis Crick Avenue, CB2 0QH Cambridge, England
| | - Georgina Garza-Ramos
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico.
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4
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Niu L, Xie L, Ji J, Lv L. A novel process using immobilized engineered strain HC01 cells with co-expressed D-hydantoinase and D-N-carbamoylase as biocatalyst for the production of D-Valine. Bioprocess Biosyst Eng 2023; 46:227-236. [PMID: 36478291 DOI: 10.1007/s00449-022-02825-6] [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: 08/01/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
The demand for D-Valine increases because of its wide range of use. A whole-cell biocatalyst for the production of D-Valine from 5'-isopropyl hydantoin by co-expression of the D-hydantoinase (hyd) gene from Pseudomonas putida YZ-26 and D-N-carbamoylase (cab) gene from Sinorhizobium sp. SS-ori in Escherichia coli BL 21 (DE3) was developed. The expression condition of the engineered strain HC01 co-expressing D-hydantoinase (HYD) and D-N-carbamoylase (CAB) was optimized. HYD and CAB reached the highest activities (4.65 and 0.75 U/ml-broth) after inducing for 8-12 h. Subsequently, the cells of HC01 were immobilized in the form of Ca2+-alginate beads, and the optimal conditions for immobilizing were obtained as 2.5% gel concentration and 0.029 g/mL cell concentration in the presence of 3% CaCl2. The thermostability of immobilized cells was 5 ℃ higher than that of free cells in the same condition. And the divalent metal ions such as Mn2+, Mg2+, Cu2+, Co2+, and Ni2+ did not significantly affect the enzymatic activity of HYD and CAB in immobilized cells. Bioconversion rate reached to 91% after a 42-h reaction when the substrate concentration was 50 mmol/L with the initial pH of 9.0 under the nitrogen protection. This method provides D-Valine with optical purity of 97% and an overall yield of 72%. Furthermore, the immobilized cells can be reused for more than 7 cycles and maintain their capacity of over 70%. Hence the immobilized cells of engineered strain HC01 could potentially be used to prepare D-Valine.
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Affiliation(s)
- Lixi Niu
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Lulu Xie
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Jiao Ji
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Lihua Lv
- Institute of Biotechnology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
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5
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Mantas MJQ, Nunn PB, Codd GA, Barker D. Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 3-N-methyl-2,3-diaminopropanoic acid (BMAA). PHYTOCHEMISTRY 2022; 200:113198. [PMID: 35447107 DOI: 10.1016/j.phytochem.2022.113198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an ancient clade of photosynthetic prokaryotes, present in many habitats throughout the world, including water resources. They can present health hazards to humans and animals due to the production of a wide range of toxins (cyanotoxins), including the diaminoacid neurotoxin, 3-N-methyl-2,3-diaminopropanoic acid (β-N-methylaminoalanine, BMAA). Knowledge of the biosynthetic pathway for BMAA, and its role in cyanobacteria, is lacking. Present evidence suggests that BMAA is derived by 3-N methylation of 2,3-diaminopropanoic acid (2,3-DAP) and, although the latter has never been reported in cyanobacteria, there are multiple pathways to its biosynthesis known in other bacteria and in plants. Here, we used bioinformatics analyses to investigate hypotheses concerning 2,3-DAP and BMAA biosynthesis in cyanobacteria. We assessed the potential presence or absence of each enzyme in candidate biosynthetic routes known in Albizia julibrissin, Lathyrus sativus seedlings, Streptomyces, Clostridium, Staphylococcus aureus, Pantoea agglomerans, and Paenibacillus larvae, in 130 cyanobacterial genomes using sequence alignment, profile hidden Markov models, substrate specificity/active site identification and the reconstruction of gene phylogenies. Most enzymes involved in pathways leading to 2,3-DAP in other species were not found in the cyanobacteria analysed. Nevertheless, two species appear to have the genes sbnA and sbnB, responsible for forming the 2,3-DAP constituent in staphyloferrin B, a siderophore from Staphylococcus aureus. It is currently undetermined whether these species are also capable of biosynthesising BMAA. It is possible that, in some cyanobacteria, the formation of 2,3-DAP and/or BMAA is associated with environmental iron-scavenging. The pam gene cluster, responsible for the biosynthesis of the BMAA-containing peptide, paenilamicin, so far appears to be restricted to Paenibacillus larvae. It was not detected in any of the cyanobacterial genomes analysed, nor was it found in 93 other Paenibacillus genomes or in the genomes of two BMAA-producing diatom species. We hypothesise that the presence, in some cyanobacterial species, of the enzymes 2,3-diaminopropionate ammonia-lyase (DAPAL) and reactive intermediate deaminase A (RidA) may explain the failure to detect 2,3-DAP in analytical studies. Overall, the taxonomic distribution of 2,3-DAP and BMAA in cyanobacteria is unclear; there may be multiple and additional routes, and roles, for the biosynthesis of 2,3-DAP and BMAA in these organisms.
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Affiliation(s)
- Maria José Q Mantas
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The King's Buildings, Edinburgh, EH9 3FL, United Kingdom.
| | - Peter B Nunn
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom.
| | - Geoffrey A Codd
- School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom; School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom.
| | - Daniel Barker
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The King's Buildings, Edinburgh, EH9 3FL, United Kingdom.
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6
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The structures of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide and acetamide suggest the basis of amide recognition. J Struct Biol 2022; 214:107859. [DOI: 10.1016/j.jsb.2022.107859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022]
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7
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Silva Teixeira CS, Sousa SF, Cerqueira NMFSA. An Unsual Cys-Glu-Lys Catalytic Triad is Responsible for the Catalytic Mechanism of the Nitrilase Superfamily: A QM/MM Study on Nit2. Chemphyschem 2021; 22:796-804. [PMID: 33463886 DOI: 10.1002/cphc.202000751] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/13/2021] [Indexed: 12/29/2022]
Abstract
Nitrilase 2 (Nit2) is a representative member of the nitrilase superfamily that catalyzes the hydrolysis of α-ketosuccinamate into oxaloacetate. It has been associated with the metabolism of rapidly dividing cells like cancer cells. The catalytic mechanism of Nit2 employs a catalytic triad formed by Cys191, Glu81 and Lys150. The Cys191 and Glu81 play an active role during the catalytic process while the Lys150 is shown to play only a secondary role. The results demonstrate that the catalytic mechanism of Nit2 involves four steps. The nucleophilic attack of Cys191 to the α-ketosuccinamate, the formation of two tetrahedral enzyme adducts and the hydrolysis of a thioacyl-enzyme intermediate, from which results the formation of oxaloacetate and enzymatic turnover. The rate limiting step of the catalytic process is the formation of the first tetrahedral intermediate with a calculated activation free energy of 18.4 kcal/mol, which agrees very well with the experimental kcat (17.67 kcal/mol).
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Affiliation(s)
- Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
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8
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Phe-140 Determines the Catalytic Efficiency of Arylacetonitrilase from Alcaligenes faecalis. Int J Mol Sci 2020; 21:ijms21217859. [PMID: 33113984 PMCID: PMC7660301 DOI: 10.3390/ijms21217859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/03/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Arylacetonitrilase from Alcaligenes faecalis ATCC8750 (NitAF) hydrolyzes various arylacetonitriles to the corresponding carboxylic acids. A systematic strategy of amino acid residue screening through sequence alignment, followed by homology modeling and biochemical confirmation was employed to elucidate the determinant of NitAF catalytic efficiency. Substituting Phe-140 in NitAF (wild-type) to Trp did not change the catalytic efficiency toward phenylacetonitrile, an arylacetonitrile. The mutants with nonpolar aliphatic amino acids (Ala, Gly, Leu, or Val) at location 140 had lower activity, and those with charged amino acids (Asp, Glu, or Arg) exhibited nearly no activity for phenylacetonitrile. Molecular modeling showed that the hydrophobic benzene ring at position 140 supports a mechanism in which the thiol group of Cys-163 carries out a nucleophilic attack on a cyanocarbon of the substrate. Characterization of the role of the Phe-140 residue demonstrated the molecular determinant for the efficient formation of arylcarboxylic acids.
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9
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Shen JD, Cai X, Liu ZQ, Zheng YG. Nitrilase: a promising biocatalyst in industrial applications for green chemistry. Crit Rev Biotechnol 2020; 41:72-93. [PMID: 33045860 DOI: 10.1080/07388551.2020.1827367] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nitrilases are widely distributed in nature and are able to hydrolyze nitriles into their corresponding carboxylic acids and ammonia. In industry, nitrilases have been used as green biocatalysts for the production of high value-added products. To date, biocatalysts are considered to be important alternatives to chemical catalysts due to increasing environmental problems and resource scarcity. This review provides an overview of recent advances of nitrilases in aspects of distribution, enzyme screening, molecular structure and catalytic mechanism, protein engineering, and their potential applications in industry.
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Affiliation(s)
- Ji-Dong Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Xue Cai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
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10
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Liu Y, Xu G, Zhou J, Ni J, Zhang L, Hou X, Yin D, Rao Y, Zhao YL, Ni Y. Structure-Guided Engineering of d-Carbamoylase Reveals a Key Loop at Substrate Entrance Tunnel. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02942] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yafei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Jieyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Jie Ni
- Warshel Institute for Computational Biology, School of Life and Health Science, Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Dejing Yin
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu China
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11
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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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12
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Conformational changes in Apolipoprotein N-acyltransferase (Lnt). Sci Rep 2020; 10:639. [PMID: 31959792 PMCID: PMC6971011 DOI: 10.1038/s41598-020-57419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/31/2019] [Indexed: 11/10/2022] Open
Abstract
Lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three integral membrane enzymes. The last step of this process, unique to Gram-negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of Lnt from Escherichia coli. In one form we observe a highly dynamic arm that is able to restrict access to the active site as well as a covalent modification to the active site cysteine consistent with the thioester acyl-intermediate. In the second form, the enzyme crystallized in an open conformation exposing the active site to the environment. In total we observe 3 unique Lnt molecules that when taken together suggest the movement of essential loops and residues are triggered by substrate binding that could control the interaction between Lnt and the incoming substrate apolipoprotein. The results provide a dynamic context for residues shown to be central for Lnt function and provide further insights into its mechanism.
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13
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Chuenchor W, Doukov TI, Chang KT, Resto M, Yun CS, Gerratana B. Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD + synthetases. Nat Commun 2020; 11:16. [PMID: 31911602 PMCID: PMC6946656 DOI: 10.1038/s41467-019-13845-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
NAD+ synthetase is an essential enzyme of de novo and recycling pathways of NAD+ biosynthesis in Mycobacterium tuberculosis but not in humans. This bifunctional enzyme couples the NAD+ synthetase and glutaminase activities through an ammonia tunnel but free ammonia is also a substrate. Here we show that the Homo sapiens NAD+ synthetase (hsNadE) lacks substrate specificity for glutamine over ammonia and displays a modest activation of the glutaminase domain compared to tbNadE. We report the crystal structures of hsNadE and NAD+ synthetase from M. tuberculosis (tbNadE) with synthetase intermediate analogues. Based on the observed exclusive arrangements of the domains and of the intra- or inter-subunit tunnels we propose a model for the inter-domain communication mechanism for the regulation of glutamine-dependent activity and NH3 transport. The structural and mechanistic comparison herein reported between hsNadE and tbNadE provides also a starting point for future efforts in the development of anti-TB drugs.
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Affiliation(s)
- Watchalee Chuenchor
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tzanko I Doukov
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, 94025, USA
| | - Kai-Ti Chang
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Melissa Resto
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Chang-Soo Yun
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Barbara Gerratana
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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14
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Biocatalytic production of D-p-hydroxyphenylglycine by optimizing protein expression and cell wall engineering in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:8839-8851. [DOI: 10.1007/s00253-019-10155-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/19/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
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15
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Mulelu AE, Kirykowicz AM, Woodward JD. Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure. Commun Biol 2019; 2:260. [PMID: 31341959 PMCID: PMC6637149 DOI: 10.1038/s42003-019-0505-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/13/2019] [Indexed: 01/17/2023] Open
Abstract
Nitrilases are helical enzymes that convert nitriles to acids and/or amides. All plants have a nitrilase 4 homolog specific for ß-cyanoalanine, while in some plants neofunctionalization has produced nitrilases with altered specificity. Plant nitrilase substrate size and specificity correlate with helical twist, but molecular details of this relationship are lacking. Here we determine, to our knowledge, the first close-to-atomic resolution (3.4 Å) cryo-EM structure of an active helical nitrilase, the nitrilase 4 from Arabidopsis thaliana. We apply site-saturation mutagenesis directed evolution to three residues (R95, S224, and L169) and generate a mutant with an altered helical twist that accepts substrates not catalyzed by known plant nitrilases. We reveal that a loop between α2 and α3 limits the length of the binding pocket and propose that it shifts position as a function of helical twist. These insights will allow us to start designing nitrilases for chemoenzymatic synthesis.
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Affiliation(s)
- Andani E. Mulelu
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa
| | - Angela M. Kirykowicz
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa
| | - Jeremy D. Woodward
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Structural Biology Research Unit, University of Cape Town, Cape Town, 7925 South Africa
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16
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Martínez-Rodríguez S, Conejero-Muriel M, Gavira JA. A novel cysteine carbamoyl-switch is responsible for the inhibition of formamidase, a nitrilase superfamily member. Arch Biochem Biophys 2019; 662:151-159. [PMID: 30528776 DOI: 10.1016/j.abb.2018.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 11/25/2022]
Abstract
Formamidases (EC 3.5.1.49) and amidases (EC 3.5.1.4) are paralogous cysteine-dependent enzymes which catalyze the conversion of amide substrates to ammonia and the corresponding carboxylic acid. Both enzymes have been suggested as an alternative pathway for ammonia production during urea shortage. Urea was proved key in the transcriptional regulation of formamidases/amidases, connecting urea level to amide metabolism. In addition, different amidases have also been shown to be inhibited by urea, pointing to urea-regulation at the enzymatic level. Although amidases have been widely studied due to its biotechnological application in the hydrolysis of aliphatic amides, up to date, only two formamidases have been extensively characterized, belonging to Helicobacter pylori (HpyAmiF) and Bacillus cereus (BceAmiF). In this work, we report the first structure of an acyl-intermediate of BceAmiF. We also report the inhibition of BceAmiF by urea, together with mass spectrometry studies confirming the S-carbamoylation of BceAmiF after urea treatment. X-ray studies of urea-soaked BceAmiF crystals showed short- and long-range rearrangements affecting oligomerization interfaces. Since cysteine-based switches are known to occur in the regulation of different metabolic and signaling pathways, our results suggest a novel S-carbamoylation-switch for the regulation of BceAmiF. This finding could relate to previous observations of unexplained modifications in the catalytic cysteine of different nitrilase superfamily members and therefore extending this regulation mechanism to the whole nitrilase superfamily.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada (Campus de Melilla), 52071, Melilla, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, 18100, Granada, Spain.
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17
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Yu H, Jiao S, Wang M, Liang Y, Tang L. Biodegradation of Nitriles by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Bellini RG, Coronado MA, Paschoal AR, Gaudencio do Rêgo T, Hungria M, Ribeiro de Vasconcelos AT, Nicolás MF. Structural analysis of a novel N-carbamoyl-d-amino acid amidohydrolase from a Brazilian Bradyrhizobium japonicum strain: In silico insights by molecular modelling, docking and molecular dynamics. J Mol Graph Model 2018; 86:35-42. [PMID: 30336451 DOI: 10.1016/j.jmgm.2018.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
In this work we performed several in silico analyses to describe the relevant structural aspects of an enzyme N-Carbamoyl-d-amino acid amidohydrolase (d-NCAase) encoded on the genome of the Brazilian strain CPAC 15 (=SEMIA 5079) of Bradyrhizobium japonicum, a nonpathogenic species belonging to the order Rhizobiales. d-NCAase has wide applications particularly in the pharmaceutical industry, since it catalyzes the production of d-amino acids such as D-p-hydroxyphenylglycine (D-HPG), an intermediate in the synthesis of β-lactam antibiotics. We applied a homology modelling approach and 50 ns of molecular dynamics simulations to predict the structure and the intersubunit interactions of this novel d-NCAase. Also, in order to evaluate the substrate binding site, the model was subjected to 50 ns of molecular dynamics simulations in the presence of N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) (a d-NCAase canonical substrate) and water-protein/water-substrate interactions analyses were performed. Overall, the structural analysis and the molecular dynamics simulations suggest that d-NCAase of B. japonicum CPAC-15 has a homodimeric structure in solution. Here, we also examined the substrate specificity of the catalytic site of our model and the interactions with water molecules into the active binding site were comprehensively discussed. Also, these simulations showed that the amino acids Lys123, His125, Pro127, Cys172, Asp174 and Arg176 are responsible for recognition of ligand in the active binding site through several chemical associations, such as hydrogen bonds and hydrophobic interactions. Our results show a favourable environment for a reaction of hydrolysis that transforms N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) into the active compound D-p-hydroxyphenylglycine (D-HPG). This work envisage the use of d-NCAase from the Brazilian Bradyrhizobium japonicum strain CPAC-15 (=SEMIA 5079) for the industrial production of D-HPG, an important intermediate for semi-synthesis of β-lactam antibiotics such as penicillins, cephalosporins and amoxicillin.
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Affiliation(s)
- Reinaldo G Bellini
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Mônika Aparecida Coronado
- Centro Multiusuário de Inovação Biomolecular, Departamento de Física, Universidade, Estadual Paulista (UNESP), São José do Rio Preto, 15054-000, SP, Brazil.
| | - Alexandre Rossi Paschoal
- Federal University of Technology - Paraná, Avenida Alberto Carazzai, 1640, 86300-000, Cornélio Procópio, PR, Brazil.
| | - Thaís Gaudencio do Rêgo
- Universidade Federal da Paraíba, Centro de Informática, Rua dos Escoteiros, S/N, João Pessoa, PB, 58055-000, Brazil.
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19
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Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism. Biochem J 2018; 475:2395-2416. [PMID: 29976570 DOI: 10.1042/bcj20180222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombinant human βUP is shown to be similarly regulated by substrate and product, but in a pH-dependent manner. Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. Only at physiological pH is the enzyme responsive to effector binding, with N-carbamoyl-β-alanine causing association to more active higher molecular mass species, and β-alanine dissociation to inactive dimers. The parallel between the pH and ligand-induced effects suggests that protonation state changes play a crucial role in the allosteric regulation mechanism. Disruption of dimer-dimer interfaces by site-directed mutagenesis generated dimeric, inactive enzyme variants. The crystal structure of the T299C variant refined to 2.08 Å resolution revealed high structural conservation between human and fruit fly βUP, and supports the hypothesis that enzyme activation by oligomer assembly involves ordering of loop regions forming the entrance to the active site at the dimer-dimer interface, effectively positioning the catalytically important Glu207 in the active site.
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20
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Cheng W, Doyle DA, El Arnaout T. The N-acyltransferase Lnt: Structure-function insights from recent simultaneous studies. Int J Biol Macromol 2018; 117:870-877. [PMID: 29859843 DOI: 10.1016/j.ijbiomac.2018.05.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 02/05/2023]
Abstract
Bacterial lipoproteins have been researched for decades due to their roles in a large number of biological functions. There were no structures of their main three membrane processing enzymes, until 2016 for Lgt and LspA, and then 2017 for Lnt with not one but three simultaneous, independent publications. We have analyzed the recent findings for this apolipoprotein N-acyltransferase Lnt, with comparisons between the novel structures, and with soluble nitrilases, to determine the significance of unique features in terms of substrate's recognition and binding mechanism influenced by exclusive residues, two transmembrane helices, and a flexible loop.
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Affiliation(s)
- Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Declan A Doyle
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Toufic El Arnaout
- School of Food Science and Environmental Health, Dublin Institute of Technology, Marlborough St, Dublin 1, Ireland.
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21
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Novikov AD, Riabchenko LE, Leonova TE, Larikova GA, Lavrov KV, Glinskii SA, Yanenko AS. Bacterial Strain Alcaligenes denitrificans C-32 Containing Two Nitrilases with Different Substrate Specificities. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683817080051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Xue YP, Jiao B, Hua DE, Cheng F, Liu ZQ, Zheng YG. Improving catalytic performance of an arylacetonitrilase by semirational engineering. Bioprocess Biosyst Eng 2017; 40:1565-1572. [DOI: 10.1007/s00449-017-1812-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/01/2017] [Indexed: 01/08/2023]
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23
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Lu G, Xu Y, Zhang K, Xiong Y, Li H, Cui L, Wang X, Lou J, Zhai Y, Sun F, Zhang XC. Crystal structure of E. coli apolipoprotein N-acyl transferase. Nat Commun 2017; 8:15948. [PMID: 28885614 PMCID: PMC5500890 DOI: 10.1038/ncomms15948] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/13/2017] [Indexed: 11/09/2022] Open
Abstract
In Gram-negative bacteria, lipid modification of proteins is catalysed in a three-step pathway. Apolipoprotein N-acyl transferase (Lnt) catalyses the third step in this pathway, whereby it transfers an acyl chain from a phospholipid to the amine group of the N-terminal cysteine residue of the apolipoprotein. Here, we report the 2.6-Å crystal structure of Escherichia coli Lnt. This enzyme contains an exo-membrane nitrilase domain fused to a transmembrane (TM) domain. The TM domain of Lnt contains eight TM helices which form a membrane-embedded cavity with a lateral opening and a periplasmic exit. The nitrilase domain is located on the periplasmic side of the membrane, with its catalytic cavity connected to the periplasmic exit of the TM domain. An amphipathic lid loop from the nitrilase domain interacts with the periplasmic lipid leaflet, forming an interfacial entrance from the lipid bilayer to the catalytic centre for both the lipid donor and acceptor substrates.
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Affiliation(s)
- Guangyuan Lu
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yingzhi Xu
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kai Zhang
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06411, USA
| | - He Li
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Lei Cui
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Xianping Wang
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jizhong Lou
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yujia Zhai
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Fei Sun
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xuejun C Zhang
- National Laboratory of Macromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,School of Life Sciences, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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24
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Park JM, Trevor Sewell B, Benedik MJ. Cyanide bioremediation: the potential of engineered nitrilases. Appl Microbiol Biotechnol 2017; 101:3029-3042. [PMID: 28265723 DOI: 10.1007/s00253-017-8204-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
Abstract
The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.
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Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | - B Trevor Sewell
- Structural Biology Research Unit, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA.
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25
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Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway. Proc Natl Acad Sci U S A 2016; 113:12438-12443. [PMID: 27791147 DOI: 10.1073/pnas.1612620113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined KM and kcat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.
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26
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Park JM, Mulelu A, Sewell BT, Benedik MJ. Probing an Interfacial Surface in the Cyanide Dihydratase from Bacillus pumilus, A Spiral Forming Nitrilase. Front Microbiol 2016; 6:1479. [PMID: 26779137 PMCID: PMC4700190 DOI: 10.3389/fmicb.2015.01479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/08/2015] [Indexed: 11/13/2022] Open
Abstract
Nitrilases are of significant interest both due to their potential for industrial production of valuable products as well as degradation of hazardous nitrile-containing wastes. All known functional members of the nitrilase superfamily have an underlying dimer structure. The true nitrilases expand upon this basic dimer and form large spiral or helical homo-oligomers. The formation of this larger structure is linked to both the activity and substrate specificity of these nitrilases. The sequences of the spiral nitrilases differ from the non-spiral forming homologs by the presence of two insertion regions. Homology modeling suggests that these regions are responsible for associating the nitrilase dimers into the oligomer. Here we used cysteine scanning across these two regions, in the spiral forming nitrilase cyanide dihydratase from Bacillus pumilus (CynD), to identify residues altering the oligomeric state or activity of the nitrilase. Several mutations were found to cause changes to the size of the oligomer as well as reduction in activity. Additionally one mutation, R67C, caused a partial defect in oligomerization with the accumulation of smaller oligomer variants. These results support the hypothesis that these insertion regions contribute to the unique quaternary structure of the spiral microbial nitrilases.
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Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station TX, USA
| | - Andani Mulelu
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station TX, USA
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27
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Sekula B, Ruszkowski M, Malinska M, Dauter Z. Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:350. [PMID: 27066023 PMCID: PMC4812014 DOI: 10.3389/fpls.2016.00350] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/07/2016] [Indexed: 05/17/2023]
Abstract
Putrescine, 1,4-diaminobutane, is an intermediate in the biosynthesis of more complexed polyamines, spermidine and spermine. Unlike other eukaryotes, plants have evolved a multistep pathway for putrescine biosynthesis that utilizes arginine. In the final reaction, N-carbamoylputrescine is hydrolyzed to putrescine by N-carbamoylputrescine amidohydrolase (CPA, EC 3.5.1.53). During the hydrolysis, consecutive nucleophilic attacks on the substrate by Cys158 and water lead to formation of putrescine and two by-products, ammonia and carbon dioxide. CPA from the model legume plant, Medicago truncatula (MtCPA), was investigated in this work. Four crystal structures were determined: the wild-type MtCPA in complex with the reaction intermediate, N-(dihydroxymethyl)putrescine as well as with cadaverine, which is a longer analog of putrescine; and also structures of MtCPA-C158S mutant unliganded and with putrescine. MtCPA assembles into octamers, which resemble an incomplete left-handed helical twist. The active site of MtCPA is funnel-like shaped, and its entrance is walled with a contribution of the neighboring protein subunits. Deep inside the catalytic cavity, Glu48, Lys121, and Cys158 form the catalytic triad. In this studies, we have highlighted the key residues, highly conserved among the plant kingdom, responsible for the activity and selectivity of MtCPA toward N-carbamoylputrescine. Moreover, since, according to previous reports, a close MtCPA relative from Arabidopsis thaliana, along with several other nitrilase-like proteins, are subjected to allosteric regulation by substrates, we have used the structural information to indicate a putative secondary binding site. Based on the docking experiment, we postulate that this site is adjacent to the entrance to the catalytic pocket.
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Affiliation(s)
- Bartosz Sekula
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of TechnologyLodz, Poland
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, ArgonneIL, USA
- *Correspondence: Milosz Ruszkowski,
| | - Maura Malinska
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, ArgonneIL, USA
- Faculty of Chemistry, University of WarsawWarsaw, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, ArgonneIL, USA
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28
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Crum MAN, Park JM, Mulelu AE, Sewell BT, Benedik MJ. Probing C-terminal interactions of the Pseudomonas stutzeri cyanide-degrading CynD protein. Appl Microbiol Biotechnol 2014; 99:3093-102. [PMID: 25549622 DOI: 10.1007/s00253-014-6335-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/10/2014] [Accepted: 12/14/2014] [Indexed: 12/01/2022]
Abstract
The cyanide dihydratases from Bacillus pumilus and Pseudomonas stutzeri share high amino acid sequence similarity throughout except for their highly divergent C-termini. However, deletion or exchange of the C-termini had different effects upon each enzyme. Here we extended previous studies and investigated how the C-terminus affects the activity and stability of three nitrilases, the cyanide dihydratases from B. pumilus (CynDpum) and P. stutzeri (CynDstut) and the cyanide hydratase from Neurospora crassa. Enzymes in which the C-terminal residues were deleted decreased in both activity and thermostability with increasing deletion lengths. However, CynDstut was more sensitive to such truncation than the other two enzymes. A domain of the P. stutzeri CynDstut C-terminus not found in the other enzymes, 306GERDST311, was shown to be necessary for functionality and explains the inactivity of the previously described CynDstut-pum hybrid. This suggests that the B. pumilus C-terminus, which lacks this motif, may have specific interactions elsewhere in the protein, preventing it from acting in trans on a heterologous CynD protein. We identify the dimerization interface A-surface region 195-206 (A2) from CynDpum as this interaction site. However, this A2 region did not rescue activity in C-terminally truncated CynDstutΔ302 or enhance the activity of full-length CynDstut and therefore does not act as a general stability motif.
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Affiliation(s)
- Mary Abou-Nader Crum
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
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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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30
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Sosedov O, Stolz A. Improvement of the amides forming capacity of the arylacetonitrilase from Pseudomonas fluorescens EBC191 by site-directed mutagenesis. Appl Microbiol Biotechnol 2014; 99:2623-35. [DOI: 10.1007/s00253-014-6061-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022]
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31
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He R, Yang Q, Li M. Acylation and deacylation mechanism of Helicobacter pylori AmiF formamidase: A computational DFT study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Gordon RD, Qiu W, Romanov V, Lam K, Soloveychik M, Benetteraj D, Battaile KP, Chirgadze YN, Pai EF, Chirgadze NY. Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacteriumStaphylococcus aureusbelonging to the Nit and NitFhit Branch of the nitrilase superfamily. J Biomol Struct Dyn 2013; 31:1057-65. [DOI: 10.1080/07391102.2012.719111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Weber BW, Kimani SW, Varsani A, Cowan DA, Hunter R, Venter GA, Gumbart JC, Sewell BT. The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning. J Biol Chem 2013; 288:28514-23. [PMID: 23946488 DOI: 10.1074/jbc.m113.503284] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All known nitrilase superfamily amidase and carbamoylase structures have an additional glutamate that is hydrogen bonded to the catalytic lysine in addition to the Glu, Lys, Cys "catalytic triad." In the amidase from Geobacillus pallidus, mutating this glutamate (Glu-142) to a leucine or aspartate renders the enzyme inactive. X-ray crystal structure determination shows that the structural integrity of the enzyme is maintained despite the mutation with the catalytic cysteine (Cys-166), lysine (Lys-134), and glutamate (Glu-59) in positions similar to those of the wild-type enzyme. In the case of the E142L mutant, a chloride ion is located in the position occupied by Glu-142 O(ε1) in the wild-type enzyme and interacts with the active site lysine. In the case of the E142D mutant, this site is occupied by Asp-142 O(δ1.) In neither case is an atom located at the position of Glu-142 O(ε2) in the wild-type enzyme. The active site cysteine of the E142L mutant was found to form a Michael adduct with acrylamide, which is a substrate of the wild-type enzyme, due to an interaction that places the double bond of the acrylamide rather than the amide carbonyl carbon adjacent to the active site cysteine. Our results demonstrate that in the wild-type active site a crucial role is played by the hydrogen bond between Glu-142 O(ε2) and the substrate amino group in positioning the substrate with the correct stereoelectronic alignment to enable the nucleophilic attack on the carbonyl carbon by the catalytic cysteine.
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Affiliation(s)
- Brandon W Weber
- From the Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences and
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Engel U, Syldatk C, Rudat J. Novel amidases of two Aminobacter sp. strains: Biotransformation experiments and elucidation of gene sequences. AMB Express 2012; 2:33. [PMID: 22738219 PMCID: PMC3546935 DOI: 10.1186/2191-0855-2-33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 05/15/2012] [Indexed: 12/02/2022] Open
Abstract
The amidase activities of two Aminobacter sp. strains (DSM24754 and DSM24755) towards the aryl-substituted substrates phenylhydantoin, indolylmethyl hydantoin, D,L-6-phenyl-5,6-dihydrouracil (PheDU) and para-chloro-D,L-6-phenyl-5,6-dihydrouracil were compared. Both strains showed hydantoinase and dihydropyrimidinase activity by hydrolyzing all substrates to the corresponding N-carbamoyl-α- or N-carbamoyl-β-amino acids. However, carbamoylase activity and thus a further degradation of these products to α- and β-amino acids was not detected. Additionally, the genes coding for a dihydropyrimidinase and a carbamoylase of Aminobacter sp. DSM24754 were elucidated. For Aminobacter sp. DSM24755 a dihydropyrimidinase gene flanked by two genes coding for putative ABC transporter proteins was detected. The deduced amino acid sequences of both dihydropyrimidinases are highly similar to the well-studied dihydropyrimidinase of Sinorhizobium meliloti CECT4114. The latter enzyme is reported to accept substituted hydantoins and dihydropyrimidines as substrates. The deduced amino acid sequence of the carbamoylase gene shows a high similarity to the very thermostable enzyme of Pseudomonas sp. KNK003A.
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Abstract
Nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. This assumption was overturned by the discovery of a nickel defense system (RcnR/RcnA) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological concern. To date, the mechanisms of nickel toxicity in microorganisms and higher eukaryotes are poorly understood. In this review, we summarize nickel homeostasis processes used by microorganisms and highlight in vivo and in vitro effects of exposure to elevated concentrations of nickel. On the basis of this evidence we propose four mechanisms of nickel toxicity: (1) nickel replaces the essential metal of metalloproteins, (2) nickel binds to catalytic residues of non-metalloenzymes; (3) nickel binds outside the catalytic site of an enzyme to inhibit allosterically and (4) nickel indirectly causes oxidative stress.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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Gradually accumulating beneficial mutations to improve the thermostability of N-carbamoyl-d-amino acid amidohydrolase by step-wise evolution. Appl Microbiol Biotechnol 2011; 90:1361-71. [DOI: 10.1007/s00253-011-3114-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/04/2011] [Accepted: 01/06/2011] [Indexed: 11/28/2022]
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Janowitz T, Ajonina I, Perbandt M, Woltersdorf C, Hertel P, Liebau E, Gigengack U. The 3-ureidopropionase of Caenorhabditis elegans, an enzyme involved in pyrimidine degradation. FEBS J 2010; 277:4100-9. [PMID: 20840592 DOI: 10.1111/j.1742-4658.2010.07805.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrimidines are important metabolites in all cells. Levels of cellular pyrimidines are controlled by multiple mechanisms, with one of these comprising the reductive degradation pathway. In the model invertebrate Caenorhabditis elegans, two of the three enzymes of reductive pyrimidine degradation have previously been characterized. The enzyme catalysing the final step of pyrimidine breakdown, 3-ureidopropionase (β-alanine synthase), had only been identified based on homology. We therefore cloned and functionally expressed the 3-ureidopropionase of C. elegans as hexahistidine fusion protein. The purified recombinant enzyme readily converted the two pyrimidine degradation products: 3-ureidopropionate and 2-methyl-3-ureidopropionate. The enzyme showed a broad pH optimum between pH 7.0 and 8.0. Activity was highest at approximately 40 °C, although the half-life of activity was only 65 s at that temperature. The enzyme showed clear Michaelis-Menten kinetics, with a K(m) of 147 ± 26 μM and a V(max) of 1.1 ± 0.1 U·mg protein(-1). The quaternary structure of the recombinant enzyme was shown to correspond to a dodecamer by 'blue native' gel electrophoresis and gel filtration. The organ specific and subcellular localization of the enzyme was determined using a translational fusion to green fluorescent protein and high expression was observed in striated muscle cells. With the characterization of the 3-ureidopropionase, the reductive pyrimidine degradation pathway in C. elegans has been functionally characterized.
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Affiliation(s)
- Tim Janowitz
- Institut für Zoophysiologie, Westfälische Wilhelms-Universität, Münster, Germany.
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Almonacid DE, Yera ER, Mitchell JBO, Babbitt PC. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol 2010; 6:e1000700. [PMID: 20300652 PMCID: PMC2837397 DOI: 10.1371/journal.pcbi.1000700] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/02/2010] [Indexed: 11/19/2022] Open
Abstract
Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.
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Affiliation(s)
- Daniel E. Almonacid
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Emmanuel R. Yera
- Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - John B. O. Mitchell
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
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40
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Buddelmeijer N, Young R. The essential Escherichia coli apolipoprotein N-acyltransferase (Lnt) exists as an extracytoplasmic thioester acyl-enzyme intermediate. Biochemistry 2010; 49:341-6. [PMID: 20000742 DOI: 10.1021/bi9020346] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli apolipoprotein N-acyltransferase (Lnt) transfers an acyl group from sn-1-glycerophospholipid to the free alpha-amino group of the N-terminal cysteine of apolipoproteins, resulting in mature triacylated lipoprotein. Here we report that the Lnt reaction proceeds through an acyl-enzyme intermediate in which a palmitoyl group forms a thioester bond with the thiol of the active site residue C387 that was cleaved by neutral hydroxylamine. Lnt(C387S) also formed a fatty acyl intermediate that was resistant to neutral hydroxylamine treatment, consistent with formation of an oxygen-ester linkage. Lnt(C387A) did not form an acyl-enzyme intermediate and, like Lnt(C387S), did not have any detectable Lnt activity, indicating that acylation cannot occur at other positions in the catalytic domain. The existence of this thioacyl-enzyme intermediate allowed us to determine whether essential residues in the catalytic domain of Lnt affect the first step of the reaction, the formation of the acyl-enzyme intermediate, or the second step in which the acyl chain is transferred to the apolipoprotein substrate. In the catalytic triad, E267 is required for the formation of the acyl-enzyme intermediate, indicating its role in enhancing the nucleophilicity of C387. E343 is also involved in the first step but is not in close proximity to the active site. W237, Y388, and E389 play a role in the second step of the reaction since acyl-Lnt is formed but N-acylation does not occur. The data presented allow discrimination between the functions of essential Lnt residues in catalytic activity and substrate recognition.
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Affiliation(s)
- Nienke Buddelmeijer
- Molecular Genetics Unit, Institut Pasteur, and CNRS URA 2172, 25 rue du docteur Roux, 75724 Paris cedex 15, France.
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41
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Yeom SJ, Lee JK, Oh DK. A positively charged amino acid at position 129 in nitrilase from Rhodococcus rhodochrous ATCC 33278 is an essential residue for the activity with meta-substituted benzonitriles. FEBS Lett 2010; 584:106-10. [PMID: 19903476 DOI: 10.1016/j.febslet.2009.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 11/03/2009] [Accepted: 11/04/2009] [Indexed: 10/20/2022]
Abstract
A positively charged amino acid (Arg, Lys, or His) at position 129 in Rhodococcus rhodochrous ATCC 33278 nitrilase is essential for the activity of aromatic nitriles. The wild-type enzyme containing Arg129 was active only for meta- and para-substituted benzonitriles with a methyl or amino group, but the R129K and R129H mutant enzymes were active only for meta-substituted benzonitriles. The lack of activity of the mutants for para-substituted benzonitriles may be attributable to steric hindrance between the para-substituent and the side chain of Lys or His.
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Affiliation(s)
- Soo-Jin Yeom
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
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42
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Carbamoylases: characteristics and applications in biotechnological processes. Appl Microbiol Biotechnol 2009; 85:441-58. [DOI: 10.1007/s00253-009-2250-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 09/07/2009] [Accepted: 09/07/2009] [Indexed: 11/26/2022]
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43
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Jiwaji M, Dorrington RA. Regulation of hydantoin-hydrolyzing enzyme expression in Agrobacterium tumefaciens strain RU-AE01. Appl Microbiol Biotechnol 2009; 84:1169-79. [PMID: 19597814 DOI: 10.1007/s00253-009-2097-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 06/12/2009] [Accepted: 06/14/2009] [Indexed: 11/28/2022]
Abstract
Optically pure D-: amino acids, like D-: hydroxyphenylglycine, are used in the semi-synthetic production of pharmaceuticals. They are synthesized industrially via the biocatalytic hydrolysis of p-hydroxyphenylhydantoin using enzymes derived from Agrobacterium tumefaciens strains. The reaction proceeds via a three-step pathway: (a) the ring-opening cleavage of the hydantoin ring by a D-: hydantoinase (encoded by hyuH), (b) conversion of the resultant D-: N-carbamylamino acid to the corresponding amino acid by a D-: N-carbamoylase (encoded by hyuC), and (c) chemical or enzymatic racemization of the un-reacted hydantoin substrate. While the structure and biochemical properties of these enzymes are well understood, little is known about their origin, their function, and their regulation in the native host. We investigated the mechanisms involved in the regulation of expression of the hydantoinase and N-carbamoylase enzyme activity in A. tumefaciens strain RU-AE01. We present evidence for a complex regulatory network that responds to the growth status of the cells, the presence of inducer, and nitrogen catabolite repression. Deletion analysis and site-directed mutagenesis were used to identify regulatory elements involved in transcriptional regulation of hyuH and hyuC expression. Finally, a comparison between the hyu gene clusters in several Agrobacterium strains provides insight into the function of D-: selective hydantoin-hydrolyzing enzyme systems in Agrobacterium species.
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Affiliation(s)
- Meesbah Jiwaji
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown, South Africa
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44
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Seffernick JL, Samanta SK, Louie TM, Wackett LP, Subramanian M. Investigative mining of sequence data for novel enzymes: a case study with nitrilases. J Biotechnol 2009; 143:17-26. [PMID: 19539670 DOI: 10.1016/j.jbiotec.2009.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 06/08/2009] [Accepted: 06/09/2009] [Indexed: 10/20/2022]
Abstract
Mining sequence data is increasingly important for biocatalysis research. However, when relying on sequence data alone, prediction of the reaction catalyzed by a specific protein sequence is often elusive, and substrate specificity is far from trivial. The present study demonstrated an approach of combining sequence data and structures from distant homologs to target identification of new nitrilases that specifically utilize hindered nitrile substrates like mandelonitrile. A total of 212 non-identical target nitrilases were identified from GenBank. Evolutionary trace and sequence clustering methods were used combinatorily to identify a set of nitrilases with presumably distinct substrate specificities. Selected encoding genes were cloned into Escherichia coli. Recombinant E. coli expressing NitA (gi91784632) from Burkholderia xenovorans LB400 was capable of growth on glutaronitrile or adiponitrile as the sole nitrogen source. Purified NitA exhibited highest activity with mandelonitrile, showing a catalytic efficiency (k(cat)/K(m)) of 3.6 x 10(4)M(-1)s(-1). A second nitrilase predicted from our studies from Bradyrhizobium zaponicum USDA 110 (gi27381513) was likewise shown to prefer mandelonitrile [Zhu, D., Mukherjee, C., Biehl, E.R., Hua, L., 2007. Discovery of a mandelonitrile hydrolase from Bradyrhizobium japonicum USDA110 by rational genome mining. J. Biotechnol. 129 (4), 645-650]. Thus, predictions from sequence analysis and distant superfamily structures yielded enzyme activities with high selectivity for mandelonitrile. These data suggest that similar data mining techniques can be used to identify other substrate-specific enzymes from published, unannotated sequences.
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Affiliation(s)
- Jennifer L Seffernick
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 140 Gortner Laboratory, St. Paul, MN 55108, USA.
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Abstract
Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture.
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Affiliation(s)
- Andrew J M Howden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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46
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Enhanced hydantoin-hydrolyzing enzyme activity in an Agrobacterium tumefaciens strain with two distinct N-carbamoylases. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2008.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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47
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Han WW, Zhan DL, Luo Q, Zhou YH, Yao Y, Li ZS, Feng Y. The substrate specificity and the catalytic mechanism of N-carbamyl-d-amino acid amidohydrolase: A theoretical investigation. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.01.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Thuku R, Brady D, Benedik M, Sewell B. Microbial nitrilases: versatile, spiral forming, industrial enzymes. J Appl Microbiol 2009; 106:703-27. [DOI: 10.1111/j.1365-2672.2008.03941.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Dent KC, Weber BW, Benedik MJ, Sewell BT. The cyanide hydratase from Neurospora crassa forms a helix which has a dimeric repeat. Appl Microbiol Biotechnol 2009; 82:271-8. [DOI: 10.1007/s00253-008-1735-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/24/2008] [Accepted: 09/25/2008] [Indexed: 10/21/2022]
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50
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Yu H, Li J, Zhang D, Yang Y, Jiang W, Yang S. Improving the thermostability of N-carbamyl-d-amino acid amidohydrolase by error-prone PCR. Appl Microbiol Biotechnol 2009; 82:279-85. [PMID: 18985337 DOI: 10.1007/s00253-008-1748-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 10/08/2008] [Accepted: 10/16/2008] [Indexed: 11/29/2022]
Affiliation(s)
- Hong Yu
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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