1
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Zhang S, Liu Y, Mohisn A, Zhang G, Wang Z, Wu S. Biodegradation of penicillin G sodium by Sphingobacterium sp. SQW1: Performance, degradation mechanism, and key enzymes. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133485. [PMID: 38377898 DOI: 10.1016/j.jhazmat.2024.133485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Biodegradation is an efficient and cost-effective approach to remove residual penicillin G sodium (PGNa) from the environment. In this study, the effective PGNa-degrading strain SQW1 (Sphingobacterium sp.) was screened from contaminated soil using enrichment technique. The effects of critical operational parameters on PGNa degradation by strain SQW1 were systematically investigated, and these parameters were optimized by response surface methodology to maximize PGNa degradation. Comparative experiments found the extracellular enzyme to completely degrade PGNa within 60 min. Combined with whole genome sequencing of strain SQW1 and LC-MS analysis of degradation products, penicillin acylase and β-lactamase were identified as critical enzymes for PGNa biodegradation. Moreover, three degradation pathways were postulated, including β-lactam hydrolysis, penicillin acylase hydrolysis, decarboxylation, desulfurization, demethylation, oxidative dehydrogenation, hydroxyl reduction, and demethylation reactions. The toxicity of PGNa biodegradation intermediates was assessed using paper diffusion method, ECOSAR, and TEST software, which showed that the biodegradation products had low toxicity. This study is the first to describe PGNa-degrading bacteria and detailed degradation mechanisms, which will provide new insights into the PGNa biodegradation.
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Affiliation(s)
- Sinan Zhang
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China; Department of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - YuXuan Liu
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Ali Mohisn
- Department of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guohui Zhang
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Zejian Wang
- Department of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Shiyong Wu
- Engineering Research Center of Resource Utilization of Carbon-containing Waste with Carbon Neutrality, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China.
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2
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Sompiyachoke K, Elias MH. Engineering quorum quenching acylases with improved kinetic and biochemical properties. Protein Sci 2024; 33:e4954. [PMID: 38520282 PMCID: PMC10960309 DOI: 10.1002/pro.4954] [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: 10/25/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/25/2024]
Abstract
Many Gram-negative bacteria use N-acyl-L-homoserine lactone (AHL) signals to coordinate phenotypes such as biofilm formation and virulence factor production. Quorum-quenching enzymes, such as AHL acylases, chemically degrade these molecules which prevents signal reception by bacteria and inhibits undesirable biofilm-related traits. These capabilities make acylases appealing candidates for controlling microbes, yet candidates with high activity levels and substrate specificity and that are capable of being formulated into materials are needed. In this work, we undertook engineering efforts against two AHL acylases, PvdQ and MacQ, to generate these improved properties using the Protein One-Stop Shop Server. The engineering of acylases is complicated by low-throughput enzymatic assays. Alleviating this challenge, we report a time-course kinetic assay for AHL acylases that monitors the real-time production of homoserine lactone. Using the assay, we identified variants of PvdQ that were significantly stabilized, with melting point increases of up to 13.2°C, which translated into high resistance against organic solvents and increased compatibility with material coatings. While the MacQ mutants were unexpectedly destabilized, they had considerably improved kinetic properties, with >10-fold increases against N-butyryl-L-homoserine lactone and N-hexanoyl-L-homoserine lactone. Accordingly, these changes resulted in increased quenching abilities using a biosensor model and greater inhibition of virulence factor production of Pseudomonas aeruginosa PA14. While the crystal structure of one of the MacQ variants, M1, did not reveal obvious structural determinants explaining the observed changes in kinetics, it allowed for the capture of an acyl-enzyme intermediate that confirms a previously hypothesized catalytic mechanism of AHL acylases.
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Affiliation(s)
- Kitty Sompiyachoke
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Mikael H. Elias
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaSt. PaulMinnesotaUSA
- Biotechnology InstituteSt. PaulMinnesotaUSA
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3
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Zhang YJ, Liang JX, Xu YS, Liu YX, Cui Y, Qiao ZY, Wang H. Covalent drugs based on small molecules and peptides for disease theranostics. Biomater Sci 2024; 12:564-580. [PMID: 37975197 DOI: 10.1039/d3bm01138k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Biomacromolecules, such as proteins, nucleic acids and polysaccharides, are widely distributed in the human body, and some of them have been recognized as the targets of drugs for disease theranostics. Drugs typically act on targets in two ways: non-covalent bond and covalent bond. Non-covalent bond-based drugs have some disadvantages, such as structural instability and environmental sensitivity. Covalent interactions between drugs and targets have a longer action time, higher affinity and controllability than non-covalent interactions of conventional drugs. With the development of artificial intelligence, covalent drugs have received more attention and have been developed rapidly in pharmaceutical research in recent years. From the perspective of covalent drugs, this review summarizes the design methods and the effects of covalent drugs. Finally, we discuss the application of covalent peptide drugs and expect to provide a new reference for cancer treatment.
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Affiliation(s)
- Ying-Jin Zhang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
| | - Jian-Xiao Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
| | - Yin-Sheng Xu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
| | - Yi-Xuan Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
| | - Yingying Cui
- Department of Food and Drug, Laiwu Vocational and Technical, College, Jinan, China
| | - Zeng-Ying Qiao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
| | - Hao Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing 100190, P.R. China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P.R. China
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4
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Sompiyachoke K, Elias MH. Engineering Quorum Quenching Acylases with Improved Kinetic and Biochemical Properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555929. [PMID: 37693529 PMCID: PMC10491313 DOI: 10.1101/2023.09.01.555929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Many Gram-negative bacteria respond to N-acyl-L-homoserine lactone (AHL) signals to coordinate phenotypes such as biofilm formation and virulence factor production. Quorum-quenching enzymes, such as acylases, chemically degrade AHL signals, prevent signal reception by bacteria, and inhibit undesirable traits related to biofilm. These capabilities make these enzymes appealing candidates for controlling microbes. Yet, enzyme candidates with high activity levels, high substrate specificity for specific interference, and that are capable of being formulated into materials are needed. In this work, we undertook engineering efforts against two AHL acylases, PvdQ and MacQ, to obtain improved acylase variants. The engineering of acylase is complicated by low-throughput enzymatic assays. To alleviate this challenge, we report a time-course kinetic assay for AHL acylase that tracks the real-time production of homoserine lactone. Using the protein one-stop shop server (PROSS), we identified variants of PvdQ that were significantly stabilized, with melting point increases of up to 13.2 °C, which translated into high resistance against organic solvents and increased compatibility with material coatings. We also generated mutants of MacQ with considerably improved kinetic properties, with >10-fold increases against N-butyryl-L-homoserine lactone and N-hexanoyl-L-homoserine lactone. In fact, the variants presented here exhibit unique combinations of stability and activity levels. Accordingly, these changes resulted in increased quenching abilities using a biosensor model and greater inhibition of virulence factor production of Pseudomonas aeruginosa PA14. While the crystal structure of one of the MacQ variants, M1, did not reveal obvious structural determinants explaining the observed changes in kinetics, it allowed for the capture of an acyl-enzyme intermediate that confirms a previously hypothesized catalytic mechanism of AHL acylases.
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Affiliation(s)
- Kitty Sompiyachoke
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, St. Paul, MN, 55108, USA
| | - Mikael H. Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, St. Paul, MN, 55108, USA
- University of Minnesota, Biotechnology Institute, St. Paul, MN, 55108, USA
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5
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Ma M, Chen X, Yue Y, Wang J, He D, Liu R. Immobilization and property of penicillin G acylase on amino functionalized magnetic Ni0.3Mg0.4Zn0.3Fe2O4 nanoparticles prepared via the rapid combustion process. Front Bioeng Biotechnol 2023; 11:1108820. [PMID: 36994365 PMCID: PMC10040772 DOI: 10.3389/fbioe.2023.1108820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Penicillin G acylase plays an important role in the biocatalytic process of semi-synthetic penicillin. In order to overcome the disadvantages of free enzymes and improve the catalytic performance of enzymes, it is a new method to immobilize enzymes on carrier materials. And magnetic materials have the characteristics of easy separation. In the present study, the Magnetic Ni0.3Mg0.4Zn0.3Fe2O4 nanoparticles were successfully prepared by a rapid-combustion method and calcined at 400°C for 2 h. The surface of the nanoparticles was modified with sodium silicate hydrate, and the PGA was covalently bound to the carrier particles through the cross-linking of glutaraldehyde. The results showed that the activity of immobilized PGA reached 7121.00 U/g. The optimum pH for immobilized PGA was 8 and the optimum temperature was 45°C, the immobilized PGA exhibited higher stability against changes in pH and temperature. The Michaelis–Menten constant (Km) values of the free and immobilized PGA were 0.00387 and 0.0101 mol/L and the maximum rate (Vmax) values were 0.387 and 0.129 μmol/min. Besides, the immobilized PGA revealed excellent cycling performance. The immobilization strategy presented PGA had the advantages of reuse, good stability, cost saving and had considerable practical significance for the commercial application of PGA.
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Affiliation(s)
- Mingyi Ma
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Xiu Chen
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, China
| | - Yao Yue
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Jie Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Dawei He
- Affiliated Kunshan Hospital, Jiangsu University, Suzhou, China
- *Correspondence: Ruijiang Liu, ; Dawei He,
| | - Ruijiang Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, China
- *Correspondence: Ruijiang Liu, ; Dawei He,
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6
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da Rocha TN, Morellon-Sterlling R, Rocha-Martin J, Bolivar JM, Gonçalves LRB, Fernandez-Lafuente R. Immobilization of Penicillin G Acylase on Vinyl Sulfone-Agarose: An Unexpected Effect of the Ionic Strength on the Performance of the Immobilization Process. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27217587. [PMID: 36364414 PMCID: PMC9654356 DOI: 10.3390/molecules27217587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Penicillin G acylase (PGA) from Escherichia coli was immobilized on vinyl sulfone (VS) agarose. The immobilization of the enzyme failed at all pH values using 50 mM of buffer, while the progressive increase of ionic strength permitted its rapid immobilization under all studied pH values. This suggests that the moderate hydrophobicity of VS groups is enough to transform the VS-agarose in a heterofunctional support, that is, a support bearing hydrophobic features (able to adsorb the proteins) and chemical reactivity (able to give covalent bonds). Once PGA was immobilized on this support, the PGA immobilization on VS-agarose was optimized with the purpose of obtaining a stable and active biocatalyst, optimizing the immobilization, incubation and blocking steps characteristics of this immobilization protocol. Optimal conditions were immobilization in 1 M of sodium sulfate at pH 7.0, incubation at pH 10.0 for 3 h in the presence of glycerol and phenyl acetic acid, and final blocking with glycine or ethanolamine. This produced biocatalysts with stabilities similar to that of the glyoxyl-PGA (the most stable biocatalyst of this enzyme described in literature), although presenting just over 55% of the initially offered enzyme activity versus the 80% that is recovered using the glyoxyl-PGA. This heterofuncionality of agarose VS beads opens new possibilities for enzyme immobilization on this support.
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Affiliation(s)
- Thays N. da Rocha
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Chemical Engineering Department, Campus do Pici, Federal University of Ceará, Bloco 709, Fortaleza CEP 60440-900, CE, Brazil
| | - Roberto Morellon-Sterlling
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Departamento de Biología Molecular, Campus UAM-CSIC, Universidad Autónoma de Madrid, Darwin 2, Cantoblanco, 28049 Madrid, Spain
| | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
| | - Juan M. Bolivar
- FQPIMA Group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., 28040 Madrid, Spain
| | - Luciana R. B. Gonçalves
- Chemical Engineering Department, Campus do Pici, Federal University of Ceará, Bloco 709, Fortaleza CEP 60440-900, CE, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain
- Center of Excellence in Bionanoscience Research, Member of the External Scientific Advisory Board, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: ; Tel.: +34-91594804
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7
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Wang X, Wu K, Zhang H, Liu J, Yang Z, Bai J, Liu H, Shao L. Efficient side-chain deacylation of polymyxin B1 in recombinant Streptomyces strains. Biotechnol Lett 2022; 44:1287-1299. [PMID: 36076042 DOI: 10.1007/s10529-022-03290-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Polymyxins are antibacterial polypeptides used as "last resort" therapy option for multidrug-resistant Gram-negative bacteria. The expansion of polymyxin-resistant infections has inspired development of novel polymyxin derivatives, and deacylation is one of the critical steps in generating those antibiotics. Deacylase from Actinoplanes utahensis hydrolyze the acyl moieties of echinocandins, and also efficiently deacylates daptomycin, ramoplanin and other important antibiotics. Here, deacylase was studied considering its potential usefulness in deacylating polymyxin B1. RESULTS All the six recombinant strains containing the deacylase gene catalyzed hydrolysis of polymyxin B1, yielding cyclic heptapeptides. The efficiency of recombinant S. albus (SAL701) was higher than that of the others, and deacylation was the most efficient at 40 °C in 0.2 M Tris buffer (pH 8.0) with 0.2 M Mg2+. The optimal substrate concentration of SAL701 was increased from 2.0 to 6.0 g/L. SAL701 was highly thermostable, showing no loss of activity at 50 °C for 12 h, and the mycelia could be recycled at least three times without loss of catalytic activity. SAL701 could not deacylate β-lactam substrate such as penicillin G and cephalosporin C. Deacylase catalyzes the amide bond 1 closest to the nucleus of polymyxin B1 rather than the other bond, suggesting that it has high catalytic site specificity. Homology modeling and the docking results implied that Thr190 in deacylase could facilitate hydrolysis with high regioselectivity. CONCLUSIONS These results show that SAL701 is effective in increasing the cyclic heptapeptide moiety of polymyxin B1. These properties of the biocatalyst may enable its development in the industrial production of polymyxins antibiotics.
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Affiliation(s)
- Xiaojing Wang
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China.,Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, China.,School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Kai Wu
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, China.,School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Hanzhi Zhang
- Abiochem Biotechnology Co., Ltd, Shanghai, China
| | - Jing Liu
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, China.,School of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Zhijun Yang
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, China.,School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Jing Bai
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
| | - Hao Liu
- Department of Antibiotics and Microorganisms, Shanghai Institute for Food and Drug Control, Shanghai, China.
| | - Lei Shao
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, China. .,School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, China.
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8
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Wang Y, Hu X, Long Z, Adams E, Li J, Xu M, Liang C, Ning B, Hu C, Zhang Y. Proteomic analysis of Penicillin G acylases and resulting residues in semi-synthetic β-lactam antibiotics using liquid chromatography - tandem mass spectrometry. J Chromatogr A 2022; 1678:463365. [PMID: 35907366 DOI: 10.1016/j.chroma.2022.463365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 12/31/2022]
Abstract
Penicillin G acylase (PGA), as a key enzyme, is increasingly used in the commercial production of semi-synthetic β-lactam antibiotics (SSBAs). With the substitution of conventional chemical synthesis by emerging bioconversion processes, more and more PGAs fermented from different types of strains such as Escherichia coli (E. coli, ATCC 11105), Achromobacter sp. CCM 4824 and Providencia rettgeri (ATCC 31052) have been used in this kind of enzymatic processes. As an intermediate reaction catalyst, PGA protein and its presence in the final products may cause a potential risk of human allergic reaction and bring challenges for both quality and process controls. To achieve qualitative and quantitative analysis of PGAs and their residues in SSBAs, a tryptic digestion coupled with liquid chromatography - tandem mass spectrometry (LC-MS/MS) method was developed and proposed because of advantages like high selectivity and sensitivity. A suitable filter aided sample preparation (FASP) method was also used to remove matrix interference and to enrich the target PGA retained in the ultrafiltration membrane for an efficient enzymatic hydrolysis and subsequent accurate MS detection. Finally, twelve batches of PGAs from eight companies were identified and categorized into two types of strains (E. coli and Achromobacter sp. CCM 4824) using proteomic analysis. In total nine batches of five types of SSBAs (amoxicillin, cephalexin, cefprozil, cefdinir and cefaclor) from eight manufacturers were selected for investigation. Trace levels of PGA residual proteins ranging from 0.01 to 0.44 ppm were detected in six batches of different SSBAs which were far lower than the safety limit of 35 ppm reported by DSM, a manufacturer with expertise in the production of SSBAs by enzymatic processes. The developed FASP with LC-MS/MS method is superior to traditional protein assays in terms of selectivity, sensitivity and accuracy. Moreover, it could provide in-depth analysis of amino acid sequences and signature peptides contributing to assignment of the strain sources of PGAs. This method could become a promising and powerful tool to monitor enzymatic process robustness and reliability of this kind of SSBAs manufacturing.
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Affiliation(s)
- Yan Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China; Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Xinyue Hu
- Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Zhen Long
- Thermo Fisher Scientific Corporation, Beijing 100080, China
| | - Erwin Adams
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven, University of Leuven, Herestraat 49, O&N2, PB 923, Leuven 3000, Belgium
| | - Jin Li
- Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Mingzhe Xu
- Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Chenggang Liang
- Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Baoming Ning
- Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Changqin Hu
- Department of Antibiotics, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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9
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Pan X, Xu L, Li Y, Wu S, Wu Y, Wei W. Strategies to Improve the Biosynthesis of β-Lactam Antibiotics by Penicillin G Acylase: Progress and Prospects. Front Bioeng Biotechnol 2022; 10:936487. [PMID: 35923572 PMCID: PMC9340067 DOI: 10.3389/fbioe.2022.936487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
β-Lactam antibiotics are widely used anti-infection drugs that are traditionally synthesized via a chemical process. In recent years, with the growing demand for green alternatives, scientists have turned to enzymatic synthesis. Penicillin G acylase (PGA) is the second most commercially used enzyme worldwide with both hydrolytic and synthetic activities toward antibiotics, which has been used to manufacture the key antibiotic nucleus on an industrial level. However, the large-scale application of PGA-catalyzed antibiotics biosynthesis is still in the experimental stage because of some key limitations, such as low substrate concentration, unsatisfactory yield, and lack of superior biocatalysts. This paper systematically reviews the strategies adopted to improve the biosynthesis of β-lactam antibiotics by adjusting the enzymatic property and manipulating the reaction system in recent 20 years, including mining of enzymes, protein engineering, solvent engineering, in situ product removal, and one-pot reaction cascade. These advances will provide important guidelines for the future use of enzymatic synthesis in the industrial production of β-lactam antibiotics.
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Affiliation(s)
- Xin Pan
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
- *Correspondence: Xin Pan, ; Yong Wu, ; Wenping Wei,
| | - Lei Xu
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yaru Li
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Sihua Wu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Japan
| | - Yong Wu
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
- *Correspondence: Xin Pan, ; Yong Wu, ; Wenping Wei,
| | - Wenping Wei
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
- *Correspondence: Xin Pan, ; Yong Wu, ; Wenping Wei,
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10
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Lancaster EB, Yang W, Johnson WH, Baas BJ, Zhang YJ, Whitman CP. Kinetic, Inhibition, and Structural Characterization of a Malonate Semialdehyde Decarboxylase-like Protein from Calothrix sp. PCC 6303: A Gateway to the non-Pro1 Tautomerase Superfamily Members. Biochemistry 2022; 61:10.1021/acs.biochem.2c00101. [PMID: 35559608 PMCID: PMC10120574 DOI: 10.1021/acs.biochem.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The amino-terminal proline (Pro1) has long been thought to be a mechanistic imperative for tautomerase superfamily (TSF) enzymes, functioning as a general base or acid in all characterized reactions. However, a global examination of more than 11,000 nonredundant sequences of the TSF uncovered 346 sequences that lack Pro1. The majority (∼85%) are found in the malonate semialdehyde decarboxylase (MSAD) subgroup where most of the 294 sequences form a separate cluster. Four sequences within this cluster retain Pro1. Because these four sequences might provide clues to assist in the identification and characterization of activities of nearby sequences without Pro1, they were examined by kinetic, inhibition, and crystallographic studies. The most promising of the four (from Calothrix sp. PCC 6303 designated 437) exhibited decarboxylase and tautomerase activities and was covalently modified at Pro1 by 3-bromopropiolate. A crystal structure was obtained for the apo enzyme (2.35 Å resolution). The formation of a 3-oxopropanoate adduct with Pro1 provides clues to build a molecular model for the bound ligand. The modeled ligand extends into a region that allows interactions with three residues (Lys37, Arg56, Glu98), suggesting that these residues can play roles in the observed decarboxylation and tautomerization activities. Moreover, these same residues are conserved in 16 nearby, non-Pro1 sequences in a sequence similarity network. Thus far, these residues have not been implicated in the mechanisms of any other TSF members. The collected observations provide starting points for the characterization of the non-Pro1 sequences.
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Affiliation(s)
- Emily B. Lancaster
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712
| | - Wanjie Yang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
| | - William H. Johnson
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712
| | - Bert-Jan Baas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712
| | - Christian P. Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712
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11
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Surpeta B, Grulich M, Palyzová A, Marešová H, Brezovsky J. Common Dynamic Determinants Govern Quorum Quenching Activity in N-Terminal Serine Hydrolases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bartlomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
| | - Michal Grulich
- Laboratory of Modulation of Gene Expression, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Andrea Palyzová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Helena Marešová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology,v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland
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12
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Linhorst A, Lübke T. The Human Ntn-Hydrolase Superfamily: Structure, Functions and Perspectives. Cells 2022; 11:cells11101592. [PMID: 35626629 PMCID: PMC9140057 DOI: 10.3390/cells11101592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
N-terminal nucleophile (Ntn)-hydrolases catalyze the cleavage of amide bonds in a variety of macromolecules, including the peptide bond in proteins, the amide bond in N-linked protein glycosylation, and the amide bond linking a fatty acid to sphingosine in complex sphingolipids. Ntn-hydrolases are all sharing two common hallmarks: Firstly, the enzymes are synthesized as inactive precursors that undergo auto-proteolytic self-activation, which, as a consequence, reveals the active site nucleophile at the newly formed N-terminus. Secondly, all Ntn-hydrolases share a structural consistent αββα-fold, notwithstanding the total lack of amino acid sequence homology. In humans, five subclasses of the Ntn-superfamily have been identified so far, comprising relevant members such as the catalytic active subunits of the proteasome or a number of lysosomal hydrolases, which are often associated with lysosomal storage diseases. This review gives an updated overview on the structural, functional, and (patho-)physiological characteristics of human Ntn-hydrolases, in particular.
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13
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Wang P, Zhang S, Zhang J, Zhu Y. Computational design of penicillin acylase variants with improved kinetic selectivity for the enzymatic synthesis of cefazolin. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Sumida Y, Yamasaki M, Nishiya Y, Kumagai S, Yamada T, Azuma M. Protein Engineering of
d
‐Succinylase from
Cupriavidus sp
. for
d
‐Amino Acid Synthesis and the Structural Implications. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yosuke Sumida
- Department of Applied Chemistry and Bioengineering Graduate School of Engineering Osaka City University 3-3-138 Sugimoto Sumiyoshi-ku Osaka 558-8585 Japan
- Biotechnology Research Laboratory Toyobo Co., Ltd. 10-24 Toyo-cho Tsuruga Fukui 914-0047 Japan
| | - Masayuki Yamasaki
- Faculty of Agriculture Ryukoku University 1-5 Yokotani, Ohe-cho Seta Otsu 520-2194 Japan
- Institute for Frontier Medical Sciences Kyoto University 53 Kawahara-cho Shogoin, Sakyo-ku Kyoto 606-8507 Japan
| | - Yoshiaki Nishiya
- Biotechnology Research Laboratory Toyobo Co., Ltd. 10-24 Toyo-cho Tsuruga Fukui 914-0047 Japan
- Department of Life Science Setsunan University 17-8 Ikeda-Nakamachi Neyagawa Osaka 572-8508 Japan
| | - Shinya Kumagai
- R&D Group, Iwate Research & Development Center SEKISUI MEDICAL Co., Ltd. 4-115, Matsuo Hachimantai Iwate 028-7305 Japan
| | - Toshihide Yamada
- R&D Group, Iwate Research & Development Center SEKISUI MEDICAL Co., Ltd. 4-115, Matsuo Hachimantai Iwate 028-7305 Japan
| | - Masayuki Azuma
- Department of Applied Chemistry and Bioengineering Graduate School of Engineering Osaka City University 3-3-138 Sugimoto Sumiyoshi-ku Osaka 558-8585 Japan
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15
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Serrano-Aguirre L, Velasco-Bucheli R, García-Álvarez B, Saborido A, Arroyo M, de la Mata I. Novel Bifunctional Acylase from Actinoplanes utahensis: A Versatile Enzyme to Synthesize Antimicrobial Compounds and Use in Quorum Quenching Processes. Antibiotics (Basel) 2021; 10:antibiotics10080922. [PMID: 34438972 PMCID: PMC8388760 DOI: 10.3390/antibiotics10080922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Many intercellular communication processes, known as quorum sensing (QS), are regulated by the autoinducers N-acyl-l-homoserine lactones (AHLs) in Gram-negative bacteria. The inactivation of these QS processes using different quorum quenching (QQ) strategies, such as enzymatic degradation of the autoinducers or the receptor blocking with non-active analogs, could be the basis for the development of new antimicrobials. This study details the heterologous expression, purification, and characterization of a novel N-acylhomoserine lactone acylase from Actinoplanes utahensis NRRL 12052 (AuAHLA), which can hydrolyze different natural penicillins and N-acyl-homoserine lactones (with or without 3-oxo substitution), as well as synthesize them. Kinetic parameters for the hydrolysis of a broad range of substrates have shown that AuAHLA prefers penicillin V, followed by C12-HSL. In addition, AuAHLA inhibits the production of violacein by Chromobacterium violaceum CV026, confirming its potential use as a QQ agent. Noteworthy, AuAHLA is also able to efficiently synthesize penicillin V, besides natural AHLs and phenoxyacetyl-homoserine lactone (POHL), a non-natural analog of AHLs that could be used to block QS receptors and inhibit signal of autoinducers, being the first reported AHL acylase capable of synthesizing AHLs.
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16
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021; 60:15972-15979. [PMID: 33844389 PMCID: PMC8361980 DOI: 10.1002/anie.202102343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
The thiol group of the cysteine side chain is arguably the most versatile chemical handle in proteins. To expand the scope of established and commercially available thiol bioconjugation reagents, we genetically encoded a second such functional moiety in form of a latent thiol group that can be unmasked under mild physiological conditions. Phenylacetamidomethyl (Phacm) protected homocysteine (HcP) was incorporated and its latent thiol group unmasked on purified proteins using penicillin G acylase (PGA). The enzymatic deprotection depends on steric accessibility, but can occur efficiently within minutes on exposed positions in flexible sequences. The freshly liberated thiol group does not require treatment with reducing agents. We demonstrate the potential of this approach for protein modification with conceptually new schemes for regioselective dual labeling, thiol bioconjugation in presence of a preserved disulfide bond and formation of a novel intramolecular thioether crosslink.
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Affiliation(s)
| | - Pascal Meyer‐Ahrens
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Annika Aust
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Anna‐Lena Feldberg
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
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17
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marie Reille‐Seroussi
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Pascal Meyer‐Ahrens
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Annika Aust
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Anna‐Lena Feldberg
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
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18
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Fellechner O, Smirnova I. Process design of a continuous biotransformation with in situ product removal by cloud point extraction. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.23967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Oliver Fellechner
- Institute of Thermal Separation Processes Hamburg University of Technology Hamburg Germany
| | - Irina Smirnova
- Institute of Thermal Separation Processes Hamburg University of Technology Hamburg Germany
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19
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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20
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Yu Z, Tian H, Sun K, Shao Y, Zhang L, Zhang S, Duan P, Liu Q, Niu S, Dong D, Hu X. Impacts of externally added Brønsted and Lewis acid on conversion of furfural to cyclopentanone over Ni/SiC catalyst. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.111187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Jiang Z, Zhang X, Chen HS, Yang P, Jiang SP. Fusiform-Shaped g-C 3 N 4 Capsules with Superior Photocatalytic Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003910. [PMID: 32964669 DOI: 10.1002/smll.202003910] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/18/2020] [Indexed: 06/11/2023]
Abstract
Carbon nitride (g-C3 N4 ) nanostructure rebuilding is an effective means to modify its photocatalytic properties, especially the hollow micron-nanostructure. The increased scattering in the body effectively improves the light utilization efficiency and improves catalytic properties. In this work, fusiform-shaped g-C3 N4 capsules are created by controlling the nucleation kinetics of supramolecular assemblies. The fusiform-shaped capsule micron-nanostructure is synthesized with ultrathin wall thickness and adjusted carbon/nitride ratios which decrease the recombination rate of photo-generated carriers. The hollow nanostructure and relatively higher specific surface area of the fusiform-shaped capsule effectively enhance light scattering inside body and lead to an enhanced carrier utilization efficiency. Moreover, the decrease of bandgap and relatively negative conduction band position affect the response of hollow fusiform-shaped g-C3 N4 capsules (Hf-g-C3 N4 ) in visible light region and improve the photo-reducing performance. In term of H2 evolution property, Hf-g-C3 N4 has been improved to 7052 µmol g-1 h-1 , which is 10.9 times higher compared with bulk structure. More importantly, Hf-g-C3 N4 can produce CH4 at the rate of 1.63 µmol g-1 h-1 without help of co-catalyst and hole sacrificial agent in the photocatalytic reduction reaction of CO2 to CH4 . At same time, the selective photocatalytic reduction of CO2 is another advantage of Hf-g-C3 N4 .
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Affiliation(s)
- Zhixiang Jiang
- School of Material Science & Engineering, University of Jinan, Jinan, 250022, P. R. China
| | - Xiao Zhang
- Fuels and Energy Technology Institute and Department of Chemical Engineering, Curtin University, Perth, WA6845, Australia
| | - Hsueh-Shih Chen
- Department of Materials Science & Engineering, National Tsing Hua University, Hsinchu City, 300, Taiwan
| | - Ping Yang
- School of Material Science & Engineering, University of Jinan, Jinan, 250022, P. R. China
| | - San Ping Jiang
- Fuels and Energy Technology Institute and Department of Chemical Engineering, Curtin University, Perth, WA6845, Australia
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22
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Garrido-González JJ, Iglesias Aparicio MM, García MM, Simón L, Sanz F, Morán JR, Fuentes de Arriba ÁL. An Enzyme Model Which Mimics Chymotrypsin and N-Terminal Hydrolases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- José J. Garrido-González
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | | | - Miguel Martínez García
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Luis Simón
- Chemical Engineering Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Francisca Sanz
- X-Ray Diffraction Service, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Joaquín R. Morán
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
| | - Ángel L. Fuentes de Arriba
- Organic Chemistry Department, University of Salamanca, Plaza de los Caídos 1-5, Salamanca E-37008, Spain
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23
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Penicillin G acylase production by Mucor griseocyanus and the partial genetic analysis of its pga gene. Int Microbiol 2020; 24:37-45. [PMID: 32705496 DOI: 10.1007/s10123-020-00137-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Penicillin acylases (penicillin amidohydrolase, EC 3.5.1.11) are a group of enzymes with many applications within the pharmaceutical industry, and one of them is the production of semi-synthetic beta-lactam antibiotics. This enzyme is mainly produced by bacteria but also by some fungi. In the present study, the filamentous fungus Mucor griseocyanus was used to produce penicillin acylase enzyme (PGA). Its ability to express PGA enzyme in submerged fermentation process was assessed, finding that this fungal strain produces the biocatalyst of interest in an extracellular way at a level of 570 IU/L at 72 h of fermentation; in this case, a saline media using lactose as carbon source and penicillin G as inducer was employed. In addition, a DNA fragment (859 bp) of the pga from a pure Mucor griseocyanus strain was amplified, sequenced, and analyzed in silico. The partial sequence of pga identified in the fungi showed high identity percentage with penicillin G acylase sequences deposited in NCBI through BLAST, especially with the β subunit of PGA from the Alcaligenes faecalis bacterium¸ which is a region involved in the catalytic function of this protein. Besides, the identification of domains in the penicillin G acylase sequence of Mucor griseocyanus showed three conserved regions of this protein. The bioinformatic results support the identity of the gen as penicillin G acylase. This is the first report that involves sequencing and in silico analysis of Mucor griseocyanus strain gene encoding PGA.
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Penicillin Acylase from Streptomyces lavendulae and Aculeacin A Acylase from Actinoplanes utahensis: Two Versatile Enzymes as Useful Tools for Quorum Quenching Processes. Catalysts 2020. [DOI: 10.3390/catal10070730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many Gram-negative bacteria produce N-acyl-homoserine lactones (AHLs), quorum sensing (QS) molecules that can be enzymatically inactivated by quorum quenching (QQ) processes; this approach is considered an emerging antimicrobial alternative. In this study, kinetic parameters of several AHLs hydrolyzed by penicillin acylase from Streptomyces lavendulae (SlPA) and aculeacin A acylase from Actinoplanes utahensis (AuAAC) have been determined. Both enzymes catalyze efficiently the amide bond hydrolysis in AHLs with different acyl chain moieties (with or without 3-oxo modification) and exhibit a clear preference for AHLs with long acyl chains (C12-HSL > C14-HSL > C10-HSL > C8-HSL for SlPA, whereas C14-HSL > C12-HSL > C10-HSL > C8-HSL for AuAAC). Involvement of SlPA and AuAAC in QQ processes was demonstrated by Chromobacterium violaceum CV026-based bioassays and inhibition of biofilm formation by Pseudomonas aeruginosa, a process controlled by QS molecules, suggesting the application of these multifunctional enzymes as quorum quenching agents, this being the first time that quorum quenching activity was shown by an aculeacin A acylase. In addition, a phylogenetic study suggests that SlPA and AuAAC could be part of a new family of actinomycete acylases, with a preference for substrates with long aliphatic acyl chains, and likely involved in QQ processes.
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25
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Saha A, Oanca G, Mondal D, Warshel A. Exploring the Proteolysis Mechanism of the Proteasomes. J Phys Chem B 2020; 124:5626-5635. [PMID: 32498514 DOI: 10.1021/acs.jpcb.0c04435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The proteasome is a key protease in the eukaryotic cells which is responsible for various important cellular processes such as the control of the cell cycle, immune responses, protein homeostasis, inflammation, apoptosis, and the response to proteotoxic stress. Acting as a major molecular machine for protein degradation, proteasome first identifies damaged or obsolete regulatory proteins by attaching ubiquitin chains and subsequently utilizes conserved pore loops of the heterohexameric ring of AAA+ (ATPases associated with diverse cellular activities) to pull and mechanically unfold and translocate the misfolded protein to the active site for proteolysis. A detailed knowledge of the reaction mechanism for this proteasomal proteolysis is of central importance, both for fundamental understanding and for drug discovery. The present study investigates the mechanism of the proteolysis by the proteasome with full consideration of the protein's flexibility and its impact on the reaction free energy. Major attention is paid to the role of the protein electrostatics in determining the activation barriers. The reaction mechanism is studied by considering a small artificial fluorogenic peptide substrate (Suc-LLVY-AMC) and evaluating the activation barriers and reaction free energies for the acylation and deacylation steps, by using the empirical valence bond method. Our results shed light on the proteolysis mechanism and thus should be important for further studies of the proteasome action.
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Affiliation(s)
- Arjun Saha
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Gabriel Oanca
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Dibyendu Mondal
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave., Los Angeles, California 90089-1062, United States
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26
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Vogel J, Wakker-Havinga M, Setroikromo R, Quax WJ. Immobilized Acylase PvdQ Reduces Pseudomonas aeruginosa Biofilm Formation on PDMS Silicone. Front Chem 2020; 8:54. [PMID: 32117880 PMCID: PMC7012999 DOI: 10.3389/fchem.2020.00054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
The bacterial biofilm plays a key role in nosocomial infections, especially those related to medical devices in sustained contact with patients. The active dispersion of bacterial cells out of biofilms acts as a reservoir for infectious diseases. The formation of such biofilms is a highly complex process, which is coordinated by many regulatory mechanisms of the pathogen including quorum sensing (QS). Many bacteria coordinate the expression of key virulence factors dependent on their population density through QS. The inhibition of this system is called quorum quenching (QQ). Thus, preventing the development of biofilms is considered a promising approach to prevent the development of hard to treat infections. Enzymatic QQ is the concept of interfering with the QS system of bacteria outside the cell. PvdQ is an acylase with an N-terminal nucleophile (Ntn-hydrolase) that is a part of the pyoverdine gene cluster (pvd). It is able to cleave irreversibly the amide bond of long chain N-acyl homoserine lactones (AHL) rendering them inactive. Long chain AHLs are the main signaling molecule in the QS system of the gram-negative pathogen Pseudomonas aeruginosa PA01, which is known for surface-associated biofilms on indwelling catheters and is also the cause of catheter-associated urinary tract infections. Furthermore, PA01 is a well characterized pathogen with respect to QS as well as QQ. In this study, we immobilized the acylase PvdQ on polydimethylsiloxane silicone (PDMS), creating a surface with quorum quenching properties. The goal is to control infections by minimizing the colonization of indwelling medical devices such as urinary catheters or intravascular catheters. The enzyme activity was confirmed by testing the degradation of the main auto-inducer that mediates QS in P. aeruginosa. In this article we report for the first time a successful immobilization of the quorum quenching acylase PvdQ on PDMS silicone. We could show that immobilized PvdQ retained its activity after the coating procedure and showed a 6-fold reduction of the auto-inducer 3-oxo-C12 in a biosensor setup. Further we report significant reduction of a P. aeruginosa PA01 biofilm on a coated PDMS surface compared to the same untreated material.
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Affiliation(s)
- Jan Vogel
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
| | - Marijke Wakker-Havinga
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
| | - Rita Setroikromo
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology Department, University of Groningen, Groningen, Netherlands
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27
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Guisan JM, López-Gallego F, Bolivar JM, Rocha-Martín J, Fernandez-Lorente G. One-Point Covalent Immobilization of Enzymes on Glyoxyl Agarose with Minimal Physico-Chemical Modification: Immobilized "Native Enzymes". Methods Mol Biol 2020; 2100:83-92. [PMID: 31939116 DOI: 10.1007/978-1-0716-0215-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The immobilization of soluble enzymes inside the porous structure of a preexisting support is one of the most interesting techniques to prepare heterogeneous biocatalysts. The main cause of inactivation of these biocatalysts is the distortion of the tridimensional structure of the immobilized enzymes. In some cases, immobilization of enzymes on preexisting supports can be used in order to improve its functional properties: stabilization by multipoint covalent immobilization, hyper-activation, and stabilization of lipases by interfacial adsorption on hydrophobic supports, etc. In other cases, the properties of the enzyme can be modified by additional interactions of the enzyme surface with the support surface: hydrophobic or electrostatic interactions.In all cases, it would be very interesting to evaluate the intrinsic tridimensional stability of native industrial enzymes. Under drastic experimental conditions, soluble enzymes may undergo undesirable aggregations, and the tridimensional stability of one enzyme is more accurately evaluated by using immobilized native enzymes. That is, immobilized derivatives associated to a minimal chemical modification of the enzyme surface placed in the proximity of a fully hydrophilic and inert support surfaces. In this chapter, the immobilization of enzymes with minimal physicochemical modification on glyoxyl agarose supports is proposed. At pH 8.5, the unique reactive amino group on the enzyme surface is the N-terminus. At the end of the immobilization, mild borohydride reduction, the primary amino terminus is simply converted into a secondary amino group, with similar physical properties, and aldehyde groups on the supports are converted into fully inert hydroxyl groups. The preparation of immobilized derivatives of penicillin G acylase (PGA) with identical properties (activity and stability) that one of the soluble enzyme is reported: preparation of immobilized native PGA.
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Affiliation(s)
- Jose M Guisan
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC, Campus UAM, Madrid, Spain.
| | - Fernando López-Gallego
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC, Campus UAM, Madrid, Spain
- Departamento de Química Orgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC-Universidad de Zaragoza, Zaragoza, Spain
| | - Juan M Bolivar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Javier Rocha-Martín
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC, Campus UAM, Madrid, Spain
| | - Gloria Fernandez-Lorente
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP), CSIC, Campus UAM, Madrid, Spain
- Department of Biotechnology and Microbiology, Institute of Food Science Research (CIAL), CSIC-UAM, Campus UAM, Madrid, Spain
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SUZUKI H, FUKUYAMA K, KUMAGAI H. Bacterial γ-glutamyltranspeptidases, physiological function, structure, catalytic mechanism and application. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:440-469. [PMID: 33177298 PMCID: PMC7725658 DOI: 10.2183/pjab.96.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
γ-Glutamyltranspeptidase (GGT) has been widely used as a marker enzyme of hepatic and biliary diseases and relations between various diseases and its activity have been studied extensively. Nevertheless, several of its fundamental enzymatic characteristics had not been elucidated. We obtained homogeneous preparation of GGTs from bacteria, characterized them, and elucidated its physiological function that is common to mammalian cells, using GGT-deficient E. coli. Prior to GGT of all living organisms, we also identified catalytic nucleophile of E. coli GGT and revealed the post-translational processing mechanism for its maturation, and also its crystal structure was determined. The reaction intermediate was trapped and the structure-based reaction mechanism was presented. As for its application, using its transferase activity, we developed the enzymatic synthesis of various γ-glutamyl compounds that are promising in food, nutraceutical and medicinal industries. We found GGT of Bacillus subtilis is salt-tolerant and can be used as a glutaminase, which is important in food industry, to enhance umami of food, such as soy sauce and miso. We succeeded in converting bacterial GGT to glutaryl-7-aminocephalosporanic acid acylase, which is an important enzyme in cephem antibiotics production, by site-directed and random mutagenesis.
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Affiliation(s)
- Hideyuki SUZUKI
- Division of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
| | - Keiichi FUKUYAMA
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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Li K, Mohammed MAA, Zhou Y, Tu H, Zhang J, Liu C, Chen Z, Burns R, Hu D, Ruso JM, Tang Z, Liu Z. Recent progress in the development of immobilized penicillin G acylase for chemical and industrial applications: A mini‐review. POLYM ADVAN TECHNOL 2019. [DOI: 10.1002/pat.4791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ke Li
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Monier Alhadi Abdelrahman Mohammed
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Yongshan Zhou
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Hongyi Tu
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Jiachen Zhang
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Chunli Liu
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Zhenbin Chen
- State Key Laboratory of Gansu Advanced Non‐ferrous Metal MaterialsLanzhou University of Technology Lanzhou China
- School of Materials Science and EngineeringLanzhou University of Technology Lanzhou China
| | - Robert Burns
- Department of Physics and EngineeringFrostburg State University Frostburg Maryland
| | - Dongdong Hu
- State Key Laboratory of Chemical EngineeringEast China University of Science and Technology Shanghai China
| | - Juan M. Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied PhysicsUniversity of Santiago de Compostela Santiago de Compostela Spain
| | - Zhenghua Tang
- Guangzhou Key Laboratory for Surface Chemistry of Energy MaterialsNew Energy Research Institute School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre Guangzhou China
- Guangdong Engineering and Technology Research Center for Surface Chemistry of Energy MaterialsSchool of Environment and Energy South China University of Technology, Guangzhou Higher Education Mega Center Guangzhou China
| | - Zhen Liu
- Department of Physics and EngineeringFrostburg State University Frostburg Maryland
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30
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Hormigo D, López-Conejo MT, Serrano-Aguirre L, García-Martín A, Saborido A, de la Mata I, Arroyo M. Kinetically controlled acylation of 6-APA catalyzed by penicillin acylase from Streptomyces lavendulae: effect of reaction conditions in the enzymatic synthesis of penicillin V. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1652274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Daniel Hormigo
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
| | - María Teresa López-Conejo
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
| | - Lara Serrano-Aguirre
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
| | - Alberto García-Martín
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
| | - Ana Saborido
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel de la Mata
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Arroyo
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Enzyme Biotechnology Group, Universidad Complutense de Madrid, Madrid, Spain
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31
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Mayer J, Pippel J, Günther G, Müller C, Lauermann A, Knuuti T, Blankenfeldt W, Jahn D, Biedendieck R. Crystal structures and protein engineering of three different penicillin G acylases from Gram-positive bacteria with different thermostability. Appl Microbiol Biotechnol 2019; 103:7537-7552. [PMID: 31227867 DOI: 10.1007/s00253-019-09977-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/16/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
Abstract
Penicillin G acylase (PGA) catalyzes the hydrolysis of penicillin G to 6-aminopenicillanic acid and phenylacetic acid, which provides the precursor for most semisynthetic penicillins. Most applications rely on PGAs from Gram-negative bacteria. Here we describe the first three crystal structures for PGAs from Gram-positive Bacilli and their utilization in protein engineering experiments for the manipulation of their thermostability. PGAs from Bacillus megaterium (BmPGA, Tm = 56.0 °C), Bacillus thermotolerans (BtPGA, Tm = 64.5 °C), and Bacillus sp. FJAT-27231 (FJAT-PGA, Tm = 74.3 °C) were recombinantly produced with B. megaterium, secreted, purified to apparent heterogeneity, and crystallized. Structures with resolutions of 2.20 Å (BmPGA), 2.27 Å (BtPGA), and 1.36 Å (FJAT-PGA) were obtained. They revealed high overall similarity, reflecting the high identity of up to approx. 75%. Notably, the active center displays a deletion of more than ten residues with respect to PGAs from Gram-negatives. This enlarges the substrate binding site and may indicate a different substrate spectrum. Based on the structures, ten single-chain FJAT-PGAs carrying artificial linkers were produced. However, in all cases, complete linker cleavage was observed. While thermostability remained in the wild-type range, the enzymatic activity dropped between 30 and 60%. Furthermore, four hybrid PGAs carrying subunits from two different enzymes were successfully produced. Their thermostabilities mostly lay between the values of the two mother enzymes. For one PGA increased, enzyme activity was observed. Overall, the three novel PGA structures combined with initial protein engineering experiments provide the basis for establishment of new PGA-based biotechnological processes.
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Affiliation(s)
- Janine Mayer
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Jan Pippel
- HZI - Helmholtz Centre for Infection Research, Structure and Function of Proteins, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Gabriele Günther
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Carolin Müller
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Anna Lauermann
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Tobias Knuuti
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Wulf Blankenfeldt
- HZI - Helmholtz Centre for Infection Research, Structure and Function of Proteins, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute of Biotechnology, Biochemistry and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Rebekka Biedendieck
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany.
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32
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Reille-Seroussi M, Mayer SV, Dörner W, Lang K, Mootz HD. Expanding the genetic code with a lysine derivative bearing an enzymatically removable phenylacetyl group. Chem Commun (Camb) 2019; 55:4793-4796. [PMID: 30945708 DOI: 10.1039/c9cc00475k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the genetically encoded incorporation of phenylacetyl protected lysine (PacK) into proteins in Escherichia coli. This unnatural side-chain modification can be enzymatically removed using either penicillin G acylase (PGA) or, surprisingly, the sirtuin SrtN from Bacillus subtilis. Our approach expands the toolbox to reversibly control protein structure and function under very mild and non-denaturing conditions, as demonstrated by triggering the activity of the nonribosomal peptide synthetase GrsA.
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Affiliation(s)
- Marie Reille-Seroussi
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany.
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33
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Modeling and molecular dynamics indicate that snake venom phospholipase B-like enzymes are Ntn-hydrolases. Toxicon 2018; 153:106-113. [DOI: 10.1016/j.toxicon.2018.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/14/2018] [Accepted: 08/27/2018] [Indexed: 12/22/2022]
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34
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Sumida Y, Iwai S, Nishiya Y, Kumagai S, Yamada T, Azuma M. Characterization of d-succinylase from Cupriavidus sp. P4-10-C and its application in d-amino acid synthesis. J Biosci Bioeng 2018; 125:282-286. [DOI: 10.1016/j.jbiosc.2017.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
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35
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Structure and function of a highly active Bile Salt Hydrolase (BSH) from Enterococcus faecalis and post-translational processing of BSH enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:507-518. [PMID: 29325872 DOI: 10.1016/j.bbapap.2018.01.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/02/2017] [Accepted: 01/04/2018] [Indexed: 12/14/2022]
Abstract
Bile Salt Hydrolase (BSH), a member of Cholylglycine hydrolase family, catalyzes the de-conjugation of bile acids and is evolutionarily related to penicillin V acylase (PVA) that hydrolyses a different substrate such as penicillin V. We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2. The analysis of the substrate binding pocket showed reduced volume owing to altered loop conformations and increased hydrophobicity contributed by a higher ratio of hydrophobic to hydrophilic groups present. The aromatic residues F18, Y20 and F65 participate in substrate binding. Thus, their mutation affects enzyme activity. Docking and Molecular Dynamics simulation studies showed effective polar complementarity present for the three hydroxyl (-OH) groups of GCA substrate in the binding site contributing to higher substrate specificity and efficient catalysis. These are unique features characteristics of this BSH enzyme and thought to contribute to its higher activity and specificity towards bile salts as well as allosteric effects. Further, mechanism of autocatalytic processing of Cholylglycine Hydrolases by the excision of an N-terminal Pre-peptide was examined by inserting different N-terminal pre-peptides in EfBSH sequence. The results suggest that two serine residues next to nucleophile cysteine are essential for autocalytic processing to remove precursor peptide. Since pre-peptide is absent in EfBSH the mutation of these serines is tolerated. This suggests that an evolution-mediated subordination of the pre-peptide excision site resulted in loss of pre-peptide in EfBSH and other related Cholylglycine hydrolases.
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36
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Rosenbaum I, Avinery R, Harnoy AJ, Slor G, Tirosh E, Hananel U, Beck R, Amir RJ. Reversible Dimerization of Polymeric Amphiphiles Acts as a Molecular Switch of Enzymatic Degradability. Biomacromolecules 2017; 18:3457-3468. [DOI: 10.1021/acs.biomac.7b01150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ido Rosenbaum
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Ram Avinery
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
- School
of Physics and Astronomy, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Assaf J. Harnoy
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Gadi Slor
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Einat Tirosh
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Department
of Physical Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Uri Hananel
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Department
of Physical Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Roy Beck
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
- School
of Physics and Astronomy, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Roey J. Amir
- Department
of Organic Chemistry, School of Chemistry, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel
Aviv University Center for Nanoscience and Nanotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
- BLAVATNIK
CENTER for Drug Discovery, Tel-Aviv University, Tel-Aviv 6997801, Israel
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37
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Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides. Sci Rep 2017; 7:8946. [PMID: 28827579 PMCID: PMC5566955 DOI: 10.1038/s41598-017-09399-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/26/2017] [Indexed: 12/18/2022] Open
Abstract
Understanding the molecular mechanisms of bacterial antibiotic resistance will help prepare against further emergence of multi-drug resistant strains. MacQ is an enzyme responsible for the multi-drug resistance of Acidovorax sp. strain MR-S7. MacQ has acylase activity against both N-acylhomoserine lactones (AHLs), a class of signalling compounds involved in quorum sensing, and β-lactam antibiotics. Thus, MacQ is crucial as a quencher of quorum sensing as well as in conferring antibiotic resistance in Acidovorax. Here, we report the X-ray structures of MacQ in ligand-free and reaction product complexes. MacQ forms a 170-kDa capsule-shaped molecule via face-to-face interaction with two heterodimers consisting of an α-chain and a β-chain, generated by the self-cleaving activity of a precursor polypeptide. The electron density of the spacer polypeptide in the hollow of the molecule revealed the close orientation of the peptide-bond atoms of Val20SP-Gly21SP to the active-site, implying a role of the residues in substrate binding. In mutational analyses, uncleaved MacQ retained degradation activity against both AHLs and penicillin G. These results provide novel insights into the mechanism of self-cleaving maturation and enzymatic function of N-terminal nucleophile hydrolases.
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38
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Zhong G, Zhao Q, Zhang Q, Liu W. 4-alkyl-L-(Dehydro)proline biosynthesis in actinobacteria involves N-terminal nucleophile-hydrolase activity of γ-glutamyltranspeptidase homolog for C-C bond cleavage. Nat Commun 2017; 8:16109. [PMID: 28706296 PMCID: PMC5519988 DOI: 10.1038/ncomms16109] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 05/30/2017] [Indexed: 12/22/2022] Open
Abstract
γ-Glutamyltranspeptidases (γ-GTs), ubiquitous in glutathione metabolism for γ-glutamyl transfer/hydrolysis, are N-terminal nucleophile (Ntn)-hydrolase fold proteins that share an autoproteolytic process for self-activation. γ-GT homologues are widely present in Gram-positive actinobacteria where their Ntn-hydrolase activities, however, are not involved in glutathione metabolism. Herein, we demonstrate that the formation of 4-Alkyl-L-(dehydro)proline (ALDP) residues, the non-proteinogenic α-amino acids that serve as vital components of many bioactive metabolites found in actinobacteria, involves unprecedented Ntn-hydrolase activity of γ-GT homologue for C–C bond cleavage. The related enzymes share a key Thr residue, which acts as an internal nucleophile for protein hydrolysis and then as a newly released N-terminal nucleophile for carboxylate side-chain processing likely through the generation of an oxalyl-Thr enzyme intermediate. These findings provide mechanistic insights into the biosynthesis of various ALDP residues/associated natural products, highlight the versatile functions of Ntn-hydrolase fold proteins, and particularly generate interest in thus far less-appreciated γ-GT homologues in actinobacteria. γ-Glutamyltranspeptidases in gram-positive bacteria are not involved in glutathione metabolism, as their counterparts in eukaryotes and gram-negative bacteria. Here, the authors show that in Actinobacteria they catalyse the unusual cleavage of a C–C bond for the biosynthesis of non-proteinogenic amino acids.
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Affiliation(s)
- Guannan Zhong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qunfei Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,State Key Laboratory of Microbial Metabolism, School of Life Science &Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qinglin Zhang
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,State Key Laboratory of Microbial Metabolism, School of Life Science &Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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39
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Long SL, Gahan CGM, Joyce SA. Interactions between gut bacteria and bile in health and disease. Mol Aspects Med 2017; 56:54-65. [PMID: 28602676 DOI: 10.1016/j.mam.2017.06.002] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/26/2017] [Accepted: 06/07/2017] [Indexed: 01/18/2023]
Abstract
Bile acids are synthesized from cholesterol in the liver and released into the intestine to aid the digestion of dietary lipids. The host enzymes that contribute to bile acid synthesis in the liver and the regulatory pathways that influence the composition of the total bile acid pool in the host have been well established. In addition, the gut microbiota provides unique contributions to the diversity of bile acids in the bile acid pool. Gut microbial enzymes contribute significantly to bile acid metabolism through deconjugation and dehydroxylation reactions to generate unconjugated bile acids and secondary bile acids. These microbial enzymes (which include bile salt hydrolase (BSH) and bile acid-inducible (BAI) enzymes) are essential for bile acid homeostasis in the host and represent a vital contribution of the gut microbiome to host health. Perturbation of the gut microbiota in disease states may therefore significantly influence bile acid signatures in the host, especially in the context of gastrointestinal or systemic disease. Given that bile acids are ligands for host cell receptors (including the FXR, TGR5 and Vitamin D Receptor) alterations to microbial enzymes and associated changes to bile acid signatures have significant consequences for the host. In this review we examine the contribution of microbial enzymes to the process of bile acid metabolism in the host and discuss the implications for microbe-host signalling in the context of C. difficile infection, inflammatory bowel disease and other disease states.
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Affiliation(s)
- Sarah L Long
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland; School of Pharmacy, University College Cork, Cork, Ireland.
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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40
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Utari PD, Vogel J, Quax WJ. Deciphering Physiological Functions of AHL Quorum Quenching Acylases. Front Microbiol 2017; 8:1123. [PMID: 28674525 PMCID: PMC5474475 DOI: 10.3389/fmicb.2017.01123] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/01/2017] [Indexed: 11/13/2022] Open
Abstract
N-Acylhomoserine lactone (AHL)-acylase (also known as amidase or amidohydrolase) is a class of enzyme that belongs to the Ntn-hydrolase superfamily. As the name implies, AHL-acylases are capable of hydrolysing AHLs, the most studied signaling molecules for quorum sensing in Gram-negative bacteria. Enzymatic degradation of AHLs can be beneficial in attenuating bacterial virulence, which can be exploited as a novel approach to fight infection of human pathogens, phytopathogens or aquaculture-related contaminations. Numerous acylases from both prokaryotic and eukaryotic sources have been characterized and tested for the interference of quorum sensing-regulated functions. The existence of AHL-acylases in a multitude of organisms from various ecological niches, raises the question of what the physiological roles of AHL-acylases actually are. In this review, we attempt to bring together recent studies to extend our understanding of the biological functions of these enzymes in nature.
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Affiliation(s)
- Putri D Utari
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| | - Jan Vogel
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
| | - Wim J Quax
- Chemical and Pharmaceutical Biology Department, University of GroningenGroningen, Netherlands
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41
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Adediran SA, Pratt RF. Penicillin acylase and O-aryloxycarbonyl hydroxamates: Two acyl-enzymes, one leading to hydrolysis, the other to inactivation. Arch Biochem Biophys 2017; 614:65-71. [PMID: 28038956 DOI: 10.1016/j.abb.2016.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/27/2022]
Abstract
O-Aryloxycarbonyl hydroxamates have previously been shown to covalently inactivate serine/amine amidohydrolases such as class C β-lactamases and a N-terminal hydrolase, the proteasome. We report here reactions between O-aryloxycarbonyl hydroxamates and another N-terminal hydrolase, penicillin acylase. O-Aryloxycarbonyl hydroxamates, as non-symmetric carbonates, have two different leaving groups attached to the reactive central carbonyl group. We propose that these compounds can bind to the active site in either of two orientations and that either leaving group can be displaced from either orientation. In the present case we detected from kinetics experiments two distinct acyl-enzymes, one of which is subject to normal hydrolysis and the other to inactivation. Non-symmetric carbonates therefore can be very versatile enzyme inactivators.
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Affiliation(s)
- S A Adediran
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - R F Pratt
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA.
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Chand D, Avinash VS, Yadav Y, Pundle AV, Suresh CG, Ramasamy S. Molecular features of bile salt hydrolases and relevance in human health. Biochim Biophys Acta Gen Subj 2017; 1861:2981-2991. [DOI: 10.1016/j.bbagen.2016.09.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/20/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023]
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43
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Wei W, Monard G, Gauld J. Computational insights into substrate binding and catalytic mechanism of the glutaminase domain of glucosamine-6-phosphate synthase (GlmS). RSC Adv 2017. [DOI: 10.1039/c7ra04906d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanistic cysteinyl of GlmS can activate its thiol using its own α-amine without the need for a bridging water.
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Affiliation(s)
- Wanlei Wei
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Gerald Monard
- Université de Lorraine
- UMR 7565 SRSMC
- F-54506 Vandoeuvre-les-Nancy
- France
| | - James W. Gauld
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
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44
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Liu D, Chen Z, Long J, Zhao Y, Du X. Immobilization of Penicillin Acylase on Macroporous Adsorption Resin CLX1180 Carrier. ADVANCES IN POLYMER TECHNOLOGY 2016. [DOI: 10.1002/adv.21717] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Donglei Liu
- State Key Laboratory of Gansu Advanced Non-ferrous Metal Materials; Lanzhou University of Technology; Lanzhou 730050 Gansu China
- School of Material Science and Engineering; Lanzhou University of Technology; Lanzhou 730050 Gansu China
| | - Zhenbin Chen
- State Key Laboratory of Gansu Advanced Non-ferrous Metal Materials; Lanzhou University of Technology; Lanzhou 730050 Gansu China
- School of Material Science and Engineering; Lanzhou University of Technology; Lanzhou 730050 Gansu China
| | - Jiapeng Long
- State Key Laboratory of Gansu Advanced Non-ferrous Metal Materials; Lanzhou University of Technology; Lanzhou 730050 Gansu China
- School of Material Science and Engineering; Lanzhou University of Technology; Lanzhou 730050 Gansu China
| | - Yingyu Zhao
- State Key Laboratory of Gansu Advanced Non-ferrous Metal Materials; Lanzhou University of Technology; Lanzhou 730050 Gansu China
- School of Material Science and Engineering; Lanzhou University of Technology; Lanzhou 730050 Gansu China
| | - Xueyan Du
- State Key Laboratory of Gansu Advanced Non-ferrous Metal Materials; Lanzhou University of Technology; Lanzhou 730050 Gansu China
- School of Material Science and Engineering; Lanzhou University of Technology; Lanzhou 730050 Gansu China
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45
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Sumida Y, Iwai S, Nishiya Y, Kumagai S, Yamada T, Azuma M. Identification and Characterization ofD-Succinylase, and a Proposed Enzymatic Method forD-Amino Acid Synthesis. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Hicks KA, Ealick SE. Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway. Acta Crystallogr D Struct Biol 2016; 72:808-16. [PMID: 27303801 PMCID: PMC4908869 DOI: 10.1107/s2059798316007099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/26/2016] [Indexed: 11/10/2022] Open
Abstract
HpxW from the ubiquitous pathogen Klebsiella pneumoniae is involved in a novel uric acid degradation pathway downstream from the formation of oxalurate. Specifically, HpxW is an oxamate amidohydrolase which catalyzes the conversion of oxamate to oxalate and is a member of the Ntn-hydrolase superfamily. HpxW is autoprocessed from an inactive precursor to form a heterodimer, resulting in a 35.5 kDa α subunit and a 20 kDa β subunit. Here, the structure of HpxW is presented and the substrate complex is modeled. In addition, the steady-state kinetics of this enzyme and two active-site variants were characterized. These structural and biochemical studies provide further insight into this class of enzymes and allow a mechanism for catalysis consistent with other members of the Ntn-hydrolase superfamily to be proposed.
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Affiliation(s)
- Katherine A. Hicks
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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47
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Huang X, Xue J, Lin M, Zhu Y. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model. PLoS One 2016; 11:e0156559. [PMID: 27243223 PMCID: PMC4887040 DOI: 10.1371/journal.pone.0156559] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/16/2016] [Indexed: 11/24/2022] Open
Abstract
Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
| | - Jing Xue
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
| | - Min Lin
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P.R. China
- * E-mail:
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48
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Overexpression of penicillin V acylase from Streptomyces lavendulae and elucidation of its catalytic residues. Appl Environ Microbiol 2016; 81:1225-33. [PMID: 25501472 DOI: 10.1128/aem.02352-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pva gene from Streptomyces lavendulae ATCC 13664, encoding a novel penicillin V acylase (SlPVA), has been isolated and characterized. The gene encodes an inactive precursor protein containing a secretion signal peptide that is activated by two internal autoproteolytic cleavages that release a 25-amino-acid linker peptide and two large domains of 18.79 kDa (alpha-subunit) and 60.09 kDA (beta-subunit). Based on sequence alignments and the three-dimensional model of SlPVA, the enzyme contains a hydrophobicpocket involved in catalytic activity, including Serbeta1, Hisbeta23, Valbeta70, and Asnbeta272, which were confirmed by site-directed mutagenesis studies. The heterologous expression of pva in S. lividans led to the production of an extracellularly homogeneous heterodimeric enzyme at a 5-fold higher concentration (959 IU/liter) than in the original host and in a considerably shorter time. According to the catalytic properties of SlPVA, the enzyme must be classified as a new member of the Ntn-hydrolase superfamily, which belongs to a novel subfamily of acylases that recognize substrates with long hydrophobic acyl chains and have biotechnological applications in semisynthetic antifungal production.
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Avinash VS, Panigrahi P, Chand D, Pundle A, Suresh CG, Ramasamy S. Structural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity. J Struct Biol 2015; 193:85-94. [PMID: 26707624 DOI: 10.1016/j.jsb.2015.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 10/22/2022]
Abstract
Penicillin V acylases (PVA) catalyze the deacylation of the beta-lactam antibiotic phenoxymethylpenicillin (Pen V). They are members of the Ntn hydrolase family and possess an N-terminal cysteine as the main catalytic nucleophile residue. They form the evolutionarily related cholylglycine hydrolase (CGH) group which includes bile salt hydrolases (BSH) responsible for bile deconjugation. Even though a few PVA and BSH structures have been reported, no structure of a functional PVA from Gram-negative bacteria is available. Here, we report the crystal structure of a highly active PVA from Gram-negative Pectobacterium atrosepticum (PaPVA) at 2.5Å resolution. Structural comparison with PVAs from Gram-positive bacteria revealed that PaPVA had a distinctive tetrameric structure and active site organization. In addition, mutagenesis of key active site residues and biochemical characterization of the resultant variants elucidated the role of these residues in substrate binding and catalysis. The importance of residue Trp23 and Trp87 side chains in binding and correct positioning of Pen V by PVAs was confirmed using mutagenesis and substrate docking with a 15ns molecular dynamics simulation. These results establish the unique nature of Gram-negative CGHs and necessitate further research about their substrate spectrum.
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Affiliation(s)
- Vellore Sunder Avinash
- Biochemical Sciences Division, National Chemical Laboratory (CSIR-NCL), Pune 411008, India
| | - Priyabrata Panigrahi
- Biochemical Sciences Division, National Chemical Laboratory (CSIR-NCL), Pune 411008, India
| | - Deepak Chand
- Biochemical Sciences Division, National Chemical Laboratory (CSIR-NCL), Pune 411008, India
| | - Archana Pundle
- Biochemical Sciences Division, National Chemical Laboratory (CSIR-NCL), Pune 411008, India
| | | | - Sureshkumar Ramasamy
- Biochemical Sciences Division, National Chemical Laboratory (CSIR-NCL), Pune 411008, India.
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50
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Grulich M, Brezovský J, ŠtĿpánek V, Palyzová A, Kyslíková E, Kyslík P. Resolution of α/β-amino acids by enantioselective penicillin G acylase from Achromobacter sp . ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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