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Nandan A, Nampoothiri KM. Molecular advances in microbial aminopeptidases. BIORESOURCE TECHNOLOGY 2017; 245:1757-1765. [PMID: 28599921 DOI: 10.1016/j.biortech.2017.05.103] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/22/2023]
Abstract
Aminopeptidases are exopeptidases that catalyze the hydrolysis of amino acid residues from the N terminus of peptides and proteins. They are widely and diversely used for protein hydrolysis in industrial and research applications. They form a large enzyme family in microorganisms and most of the sequenced microbial genomes contain several aminopeptidase coding genes. Various approaches are being used to enhance the yield and desired properties of these enzymes to make it more suited for industrial applications. Novel aminopeptidases are being developed by site directed mutagenesis and recombinant DNA technology with improved substrate specificity and stability. This review focuses on its classification and recent advancements in the molecular studies pertaining to this enzyme.
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Affiliation(s)
- Arya Nandan
- CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India
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Gao X, Cui W, Tian Y, Zhou Z. Over-expression, secretion, biochemical characterisation, and structure analysis of Bacillus subtilis aminopeptidase. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:2810-2815. [PMID: 23426795 DOI: 10.1002/jsfa.6105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/21/2013] [Accepted: 02/20/2013] [Indexed: 06/01/2023]
Abstract
BACKGROUND Aminopeptidases have great application in the food industry. Current research on the expression of aminopeptidases mainly focuses on the Escherichia coli expression system. However, the application of recombinant E. coli in the food industry is restricted due to its pathogenicity and low secretory efficiency, which should be concerned in the industrial production of aminopeptidases. RESULTS The gene of aminopeptidase from Bacillus subtilis Zj016 (BSAP) was identified. Over-expression and secretion of BSAP were achieved in a B. subtilis expression system with the signal peptide of itself. The yield researched 52 ± 1.9 U mL(-1) , which was 18 times that of the wild-type microbe. The purified enzyme was stable at pH 7.5-9.0 and below 60°C, and was inhibited by several metal ions except appropriate Co(2+) . BSAP was most active toward p-nitroaniline derivatives of Leu, Arg and Lys. Homology modelling and structure analysis showed that there was a flexible protease-associated domain in the predicted structure of BSAP. CONCLUSIONS The study presented a simple procedure for over-expression and purification of BSAP. The substrate specificity and structure information were indicated based on the characterisation and homology modelling. This will be useful for further research of aminopeptidases not only from an academic standpoint but also from an applied point of view.
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Affiliation(s)
- Xinxing Gao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Ave., Wuxi, Jiangsu, 214122, China
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Gao X, Cui W, Ding N, Liu Z, Tian Y, Zhou Z. Structure-based approach to alter the substrate specificity of Bacillus subtilis aminopeptidase. Prion 2013; 7:328-34. [PMID: 23787698 DOI: 10.4161/pri.25147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aminopeptidases can selectively catalyze the cleavage of the N-terminal amino acid residues from peptides and proteins. Bacillus subtilis aminopeptidase (BSAP) is most active toward p-nitroanilides (pNAs) derivatives of Leu, Arg, and Lys. The BSAP with broad substrate specificity is expected to improve its application. Based on an analysis of the predicted structure of BSAP, four residues (Leu 370, Asn 385, Ile 387, and Val 396) located in the substrate binding region were selected for saturation mutagenesis. The hydrolytic activity toward different aminoacyl-pNAs of each mutant BSAP in the culture supernatant was measured. Although the mutations resulted in a decrease of hydrolytic activity toward Leu-pNA, N385L BSAP exhibited higher hydrolytic activities toward Lys-pNA (2.2-fold) and Ile-pNA (9.1-fold) than wild-type BSAP. Three mutant enzymes (I387A, I387C and I387S BSAPs) specially hydrolyzed Phe-pNA, which was undetectable in wild-type BSAP. Among these mutant BSAPs, N385L and I387A BSAPs were selected for further characterized and used for protein hydrolysis application. Both of N385L and I387A BSAPs showed higher hydrolysis efficiency than the wild-type BASP and a combination of the wild-type and N385L and I387A BSAPs exhibited the highest hydrolysis efficiency for protein hydrolysis. This study will greatly facilitate studies aimed on change the substrate specificity and our results obtained here should be useful for BSAP application in food industry.
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Affiliation(s)
- Xinxing Gao
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology, Jiangnan University; Wuxi, Jiangsu, PR China
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Taguchi H, Wakamatsu M, Aso K, Ono S, Shin T, Akamatsu T. A simple assay for 6-aminohexanoate-oligomer-hydrolase using N-(4-nitrophenyl)-6-aminohexanamide. J Biosci Bioeng 2012; 114:586-8. [PMID: 22867796 DOI: 10.1016/j.jbiosc.2012.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 07/06/2012] [Accepted: 07/10/2012] [Indexed: 11/30/2022]
Abstract
We synthesized N-(4-nitrophenyl)-6-aminohexanamide (AHpNA) and used it as a substrate in a kinetic study of 6-aminohexanoate-hydrolase (NylB), a nylon oligomer-hydrolyzing enzyme. NylBs derived from Arthrobacter sp. KI72 and Pseudomonas sp. NK87 hydrolyzed AHpNA as well as a 6-aminohexanoic acid dimer, a known substrate for NylB. The K(m) values of the NylB from Arthrobacter sp. KI72 and Pseudomonas sp. NK87 for AHpNA were 0.5 mM and 2.0 mM, respectively.
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Affiliation(s)
- Hisataka Taguchi
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan.
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Arima J, Kono M, Kita M, Mori N. A mutant leucine aminopeptidase from Streptomyces cinnamoneus with enhanced L-aspartyl L-amino acid methyl ester synthetic activity. Biotechnol Lett 2012; 34:1093-9. [PMID: 22354473 DOI: 10.1007/s10529-012-0877-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/08/2012] [Indexed: 11/25/2022]
Abstract
L-aspartyl L-amino acid methyl ester was synthesized using a mutant of a thermostable leucine aminopeptidase from Streptomyces cinnamoneus, D198 K SSAP, obtained in previously. A peptide of high-intensity sweetener, L-aspartyl-L-phenylalanine methyl ester, was selected as a model for demonstrating the synthesis of L-aspartyl L-amino acid methyl ester. The hydrolytic activities of D198 K SSAP toward L-aspartyl-L-phenylalanine and its methyl ester were, respectively, 74-fold and fourfold higher than those of wild type. Similarly, the initial rate of the enzyme for L-aspartyl-L-phenylalanine methyl ester synthesis was over fivefold higher than that of wild-type SSAP in 90% methanol (v/v) in a one-pot reaction. Furthermore, other L-aspartyl L-amino acid methyl esters were synthesized efficiently using D198 K SSAP. Results show that the substitution of Asp198 of SSAP with Lys is effective for synthesizing L-aspartyl L-amino acid methyl ester.
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Affiliation(s)
- Jiro Arima
- Department of Agricultural, Biological, and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori, Japan.
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Biochemical characterization of L-carnitine dehydrogenases from Rhizobium sp. and Xanthomonas translucens. Biosci Biotechnol Biochem 2010; 74:1237-42. [PMID: 20530902 DOI: 10.1271/bbb.100072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently, we obtained two L-carnitine dehydrogenases (CDHs) from soil isolates, Rhizobium sp. (Rs-CDH) and Xanthomonas translucens (Xt-CDH). The respective molecular masses of Rs-CDH and Xt-CDH were approximately 50 kDa and 37 kDa. In this study, the genes encoding both enzymes were cloned. Their primary structures exhibited high identities with those of 3-hydroxyacyl-CoA dehydrogenases. In addition, Rs-CDH had a 180-residue long extra sequence in its C-terminal region. Except for the initial 20 residues, the extra sequence exhibited similarity to thioesterase. The activity of Rs-CDH was affected only slightly by deletion of thioesterase domain, but it was eliminated by the deletion of the whole C-terminal extra sequence. A further deletion experiment indicated that the region of Ala330-Pro335 of Rs-CDH has important functions in catalytic activity. Moreover, based on the deletion experiment on Xt-CDH, the five-residue tail is considered to have a function similar to Ala330-Pro335 of Rs-CDH.
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Akioka M, Nakano H, Horikiri A, Tsujimoto Y, Matsui H, Shimizu T, Nakatsu T, Kato H, Watanabe K. Overexpression, purification, crystallization and preliminary X-ray crystallographic studies of a proline-specific aminopeptidase from Aneurinibacillus sp. strain AM-1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1266-8. [PMID: 17142913 PMCID: PMC2225360 DOI: 10.1107/s1744309106047543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 11/09/2006] [Indexed: 11/10/2022]
Abstract
To elucidate the structure and molecular mechanism of a characteristic proline-specific aminopeptidase produced by the thermophile Aneurinibacillus sp. strain AM-1, its gene was cloned and the recombinant protein was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 1.8 A resolution from the recombinant aminopeptidase crystal. The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 93.62, b = 68.20, c = 76.84 A. A complete data set was also obtained from crystals of SeMet-substituted aminopeptidase. Data in the resolution range 20-2.1 A from the MAD data set from the SeMet-substituted crystal were used for phase determination.
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Affiliation(s)
- Makoto Akioka
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Hiroaki Nakano
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Aya Horikiri
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Yoshiyuki Tsujimoto
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Hiroshi Matsui
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
| | - Tetsuya Shimizu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Toru Nakatsu
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Hiroaki Kato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo, Kyoto 606-8501, Japan
| | - Kunihiko Watanabe
- Department of Applied Biochemistry, Kyoto Prefectural University, Shimogamo, Sakyo, Kyoto 606-8522, Japan
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Arima J, Uesugi Y, Iwabuchi M, Hatanaka T. Change in substrate preference of Streptomyces aminopeptidase through modification of the environment around the substrate binding site. Appl Environ Microbiol 2006; 72:7962-7. [PMID: 17028223 PMCID: PMC1694256 DOI: 10.1128/aem.01460-06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We attempted to alter the substrate preference of aminopeptidase from Streptomyces septatus TH-2 (SSAP). Because Asp198 and Phe221 of SSAP are located in the substrate binding site, we screened 2,000 mutant enzymes with D198X/F221X mutations. By carrying out this examination, we obtained two enzymes; one specifically hydrolyzed an arginyl derivative, and the other specifically hydrolyzed a cystinyl derivative (65- and 12.5-fold higher k(cat) values for hydrolysis of p-nitroanilide derivatives than those of the wild type, respectively).
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Affiliation(s)
- Jiro Arima
- Research Institute for Biological Sciences (RIBS), Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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Arima J, Uesugi Y, Uraji M, Iwabuchi M, Hatanaka T. Dipeptide synthesis by an aminopeptidase from Streptomyces septatus TH-2 and its application to synthesis of biologically active peptides. Appl Environ Microbiol 2006; 72:4225-31. [PMID: 16751535 PMCID: PMC1489603 DOI: 10.1128/aem.00150-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dipeptide synthesis by aminopeptidase from Streptomyces septatus TH-2 (SSAP) was demonstrated using free amino acid as an acyl donor and aminoacyl methyl ester as an acyl acceptor in 98% methanol (MeOH). SSAP retained its activity after more than 100 h in 98% MeOH, and in the case of phenylalanyl-phenylalanine methyl ester synthesis, the enzyme reaction reached equilibrium when more than 50% of the free phenylalanine was converted to the product. In an investigation of the specificity of SSAP toward acyl donors and acyl acceptors, SSAP showed a broad specificity toward various free amino acids and aminoacyl methyl esters. Furthermore, we applied SSAP to the synthesis of several biologically active peptides, such as aspartyl-phenylalanine, alanyl-tyrosine, and valyl-tyrosine methyl esters.
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Affiliation(s)
- Jiro Arima
- Research Institute for Biological Sciences (RIBS), Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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Arima J, Uesugi Y, Uraji M, Yatsushiro S, Tsuboi S, Iwabuchi M, Hatanaka T. Modulation of Streptomyces Leucine Aminopeptidase by Calcium. J Biol Chem 2006; 281:5885-94. [PMID: 16407307 DOI: 10.1074/jbc.m509025200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Streptomyces griseus leucine aminopeptidase (SGAP), which has two zinc atoms in its active site, is clinically important as a model for understanding the structure and mechanism of action of other metallopeptidases. SGAP is a calcium-activated and calcium-stabilized enzyme, and its activation by calcium correlates with substrate specificity. In our previous study, we found a non-calcium-modulated leucine aminopeptidase secreted by Streptomyces septatus, the primary structure of which showed 71% identity with SGAP. In this study, we constructed chimeras of SGAP and S. septatus aminopeptidase by using an in vivo DNA shuffling system and several mutant enzymes by site-directed mutagenesis to identify the key residues in this modulation by calcium. We identified the key residues Asp-173 and Asp-174 of SGAP associated with both SGAP activation and stabilization by calcium. We also showed that the known calcium-binding site, which is composed of Asp-3, Ile-4, Asp-262, and Asp-266 of SGAP, only contributes to SGAP stabilization by calcium. Furthermore, we identified an important residue, Glu-196, that functions in cooperation with Asp-173, Asp-174, and calcium to increase the catalytic activity of SGAP.
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Affiliation(s)
- Jiro Arima
- Research Institute for Biological Sciences, Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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Arima J, Uesugi Y, Uraji M, Iwabuchi M, Hatanaka T. The role of Glu196 in the environment around the substrate binding site of leucine aminopeptidase fromStreptomyces griseus. FEBS Lett 2006; 580:912-7. [PMID: 16427629 DOI: 10.1016/j.febslet.2006.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 12/27/2005] [Accepted: 01/02/2006] [Indexed: 11/26/2022]
Abstract
To investigate the role of Glu196 of leucine aminopeptidase from Streptomyces griseus (SGAP) in SGAP activation by calcium and substrate specificity, we constructed E196X SGAP by saturation mutagenesis. Most mutations led to the abrogation of SGAP activation by calcium, and substitution with Lys led to a marked increase in activity toward Asp-p-nitroanilide (pNA) and a decrease in that toward Lys-pNA. A similar result was obtained from the investigation using non-calcium-activated enzyme from Streptomyces septatus (SSAP). These results indicate that Glu196 of SGAP is associated with the environment around the substrate binding site besides its role in SGAP activation by calcium.
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Affiliation(s)
- Jiro Arima
- Research Institute for Biological Sciences (RIBS), Okayama, Kaga-gun, Okayama 716-1241, Japan
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