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Structure determinants defining the specificity of papain-like cysteine proteases. Comput Struct Biotechnol J 2022; 20:6552-6569. [DOI: 10.1016/j.csbj.2022.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
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Silva NCM, De Sá LFR, Oliveira EAG, Costa MN, Ferreira ATS, Perales J, Fernandes KVS, Xavier-Filho J, Oliveira AEA. Albizia lebbeck Seed Coat Proteins Bind to Chitin and Act as a Defense against Cowpea Weevil Callosobruchus maculatus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3514-3522. [PMID: 27078512 DOI: 10.1021/acs.jafc.6b00549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The seed coat is an external tissue that participates in defense against insects. In some nonhost seeds, including Albizia lebbeck, the insect Callosobruchus maculatus dies during seed coat penetration. We investigated the toxicity of A. lebbeck seed coat proteins to C. maculatus. A chitin-binding protein fraction was isolated from seed coat, and mass spectrometry showed similarity to a C1 cysteine protease. By ELM program an N-glycosylation interaction motif was identified in this protein, and by molecular docking the potential to interact with N-acetylglucosamine (NAG) was shown. The chitin-binding protein fraction was toxic to C. maculatus and was present in larval midgut and feces but not able to hydrolyze larval gut proteins. It did not interfere, though, with the intestinal cell permeability. These results indicate that the toxicity mechanism of this seed coat fraction may be related to its binding to chitin, present in the larvae gut, disturbing nutrient absorption.
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Affiliation(s)
- Nadia C M Silva
- Laboratório de Quı́mica e Função de Proteı́nas e Peptı́deos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF , 28013602 Campos dos Goytacazes, RJ, Brazil
| | - Leonardo F R De Sá
- Laboratório de Quı́mica e Função de Proteı́nas e Peptı́deos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF , 28013602 Campos dos Goytacazes, RJ, Brazil
| | - Eduardo A G Oliveira
- Laboratório de Quı́mica e Função de Proteı́nas e Peptı́deos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF , 28013602 Campos dos Goytacazes, RJ, Brazil
| | - Monique N Costa
- Laboratório de Toxinologia, Fundação Oswaldo Cruz , Rio de Janeiro, FIOCRUZ-RJ, Brazil
| | - Andre T S Ferreira
- Laboratório de Toxinologia, Fundação Oswaldo Cruz , Rio de Janeiro, FIOCRUZ-RJ, Brazil
| | - Jonas Perales
- Laboratório de Toxinologia, Fundação Oswaldo Cruz , Rio de Janeiro, FIOCRUZ-RJ, Brazil
| | - Kátia V S Fernandes
- Laboratório de Quı́mica e Função de Proteı́nas e Peptı́deos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF , 28013602 Campos dos Goytacazes, RJ, Brazil
| | - Jose Xavier-Filho
- Laboratório de Quı́mica e Função de Proteı́nas e Peptı́deos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF , 28013602 Campos dos Goytacazes, RJ, Brazil
| | - Antonia E A Oliveira
- Laboratório de Quı́mica e Função de Proteı́nas e Peptı́deos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF , 28013602 Campos dos Goytacazes, RJ, Brazil
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Ghosh A, Raha S. Molecular and functional characterisation of a stress responsive cysteine protease, EhCP6 from Entamoeba histolytica. Protein Expr Purif 2015; 109:55-61. [DOI: 10.1016/j.pep.2015.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 11/30/2022]
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Enhancement of proteolytic activity of a thermostable papain-like protease by structure-based rational design. PLoS One 2013; 8:e62619. [PMID: 23671614 PMCID: PMC3643963 DOI: 10.1371/journal.pone.0062619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
Ervatamins (A, B and C) are papain-like cysteine proteases from the plant Ervatamia coronaria. Among Ervatamins, Ervatamin-C is a thermostable protease, but it shows lower catalytic efficiency. In contrast, Ervatamin-A which has a high amino acid sequence identity (∼90%) and structural homology (Cα rmsd 0.4 Å) with Ervatamin-C, has much higher catalytic efficiency (∼57 times). From the structural comparison of Ervatamin-A and -C, two residues Thr32 and Tyr67 in the catalytic cleft of Ervatamin-A have been identified whose contributions for higher activity of Ervatamin-A are established in our earlier studies. In this study, these two residues have been introduced in Ervatamin-C by site directed mutagenesis to enhance the catalytic efficiency of the thermostable protease. Two single mutants (S32T and A67Y) and one double mutant (S32T/A67Y) of Ervatamin-C have been generated and characterized. All the three mutants show ∼ 8 times higher catalytic efficiency (k cat/K m) than the wild-type. The thermostability of all the three mutant enzymes remained unchanged. The double mutant does not achieve the catalytic efficiency of the template enzyme Ervatamin-A. By modeling the structure of the double mutant and probing the role of active site residues by docking a substrate, the mechanistic insights of higher activity of the mutant protease have been addressed. The in-silico study demonstrates that the residues beyond the catalytic cleft also influence the substrate binding and positioning of the substrate at the catalytic centre, thus controlling the catalytic efficiency of an enzyme.
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Roy S, Choudhury D, Aich P, Dattagupta JK, Biswas S. The structure of a thermostable mutant of pro-papain reveals its activation mechanism. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1591-603. [PMID: 23151624 DOI: 10.1107/s0907444912038607] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/08/2012] [Indexed: 11/10/2022]
Abstract
Papain is the archetype of a broad class of cysteine proteases (clan C1A) that contain a pro-peptide in the zymogen form which is required for correct folding and spatio-temporal regulation of proteolytic activity in the initial stages after expression. This study reports the X-ray structure of the zymogen of a thermostable mutant of papain at 2.6 Å resolution. The overall structure, in particular that of the mature part of the protease, is similar to those of other members of the family. The structure provides an explanation for the molecular basis of the maintenance of latency of the proteolytic activity of the zymogen by its pro-segment at neutral pH. The structural analysis, together with biochemical and biophysical studies, demonstrated that the pro-segment of the zymogen undergoes a rearrangement in the form of a structural loosening at acidic pH which triggers the proteolytic activation cascade. This study further explains the bimolecular stepwise autocatalytic activation mechanism by limited proteolysis of the zymogen of papain at the molecular level. The possible factors responsible for the higher thermal stability of the papain mutant have also been analyzed.
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Affiliation(s)
- Sumana Roy
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, India
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Ramos-Martínez EM, Herrera-Ramírez AC, Badillo-Corona JA, Garibay-Orijel C, González-Rábade N, Oliver-Salvador MDC. Isolation of cDNA from Jacaratia mexicana encoding a mexicain-like cysteine protease gene. Gene 2012; 502:60-8. [DOI: 10.1016/j.gene.2012.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
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Nandi TK, Bairagya HR, Mukhopadhyay BP, Mallik P, Sukul D, Bera AK. Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid–base coupled mechanism in plant thiol protease. J Mol Model 2011; 18:2633-44. [DOI: 10.1007/s00894-011-1277-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 10/09/2011] [Indexed: 10/15/2022]
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Dutta S, Choudhury D, Dattagupta JK, Biswas S. C-Terminal extension of a plant cysteine protease modulates proteolytic activity through a partial inhibitory mechanism. FEBS J 2011; 278:3012-24. [PMID: 21707922 DOI: 10.1111/j.1742-4658.2011.08221.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The amino acid sequence of ervatamin-C, a thermostable cysteine protease from a tropical plant, revealed an additional 24-amino-acid extension at its C-terminus (CT). The role of this extension peptide in zymogen activation, catalytic activity, folding and stability of the protease is reported. For this study, we expressed two recombinant forms of the protease in Escherichia coli, one retaining the CT-extension and the other with it truncated. The enzyme with the extension shows autocatalytic zymogen activation at a higher pH of 8.0, whereas deletion of the extension results in a more active form of the enzyme. This CT-extension was not found to be cleaved during autocatalysis or by limited proteolysis by different external proteases. Molecular modeling and simulation studies revealed that the CT-extension blocks some of the substrate-binding unprimed subsites including the specificity-determining subsite (S2) of the enzyme and thereby partially occludes accessibility of the substrates to the active site, which also corroborates the experimental observations. The CT-extension in the model structure shows tight packing with the catalytic domain of the enzyme, mediated by strong hydrophobic and H-bond interactions, thus restricting accessibility of its cleavage sites to the protease itself or to the external proteases. Kinetic stability analyses (T(50) and t(1/2) ) and refolding experiments show similar thermal stability and refolding efficiency for both forms. These data suggest that the CT-extension has an inhibitory role in the proteolytic activity of ervatamin-C but does not have a major role either in stabilizing the enzyme or in its folding mechanism.
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Affiliation(s)
- Sruti Dutta
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
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Dutta S, Ghosh R, Dattagupta J, Biswas S. Heterologous expression of a thermostable plant cysteine protease in Escherichia coli both in soluble and insoluble forms. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.04.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Choudhury D, Biswas S, Roy S, Dattagupta JK. Improving thermostability of papain through structure-based protein engineering. Protein Eng Des Sel 2010; 23:457-67. [PMID: 20304972 DOI: 10.1093/protein/gzq016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Debi Choudhury
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
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Ghosh R, Chakraborty S, Chakrabarti C, Dattagupta JK, Biswas S. Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria. FEBS J 2007; 275:421-34. [PMID: 18167146 DOI: 10.1111/j.1742-4658.2007.06211.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple proteases of the same family are quite often present in the same species in biological systems. These multiple proteases, despite having high homology in their primary and tertiary structures, show deviations in properties such as stability, activity, and specificity. It is of interest, therefore, to compare the structures of these multiple proteases in a single species to identify the structural changes, if any, that may be responsible for such deviations. Ervatamin-A, ervatamin-B and ervatamin-C are three such papain-like cysteine proteases found in the latex of the tropical plant Ervatamia coronaria, and are known not only for their high stability over a wide range of temperature and pH, but also for variations in activity and specificity among themselves and among other members of the family. Here we report the crystal structures of ervatamin-A and ervatamin-C, complexed with an irreversible inhibitor 1-[l-N-(trans-epoxysuccinyl)leucyl]amino-4-guanidinobutane (E-64), together with enzyme kinetics and molecular dynamic simulation studies. A comparison of these results with the earlier structures helps in a correlation of the structural features with the corresponding functional properties. The specificity constants (k(cat)/K(m)) for the ervatamins indicate that all of these enzymes have specificity for a branched hydrophobic residue at the P2 position of the peptide substrates, with different degrees of efficiency. A single amino acid change, as compared to ervatamin-C, in the S2 pocket of ervatamin-A (Ala67-->Tyr) results in a 57-fold increase in its k(cat)/K(m) value for a substrate having a Val at the P2 position. Our studies indicate a higher enzymatic activity of ervatamin-A, which has been subsequently explained at the molecular level from the three-dimensional structure of the enzyme and in the context of its helix polarizibility and active site plasticity.
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Affiliation(s)
- Raka Ghosh
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
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