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Mori T, Masuzawa N, Kondo K, Nakanishi Y, Chida S, Uehara D, Katahira M, Takeda M. A heterodimeric hyaluronate lyase secreted by the activated sludge bacterium Haliscomenobacter hydrossis. Biosci Biotechnol Biochem 2023; 87:256-266. [PMID: 36535637 DOI: 10.1093/bbb/zbac207] [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: 09/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Haliscomenobacter hydrossis is a filamentous bacterium common in activated sludge. The bacterium was found to utilize hyaluronic acid, and hyaluronate lyase activity was detected in its culture. However, no hyaluronate lyase gene was found in the genome, suggesting the bacterium secretes a novel hyaluronate lyase. The purified enzyme exhibited two bands on SDS-PAGE and a single peak on gel filtration chromatography, suggesting a heterodimeric composition. N-terminal amino acid sequence and mass spectrometric analyses suggested that the subunits are molybdopterin-binding and [2Fe-2S]-binding subunits of a xanthine oxidase family protein. The presence of the cofactors was confirmed using spectrometric analysis. Oxidase activity was not detected, revealing that the enzyme is not an oxidase but a hyaluronate lyase. Nuclear magnetic resonance analysis of the enzymatic digest revealed that the enzyme breaks hyaluronic acid to 3-(4-deoxy-β-d-gluc-4-enuronosyl)-N-acetyl-d-glucosamine. As hyaluronate lyases (EC 4.2.2.1) are monomeric or trimeric, the enzyme is the first heterodimeric hyaluronate lyase.
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Affiliation(s)
- Tomomi Mori
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Nozomi Masuzawa
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Yuta Nakanishi
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Shun Chida
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Daiki Uehara
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Minoru Takeda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
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Sindelar M, Jilkova J, Kubala L, Velebny V, Turkova K. Hyaluronidases and hyaluronate lyases: From humans to bacteriophages. Colloids Surf B Biointerfaces 2021; 208:112095. [PMID: 34507069 DOI: 10.1016/j.colsurfb.2021.112095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/05/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Hyaluronan is a non-sulfated negatively-charged linear polymer distributed in most parts of the human body, where it is located around cells in the extracellular matrix of connective tissues and plays an essential role in the organization of tissue architecture. Moreover, hyaluronan is involved in many biological processes and used in many clinical, cosmetic, pharmaceutic, and biotechnological applications worldwide. As interest in hyaluronan applications increases, so does interest in hyaluronidases and hyaluronate lyases, as these enzymes play a major part in hyaluronan degradation. Many hyaluronidases and hyaluronate lyases produced by eukaryotic cells, bacteria, and bacteriophages have so far been described and annotated, and their ability to cleave hyaluronan has been experimentally proven. These enzymes belong to several carbohydrate-active enzyme families, share very low sequence identity, and differ in their cleaving mechanisms and in their structural and functional properties. This review presents a summary of annotated and characterized hyaluronidases and hyaluronate lyases isolated from different sources belonging to distinct protein families, with a main focus on the binding and catalytic residues of the discussed enzymes in the context of their biochemical properties. In addition, the application potential of individual groups of hyaluronidases and hyaluronate lyases is evaluated.
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Affiliation(s)
- Martin Sindelar
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jana Jilkova
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Lukas Kubala
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 65691, Brno, Czech Republic
| | - Vladimir Velebny
- Contipro a.s., Dolní Dobrouč 401, 56102, Dolní Dobrouč, Czech Republic
| | - Kristyna Turkova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 65691, Brno, Czech Republic.
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Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol 2017; 101:3103-3119. [PMID: 28337580 PMCID: PMC5380687 DOI: 10.1007/s00253-017-8224-6] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/23/2017] [Accepted: 03/04/2017] [Indexed: 11/24/2022]
Abstract
Bacteriophages are bacterial viruses that infect the host after successful receptor recognition and adsorption to the cell surface. The irreversible adherence followed by genome material ejection into host cell cytoplasm must be preceded by the passage of diverse carbohydrate barriers such as capsule polysaccharides (CPSs), O-polysaccharide chains of lipopolysaccharide (LPS) molecules, extracellular polysaccharides (EPSs) forming biofilm matrix, and peptidoglycan (PG) layers. For that purpose, bacteriophages are equipped with various virion-associated carbohydrate active enzymes, termed polysaccharide depolymerases and lysins, that recognize, bind, and degrade the polysaccharide compounds. We discuss the existing diversity in structural locations, variable architectures, enzymatic specificities, and evolutionary aspects of polysaccharide depolymerases and virion-associated lysins (VALs) and illustrate how these aspects can correlate with the host spectrum. In addition, we present methods that can be used for activity determination and the application potential of these enzymes as antibacterials, antivirulence agents, and diagnostic tools.
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Affiliation(s)
- Agnieszka Latka
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.,Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Grazyna Majkowska-Skrobek
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B. Bacteriophages and phage-derived proteins--application approaches. Curr Med Chem 2016; 22:1757-73. [PMID: 25666799 PMCID: PMC4468916 DOI: 10.2174/0929867322666150209152851] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Currently, the bacterial resistance, especially to most commonly used antibiotics has proved to be a severe therapeutic problem. Nosocomial and community-acquired infections are usually caused by multidrug resistant strains. Therefore, we are forced to develop an alternative or supportive treatment for successful cure of life-threatening infections. The idea of using natural bacterial pathogens such as bacteriophages is already well known. Many papers have been published proving the high antibacterial efficacy of lytic phages tested in animal models as well as in the clinic. Researchers have also investigated the application of non-lytic phages and temperate phages, with promising results. Moreover, the development of molecular biology and novel generation methods of sequencing has opened up new possibilities in the design of engineered phages and recombinant phage-derived proteins. Encouraging performances were noted especially for phage enzymes involved in the first step of viral infection responsible for bacterial envelope degradation, named depolymerases. There are at least five major groups of such enzymes – peptidoglycan hydrolases, endosialidases, endorhamnosidases, alginate lyases and hyaluronate lyases – that have application potential. There is also much interest in proteins encoded by lysis cassette genes (holins, endolysins, spanins) responsible for progeny release during the phage lytic cycle. In this review, we discuss several issues of phage and phage-derived protein application approaches in therapy, diagnostics and biotechnology in general.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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The C-terminus hot spot region helps in the fibril formation of bacteriophage-associated hyaluronate lyase (HylP2). Sci Rep 2015; 5:14429. [PMID: 26395159 PMCID: PMC4585773 DOI: 10.1038/srep14429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/21/2015] [Indexed: 11/09/2022] Open
Abstract
The bacteriophage encoded hyaluronate lyases (HylP and HylP2) degrade hyaluronan and other glycosaminoglycans. HylP2 forms a functional fibril under acidic conditions in which its N-terminus is proposed to form the fibrillar core, leading to nucleation and acceleration of fibril formation. Here we report the presence of a hot spot region (A144GVVVY149) towards the carboxy terminus of HylP2, essential for the acceleration of fibril formation. The 'hot spot' is observed to be inherently mutated for valines (A178AMVMY183) in case of HylP. The N- terminal swapped chimeras between these phage HLs ((N)HylP2(C)HylP and (N)HylP(C)HylP2) or HylP did not form fibrils at acidic pH. However, seeding of prefibrils of HylP2 recompensed nucleation and led to fibrillation in (N)HylP(C)HylP2. The V147A mutation in the 'hot spot' region abolished fibril formation in HylP2. The M179V and M181V double mutations in the 'hot spot' region of HylP led to fibrillation with the seeding of prefibrils. It appears that fibrillation in HylP2 even though is initiated by the N-terminus, is accelerated by the conserved 'hot spot' region in the C-terminus. A collagenous (Gly-X-Y)10 motif in the N-terminus and a mutated 'hot spot' region in the C-terminus of HylP affect fibrillar nucleation and acceleration respectively.
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Singh SK, Malhotra S, Akhtar MS. Characterization of hyaluronic acid specific hyaluronate lyase (HylP) from Streptococcus pyogenes. Biochimie 2014; 102:203-10. [DOI: 10.1016/j.biochi.2014.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 03/25/2014] [Indexed: 11/30/2022]
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Khan AH, Mohamed Omar YM, Kakar MA, Bangulzai N. Crystallization and preliminary crystallographic analysis of recombinant hyaluronate lyase from Streptococcus suis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:673-5. [PMID: 23722851 PMCID: PMC3668592 DOI: 10.1107/s1744309113012554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/07/2013] [Indexed: 11/10/2022]
Abstract
Hyaluronate lyase is an important surface enzyme of many streptococcal species. The enzyme degrades several biologically important connective tissue components, which facilitates the spreading of the bacteria throughout the host tissues and presumably provides energy and a carbon source for bacterial cells. Recombinant hyaluronate lyase was expressed in Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group P222(1), with unit-cell parameters a = 58.08, b = 101.32, c = 103.47 Å and one molecule in the asymmetric unit. Diffraction data were collected to 2.50 Å resolution.
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Affiliation(s)
- Abdul Hamid Khan
- Department of Microbiology, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Pakistan.
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B, Delattre AS, Lavigne R. Learning from bacteriophages - advantages and limitations of phage and phage-encoded protein applications. Curr Protein Pept Sci 2012; 13:699-722. [PMID: 23305359 PMCID: PMC3594737 DOI: 10.2174/138920312804871193] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/12/2012] [Accepted: 09/20/2012] [Indexed: 12/18/2022]
Abstract
The emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. The bacteria causing both hospital and community-acquired infections are most often multidrug resistant. In view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. The presented review focuses on the major characteristics of bacteriophages and phage-encoded proteins affecting their usefulness as antimicrobial agents. We discuss several issues such as mode of action, pharmacodynamics, pharmacokinetics, resistance and manufacturing aspects of bacteriophages and phage-encoded proteins application.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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El-Safory NS, Fazary AE, Lee CK. Hyaluronidases, a group of glycosidases: Current and future perspectives. Carbohydr Polym 2010. [DOI: 10.1016/j.carbpol.2010.02.047] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mishra V, Ali V, Nozaki T, Bhakuni V. Entamoeba histolytica Phosphoserine aminotransferase (EhPSAT): insights into the structure-function relationship. BMC Res Notes 2010; 3:52. [PMID: 20199659 PMCID: PMC2850911 DOI: 10.1186/1756-0500-3-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 03/03/2010] [Indexed: 11/29/2022] Open
Abstract
Background Presence of phosphorylated Serine biosynthesis pathway upstream to the de novo cysteine biosynthesis pathway makes PSAT a crucial enzyme. Besides this, phoshoserine produced by the enzyme can also be taken up directly by cysteine synthase as a substrate. PSAT is a PLP dependent enzyme where the cofactor serves as an epicenter for functional catalysis with the active site architecture playing crucial role in optimum function of the enzyme. Findings EhPSAT is a homodimer of molecular mass 86 kDa. To understand the structural modulations associated with pH dependent changes in functional activity of EhPSAT detailed biophysical studies were carried out. pH alterations had no significant effect on the secondary structure, cofactor orientation and oligomeric configuration of the enzyme however, pH dependent compaction in molecular dimensions was observed. Most interestingly, a direct correlation between pH induced modulation of functional activity and orientation of Trp 101 present in the active site of the enzyme was observed. Sodium halides nullified the pH induced global changes in the enzyme, however differential effect of these salts on the active site microenvironment and functional activity of the enzyme was observed. Conclusions The study unequivocally demonstrates that pH induced selective modification of active site microenvironment and not global change in structure or oligomeric status of the enzyme is responsible for the pH dependent change in enzymatic activity of PSAT.
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Affiliation(s)
- Vibhor Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil Palace, Council of scientific and industrial research (CSIR), Lucknow 226001, India.
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Polysaccharide binding sites in hyaluronate lyase - crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose. FEBS J 2009; 276:3392-402. [DOI: 10.1111/j.1742-4658.2009.07065.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mishra P, Bhakuni V. Self-assembly of bacteriophage-associated hyaluronate lyase (HYLP2) into an enzymatically active fibrillar film. J Biol Chem 2009; 284:5240-9. [PMID: 18849564 DOI: 10.1074/jbc.m806730200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The in vitro assembly of a soluble protein into its mature fibrillar form is usually accompanied by loss of its functional activity. Our study is the first demonstration of a natural enzyme (HylP2) retaining its enzymatic activity on conversion from pre-fibril to mature fibril and supports the contention that minor conformational changes in the native folded form of a protein can lead to the formation of a functional fibril. Hyaluronate lyase (HylP2) is a natural enzyme of bacteriophage 10403 of Streptococcus pyogenes. At pH 5.0, the enzyme undergoes partial unfolding localized in its N-terminal domain while the C-terminal domain maintains its folded trimeric conformation. This structural variant of HylP2 retains about 70% enzymatic activity with hyaluronan. It further self-assembles into a fibrillar film in vitro through solvent-exposed nonpolar surfaces and intermolecular beta-sheet formation by the beta-strands in the protein. Interestingly, the mature fibrillar film of HylP2 also retains about 60 and 20% enzymatic activity for hyaluronic acid and chondroitin sulfate, respectively. The possession of broad substrate specificity by the fibrillar form of HylP2 indicates that fluctuations in pH, which do not lead to loss of functionality of HylP2, might assist in bacterial pathogenesis. The formation of fibrillar film-like structure has been observed for the first time among the hyaluronidase enzymes. After acquiring this film-like structure in bacteriophage, HylP2 still retains its enzymatic activity, which establishes that these fibrils are a genuinely acquired protein fold/structure.
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Affiliation(s)
- Parul Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Lucknow 226001, India
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Cation induced differential effect on structural and functional properties of Mycobacterium tuberculosis alpha-isopropylmalate synthase. BMC STRUCTURAL BIOLOGY 2007; 7:39. [PMID: 17577419 PMCID: PMC1919377 DOI: 10.1186/1472-6807-7-39] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 06/19/2007] [Indexed: 11/10/2022]
Abstract
BACKGROUND Alpha-isopropylmalate synthase (MtalphaIPMS), an enzyme that catalyzes the first committed step of the leucine biosynthetic pathway of Mycobacterium tuberculosis is a potential drug target for the anti-tuberculosis drugs. Cations induce differential effect of activation and inhibition of MtalphaIPMS. To date no concrete mechanism for such an opposite effect of similarly charged cations on the functional activity of enzyme has been presented. RESULTS Effect of cations on the structure and function of the MtalphaIPMS has been studied in detail. The studies for the first time demonstrate that different cations interact specifically at different sites in the enzyme and modulate the enzyme structure differentially. The inhibitors Zn2+ and Cd2+ ions interact directly with the catalytic domain of the enzyme and induce unfolding/denaturation of the domain. The activator K+ also interacts with the catalytic TIM barrel domain however, it does not induce any significant effect on the enzyme structure. Studies with isolated catalytic TIM barrel domain showed that it can carry out the catalytic function on its own but probably requires the non-catalytic C-terminal domain for optimum functioning. An important observation was that divalent cations induce significant interaction between the regulatory and the catalytic domain of MtalphaIPMS thus inducing structural cooperativity in the enzyme. This divalent cation induced structural cooperativity might result in modulation of activity of the catalytic domain by regulatory domain. CONCLUSION The studies for the first time demonstrate that different cations bind at different sites in the enzyme leading to their differential effects on the structure and functional activity of the enzyme.
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