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41 results on '"Zamocky, Marcel"'

3. Stromal Ascorbate Peroxidase (OsAPX7) Modulates Drought Stress Tolerance in Rice (Oryza sativa)

Author

Jardim-Messeder, Douglas, primary, Caverzan, Andreia, additional, Balbinott, Natalia, additional, Menguer, Paloma K., additional, Paiva, Ana L. S., additional, Lemos, Moaciria, additional, Cunha, Juliana R., additional, Gaeta, Marcos L., additional, Costa, Miguel, additional, Zamocky, Marcel, additional, Saibo, Nelson J. M., additional, Silveira, Joaquim A. G., additional, Margis, Rogério, additional, and Margis-Pinheiro, Márcia, additional

Published
2023
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19. PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae

Author

Oliva, Michele, Theiler, Grégory, Zamocky, Marcel, Koua, Dominique, Margis-Pinheiro, Marcia, Passardi, Filippo, Dunand, Christophe, Oliva, Michele, Theiler, Grégory, Zamocky, Marcel, Koua, Dominique, Margis-Pinheiro, Marcia, Passardi, Filippo, and Dunand, Christophe

Abstract

Peroxidases are enzymes that are implicated in several biological processes and are detected in all living organisms. The increasing number of sequencing projects and the poor quality of annotation justified the creation of an efficient tool that was suitable for collecting and annotating the huge quantity of data. Started in 2004 to collect only class III peroxidases, PeroxiBase has undergone important updates since then and, currently, the majority of peroxidase sequences from all kingdoms of life is stored in the database. In addition, the web site (http://peroxibase.isb-sib.ch) provides a series of bioinformatics tools and facilities suitable for analysing these stored sequences. In particular, the high number of isoforms in each organism makes phylogenetic studies extremely useful to elucidate the complex evolution of these enzymes, not only within the plant kingdom but also between the different kingdoms. This paper provides a general overview of PeroxiBase, focusing on its tools and the stored data. The main goal is to give researchers some guidelines to extract classified and annotated sequences from the data base in a quick and easy way in order to perform alignments and phylogenetic analysis. The description of the database is accompanied by the updates we have recently carried out in order to improve its completeness and make it more user-friendly

Published
2017

20. Interaction with the redox cofactor MYW and functional role of a mobile arginine in eukaryotic catalase-peroxidase

Author

Gasselhuber, Bernhard, Graf, Michael M.H., Jakopitsch, Christa, Zamocky, Marcel, Nicolussi, Andrea, Furtmüller, Paul G., Oostenbrink, Chris, Carpena, Xavi, and Obinger, Christian

Subjects
bacteria
Abstract

Catalase-peroxidases (KatGs) are unique bifunctional heme peroxidases with an additional posttranslationally formed redox-active Met-Tyr-Trp cofactor that is essential for catalase activity. On the basis of studies of bacterial KatGs, controversial mechanisms of hydrogen peroxide oxidation were proposed. The recent discovery of eukaryotic KatGs with differing pH optima of catalase activity now allows us to scrutinize those postulated reaction mechanisms. In our study, secreted KatG from the fungus Magnaporthe grisea (MagKatG2) was used to analyze the role of a remote KatG-typical mobile arginine that was shown to interact with the Met-Tyr-Trp adduct in a pH-dependent manner in bacterial KatGs. Here we present crystal structures of MagKatG2 at pH 3.0, 5.5, and 7.0 and investigate the mobility of Arg461 by molecular dynamics simulation. Data suggest that at pH ≥4.5 Arg461 mostly interacts with the deprotonated adduct Tyr. Elimination of Arg461 by mutation to Ala slightly increases the thermal stability but does not alter the active site architecture or the kinetics of cyanide binding. However, the variant Arg461Ala lost the wild-type-typical optimum of catalase activity at pH 5.25 (k = 6450 s) but exhibits a broad plateau between pH 4.5 and 7.5 (k = 270 s at pH 5.5). Moreover, significant differences in the kinetics of interconversion of redox intermediates of wild-type and mutant protein mixed with either peroxyacetic acid or hydrogen peroxide are observed. These findings together with published data from bacterial KatGs allow us to propose a role of Arg461 in the HO oxidation reaction of KatG.

Published
2016

22. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation

Author

Gasselhuber, Bernhard, primary, Carpena, Xavi, additional, Graf, Michael M. H., additional, Pirker, Katharina F., additional, Nicolussi, Andrea, additional, Sündermann, Axel, additional, Hofbauer, Stefan, additional, Zamocky, Marcel, additional, Furtmüller, Paul G., additional, Jakopitsch, Christa, additional, Oostenbrink, Chris, additional, Fita, Ignacio, additional, and Obinger, Christian, additional

Published
2015
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23. A Stable Bacterial Peroxidase with Novel Halogenating Activity and an Autocatalytically Linked Heme Prosthetic Group

Author

Auer, Markus, primary, Gruber, Clemens, additional, Bellei, Marzia, additional, Pirker, Katharina F., additional, Zamocky, Marcel, additional, Kroiss, Daniela, additional, Teufer, Stefan A., additional, Hofbauer, Stefan, additional, Soudi, Monika, additional, Battistuzzi, Gianantonio, additional, Furtmüller, Paul G., additional, and Obinger, Christian, additional

Published
2013
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33. PeroxiBase: The peroxidase database

Author

Passardi, Filippo, primary, Theiler, Grégory, additional, Zamocky, Marcel, additional, Cosio, Claudia, additional, Rouhier, Nicolas, additional, Teixera, Felipe, additional, Margis-Pinheiro, Marcia, additional, Ioannidis, Vassilios, additional, Penel, Claude, additional, Falquet, Laurent, additional, and Dunand, Christophe, additional

Published
2007
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37. Continuous Enzymatic Regeneration of Electron Acceptors Used by Flavoenzymes: Cellobiose Dehydrogenase-Catalyzed Production of Lactobionic Acid as an Example.

Author

Ludwig, Roland, Ozga, Magdalena, Zamocky, Marcel, Peterbauer, Clemens, Kulbe, Klaus D., and Haltrich, Dietmar

Subjects
DEHYDROGENASES, LACTOSE, LACCASE, FLAVOPROTEINS, ENZYMES, BIOTECHNOLOGY, BIOTRANSFORMATION (Metabolism)
Abstract

An efficient enzymatic bioprocess is described in which lactose, an abundant renewable resource produced by the dairy industry, is completely and efficiently converted with a specific productivity of up to 32 g (kU h) -1 into lactobionic acid, without the formation of any by-products. The key biocatalyst of this new process is the fungal enzyme cellobiose dehydrogenase which oxidizes several β-1,4-linked disaccharides including lactose specifically at position C-1 of the reducing sugar moiety to the corresponding lactones. The electron acceptor employed in this reaction is continuously regenerated with the help of laccase, a H 2 O-producing, copper-containing oxidase, and therefore has to be added in low, catalytic amounts only. Redox mediators that were successfully employed in this novel process and hence are compatible with the laccase regeneration system include benzoquinone, ABTS, ferricyanide, or ferrocene, amongst others. Factors affecting operational stability of the biocatalysts employed in this process include the redox mediator used, the temperature, and importantly the volumetric gas flow necessary for maintaining the dissolved oxygen tension. Lactobionic acid is a mild and sweet tasting acid with excellent chelating properties. These useful characteristics have lead to a growing number of patents for diverse applications in the food, pharmaceutical and detergent industries. [ABSTRACT FROM AUTHOR]

Published
2004
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38. Structure of catalase-A from Saccharomyces cerevisiae11Edited by R. Huber

Author

MateMate´, Maria J., Zamocky, Marcel, Nykyri, Leena M., Herzog, Christian, Alzari, Pedro M., Betzel, Christian, Koller, Franz, and Fita, Ignacio

Abstract

The structure of the peroxisomal catalase A from the budding yeast Saccharomyces cerevisiae, with 515 residues per subunit, has been determined and refined to 2.4 A˚ resolution. The crystallographic agreement factors R and Rfree are 15.4 % and 19.8 %, respectively. A tetramer with accurate 222-molecular symmetry is located in the asymmetric unit of the crystal. The conformation of the central core of catalase A, about 300 residues, remains similar to the structure of catalases from distantly related organisms. In contrast, catalase A lacks a carboxy-terminal domain equivalent to that found in catalase from Penicillium vitalae, the only other fungal catalase structure available. Structural peculiarities related with the heme and NADP(H) binding pockets can be correlated with biochemical characteristics of the catalase A enzyme. The network of molecular cavities and channels, filled with solvent molecules, supports the existence of one major substrate entry and at least two possible alternative pathways to the heme active site. The structure of the variant protein Val111Ala, also determined by X-ray crystallography at 2.8 A˚ resolution, shows a few, well-localized, differences with respect to the wild-type enzyme. These differences, that include the widening of the entry channel in its narrowest point, provide an explanation for both the increased peroxidatic activity and the reduced catalatic activity of this mutant.

Published
1999
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39. PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae

Author

Oliva, Michele, Theiler, Grégory, Zamocky, Marcel, Koua, Dominique, Margis-Pinheiro, Marcia, Passardi, Filippo, Dunand, Christophe, Oliva, Michele, Theiler, Grégory, Zamocky, Marcel, Koua, Dominique, Margis-Pinheiro, Marcia, Passardi, Filippo, and Dunand, Christophe

Abstract

Peroxidases are enzymes that are implicated in several biological processes and are detected in all living organisms. The increasing number of sequencing projects and the poor quality of annotation justified the creation of an efficient tool that was suitable for collecting and annotating the huge quantity of data. Started in 2004 to collect only class III peroxidases, PeroxiBase has undergone important updates since then and, currently, the majority of peroxidase sequences from all kingdoms of life is stored in the database. In addition, the web site (http://peroxibase.isb-sib.ch) provides a series of bioinformatics tools and facilities suitable for analysing these stored sequences. In particular, the high number of isoforms in each organism makes phylogenetic studies extremely useful to elucidate the complex evolution of these enzymes, not only within the plant kingdom but also between the different kingdoms. This paper provides a general overview of PeroxiBase, focusing on its tools and the stored data. The main goal is to give researchers some guidelines to extract classified and annotated sequences from the data base in a quick and easy way in order to perform alignments and phylogenetic analysis. The description of the database is accompanied by the updates we have recently carried out in order to improve its completeness and make it more user-friendly

40. A new type strain of Pseudomonas putida NM-CH-I15-I isolated from a nickel-contaminated soil in southwest Slovakia harbouring the czcA-NM15I resistance determinant.

Author

Mihalikova N, Harichova J, Zamocky M, Kamlarova A, and Ferianc P

Subjects
Bacterial Typing Techniques, DNA, Bacterial genetics, Pseudomonas putida isolation & purification, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Slovakia, Soil Pollutants, Nickel, Phylogeny, Pseudomonas putida classification, Soil Microbiology
Abstract

A soil bacterium MR-CH-I15-I was on the base of phylogenetic analysis of almost the whole (1,492 bp) 16S rRNA sequence and sequences of selected 9 marker genes identified as Pseudomonas putida strain NM-CH-I15-I. The bacterium exhibited typical morphological features and biochemical properties for this species, the highest resistance to nickel and copper and multidrug resistance to different antibiotic groups. In addition, the whole czcA-NM15I heavy-metal resistance gene sequence (3,126 bp, 1,042 amino acids, MW 112, 138 Da) was obtained and on the base of phylogenetic analysis was assigned to CzcA protein from Pseudomonas reidholzensis with 93% similarity. This gene was significantly induced mainly by the addition of zinc, cadmium and cobalt and in a lesser extent of nickel. Furthermore, an increased expression of the CzcA-NM15I protein was confirmed by immunoblot analysis after heterologous expression of the czcA-NM15I synthetic variant gene in E. coli BL21 (DE3). Finally, the location of amino acids (R83, R673, D402, D408, D619, E415, E568) in the homology model of the CzcA-NM15I protein suggested that these amino acids may play an important role in the transport of cations such as cobalt, zinc or cadmium. This soil bacterium can represent a new type strain of P. putida NM-CH-I15-I.

Published
2020
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41. Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase.

Author

Gasselhuber B, Graf MM, Jakopitsch C, Zamocky M, Nicolussi A, Furtmüller PG, Oostenbrink C, Carpena X, and Obinger C

Subjects
Arginine genetics, Bacterial Proteins chemistry, Bacterial Proteins genetics, Calorimetry, Differential Scanning, Catalytic Domain, Circular Dichroism, Crystallography, X-Ray, Hydrogen Peroxide chemistry, Kinetics, Molecular Dynamics Simulation, Mutagenesis, Site-Directed, Mutation genetics, Oxidants metabolism, Oxidation-Reduction, Peroxidases chemistry, Peroxidases genetics, Arginine chemistry, Bacterial Proteins metabolism, Hydrogen Peroxide metabolism, Magnaporthe enzymology, Peroxidases metabolism
Abstract

Catalase-peroxidases (KatGs) are unique bifunctional heme peroxidases with an additional posttranslationally formed redox-active Met-Tyr-Trp cofactor that is essential for catalase activity. On the basis of studies of bacterial KatGs, controversial mechanisms of hydrogen peroxide oxidation were proposed. The recent discovery of eukaryotic KatGs with differing pH optima of catalase activity now allows us to scrutinize those postulated reaction mechanisms. In our study, secreted KatG from the fungus Magnaporthe grisea (MagKatG2) was used to analyze the role of a remote KatG-typical mobile arginine that was shown to interact with the Met-Tyr-Trp adduct in a pH-dependent manner in bacterial KatGs. Here we present crystal structures of MagKatG2 at pH 3.0, 5.5, and 7.0 and investigate the mobility of Arg461 by molecular dynamics simulation. Data suggest that at pH ≥4.5 Arg461 mostly interacts with the deprotonated adduct Tyr. Elimination of Arg461 by mutation to Ala slightly increases the thermal stability but does not alter the active site architecture or the kinetics of cyanide binding. However, the variant Arg461Ala lost the wild-type-typical optimum of catalase activity at pH 5.25 (kcat = 6450 s(-1)) but exhibits a broad plateau between pH 4.5 and 7.5 (kcat = 270 s(-1) at pH 5.5). Moreover, significant differences in the kinetics of interconversion of redox intermediates of wild-type and mutant protein mixed with either peroxyacetic acid or hydrogen peroxide are observed. These findings together with published data from bacterial KatGs allow us to propose a role of Arg461 in the H2O2 oxidation reaction of KatG.

Published
2016
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