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Barozi V, Musyoka TM, Sheik Amamuddy O, Tastan Bishop Ö. Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric Mycobacterium tuberculosis KatG via Post-molecular Dynamics Analyses Including Combined Dynamic Residue Network Metrics. ACS OMEGA 2022; 7:13313-13332. [PMID: 35474779 PMCID: PMC9025985 DOI: 10.1021/acsomega.2c01036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/22/2022] [Indexed: 05/12/2023]
Abstract
Resistance mutations in Mycobacterium tuberculosis (Mtb) catalase peroxidase protein (KatG), an essential enzyme in isoniazid (INH) activation, reduce the sensitivity of Mtb to first-line drugs, hence presenting challenges in tuberculosis (TB) management. Thus, understanding the mutational imposed resistance mechanisms remains of utmost importance in the quest to reduce the TB burden. Herein, effects of 11 high confidence mutations in the KatG structure and residue network communication patterns were determined using extensive computational approaches. Combined traditional post-molecular dynamics analysis and comparative essential dynamics revealed that the mutant proteins have significant loop flexibility around the heme binding pocket and enhanced asymmetric protomer behavior with respect to wild-type (WT) protein. Heme contact analysis between WT and mutant proteins identified a reduction to no contact between heme and residue His270, a covalent bond vital for the heme-enabled KatG catalytic activity. Betweenness centrality calculations showed large hub ensembles with new hubs especially around the binding cavity and expanded to the dimerization domain via interface in the mutant systems, providing possible compensatory allosteric communication paths for the active site as a result of the mutations which may destabilize the heme binding pocket and the loops in its vicinity. Additionally, an interesting observation came from Eigencentrality hubs, most of which are located in the C-terminal domain, indicating relevance of the domain in the protease functionality. Overall, our results provide insight toward the mechanisms involved in KatG-INH resistance in addition to identifying key regions in the enzyme functionality, which can be used for future drug design.
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Affiliation(s)
- Victor Barozi
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
| | - Thommas Mutemi Musyoka
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
| | - Olivier Sheik Amamuddy
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
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Li G, Fan A, Peng G, Keyhani NO, Xin J, Cao Y, Xia Y. A bifunctional catalase-peroxidase,MakatG1, contributes to virulence ofMetarhizium acridumby overcoming oxidative stress on the host insect cuticle. Environ Microbiol 2017; 19:4365-4378. [DOI: 10.1111/1462-2920.13932] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 09/14/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Guohong Li
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Anni Fan
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Guoxiong Peng
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Nemat O. Keyhani
- School of Life Sciences; Chongqing University; Chongqing China
- Department of Microbiology and Cell Science; University of Florida; Gainesville FL USA
| | - Jiankang Xin
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Yueqing Cao
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
| | - Yuxian Xia
- School of Life Sciences; Chongqing University; Chongqing China
- Chongqing Engineering Research Center for Fungal Insecticides; Chongqing China
- Key Laboratory of Gene Function and Regulation Technologies under Chongqing Municipal Education Commission; Chongqing China
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Gasselhuber B, Graf MMH, Jakopitsch C, Zamocky M, Nicolussi A, Furtmüller PG, Oostenbrink C, Carpena X, Obinger C. Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase. Biochemistry 2016; 55:3528-41. [PMID: 27293030 PMCID: PMC4928148 DOI: 10.1021/acs.biochem.6b00436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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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.
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Affiliation(s)
- Bernhard Gasselhuber
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Michael M H Graf
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Marcel Zamocky
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria.,Institute of Molecular Biology, Slovak Academy of Sciences , Dubravska cesta 21, SK-84551 Bratislava, Slovakia
| | - Andrea Nicolussi
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute for Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
| | - Xavi Carpena
- Institut de Biologia Molecular (IBMB-CSIC) , Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences , Muthgasse 18, A-1190 Vienna, Austria
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Wang Y, Goodwin DC. Integral role of the I'-helix in the function of the "inactive" C-terminal domain of catalase-peroxidase (KatG). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:362-71. [PMID: 23084782 DOI: 10.1016/j.bbapap.2012.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 11/19/2022]
Abstract
Catalase-peroxidases (KatGs) have two peroxidase-like domains. The N-terminal domain contains the heme-dependent, bifunctional active site. Though the C-terminal domain lacks the ability to bind heme or directly catalyze any reaction, it has been proposed to serve as a platform to direct the folding of the N-terminal domain. Toward such a purpose, its I'-helix is highly conserved and appears at the interface between the two domains. Single and multiple substitution variants targeting highly conserved residues of the I'-helix were generated for intact KatG as well as the stand-alone C-terminal domain (KatG(C)). Single variants of intact KatG produced only subtle variations in spectroscopic and catalytic properties of the enzyme. However, the double and quadruple variants showed substantial increases in hexa-coordinate low-spin heme and diminished enzyme activity, similar to that observed for the N-terminal domain on its own (KatG(N)). The analogous variants of KatG(C) showed a much more profound loss of function as evaluated by their ability to return KatG(N) to its active conformation. All of the single variants showed a substantial decrease in the rate and extent of KatG(N) reactivation, but with two substitutions, KatG(C) completely lost its capacity for the reactivation of KatG(N). These results suggest that the I'-helix is central to direct structural adjustments in the adjacent N-terminal domain and supports the hypothesis that the C-terminal domain serves as a platform to direct N-terminal domain conformation and bifunctionality.
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Affiliation(s)
- Yu Wang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
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Zámocký M, García-Fernández Q, Gasselhuber B, Jakopitsch C, Furtmüller PG, Loewen PC, Fita I, Obinger C, Carpena X. High conformational stability of secreted eukaryotic catalase-peroxidases: answers from first crystal structure and unfolding studies. J Biol Chem 2012; 287:32254-62. [PMID: 22822072 PMCID: PMC3442556 DOI: 10.1074/jbc.m112.384271] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/03/2012] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidases (KatGs) are bifunctional heme enzymes widely spread in archaea, bacteria, and lower eukaryotes. Here we present the first crystal structure (1.55 Å resolution) of an eukaryotic KatG, the extracellular or secreted enzyme from the phytopathogenic fungus Magnaporthe grisea. The heme cavity of the homodimeric enzyme is similar to prokaryotic KatGs including the unique distal (+)Met-Tyr-Trp adduct (where the Trp is further modified by peroxidation) and its associated mobile arginine. The structure also revealed several conspicuous peculiarities that are fully conserved in all secreted eukaryotic KatGs. Peculiarities include the wrapping at the dimer interface of the N-terminal elongations from the two subunits and cysteine residues that cross-link the two subunits. Differential scanning calorimetry and temperature- and urea-mediated unfolding followed by UV-visible, circular dichroism, and fluorescence spectroscopy combined with site-directed mutagenesis demonstrated that secreted eukaryotic KatGs have a significantly higher conformational stability as well as a different unfolding pattern when compared with intracellular eukaryotic and prokaryotic catalase-peroxidases. We discuss these properties with respect to the structure as well as the postulated roles of this metalloenzyme in host-pathogen interactions.
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Affiliation(s)
- Marcel Zámocký
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
- the Laboratory of Molecular Microbiology, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Queralt García-Fernández
- the Institute for Research in Biomedicine (IRB Barcelona) and Institut de Biologia Molecular de Barcelona (IBMB) from Consell Superior d'Investigacions Científiques (CSIC), Parc Científic, 08028 Barcelona, Spain, and
| | - Bernhard Gasselhuber
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Peter C. Loewen
- the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ignacio Fita
- the Institute for Research in Biomedicine (IRB Barcelona) and Institut de Biologia Molecular de Barcelona (IBMB) from Consell Superior d'Investigacions Científiques (CSIC), Parc Científic, 08028 Barcelona, Spain, and
| | - Christian Obinger
- From the Department of Chemistry, Division of Biochemistry, BOKU, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Xavi Carpena
- the Institute for Research in Biomedicine (IRB Barcelona) and Institut de Biologia Molecular de Barcelona (IBMB) from Consell Superior d'Investigacions Científiques (CSIC), Parc Científic, 08028 Barcelona, Spain, and
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Zámocký M, Droghetti E, Bellei M, Gasselhuber B, Pabst M, Furtmüller PG, Battistuzzi G, Smulevich G, Obinger C. Eukaryotic extracellular catalase-peroxidase from Magnaporthe grisea - Biophysical/chemical characterization of the first representative from a novel phytopathogenic KatG group. Biochimie 2012; 94:673-83. [PMID: 21971530 PMCID: PMC3317519 DOI: 10.1016/j.biochi.2011.09.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 09/21/2011] [Indexed: 12/04/2022]
Abstract
All phytopathogenic fungi have two catalase-peroxidase paralogues located either intracellularly (KatG1) or extracellularly (KatG2). Here, for the first time a secreted bifunctional, homodimeric catalase-peroxidase (KatG2 from the rice blast fungus Magnaporthe grisea) has been produced heterologously with almost 100% heme occupancy and comprehensively investigated by using a broad set of methods including UV-Vis, ECD and resonance Raman spectroscopy (RR), thin-layer spectroelectrochemistry, mass spectrometry, steady-state & presteady-state spectroscopy. RR spectroscopy reveals that MagKatG2 shows a unique mixed-spin state, non-planar heme b, and a proximal histidine with pronounced imidazolate character. At pH 7.0 and 25 °C, the standard reduction potential E°' of the Fe(III)/Fe(II) couple for the high-spin native protein was found to fall in the range typical for the KatG family. Binding of cyanide was relatively slow at pH 7.0 and 25 °C and with a K(d) value significantly higher than for the intracellular counterpart. Demonstrated by mass spectrometry MagKatG2 has the typical Trp118-Tyr251-Met277 adduct that is essential for its predominantly catalase activity at the unique acidic pH optimum. In addition, MagKatG2 acts as a versatile peroxidase using both one- and two-electron donors. Based on these data, structure-function relationships of extracellular eukaryotic KatGs are discussed with respect to intracellular KatGs and possible role(s) in host-pathogen interaction.
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Key Words
- extracellular catalase–peroxidase
- peroxidases–catalase superfamily
- phytopathogen
- oxidative stress
- resonance raman spectroscopy
- reduction potential
- 5c, five-coordinated
- 6c, six-coordinated
- apx, ascorbate peroxidase
- arp, arthromyces ramosus peroxidase
- bp1, barley peroxidase type 1
- cai, codon adaptation index
- caps, 3-(cyclohexylamino)propane-1-sulfonic acid
- ccd, charge-coupled device
- ccp, cytochrome c peroxidase
- cip, coprinus cinereus peroxidase
- ct, charge transfer
- l-dopa, 3,4-dihydroxy-l-phenylalanine
- e°′, reduction potential, referred to the standard hydrogen electrode, measured at ph 7.0
- ecd, electronic cd
- esi, electrospray ionization
- ha, hydroxyapatite
- hgt, horizontal gene transfer
- hrp, horseradish peroxidase
- hs, high-spin
- katg, catalase–peroxidase
- iptg, isopropyl-β-thiogalactopyranoside
- katg1, intracellular eukaryotic catalase–peroxidase
- katg2, extracellular eukaryotic catalase–peroxidase
- lc, liquid chromatography
- lip, lignin peroxidase
- ls, low-spin
- magkatg2, catalase–peroxidase from magnaporthe grisea
- mcac, metal chelate affinity chromatography
- mcd, monochlorodimedone
- mops, 4-morpholinepropane sulfonic acid
- mnp, manganese peroxidase
- nj, neighbor-joining method
- ottle, optically transparent thin-layer electrochemistry
- qs, quantum mixed-spin
- rr, resonance raman
- rt-pcr, reverse-transcription pcr
- sbp, soybean peroxidase
- she, standard hydrogen electrode
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Affiliation(s)
- Marcel Zámocký
- Division of Biochemistry, Department of Chemistry, Vienna Institute of Biotechnology at BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
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