1
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Zhao G, Wang W, Zheng L, Chen L, Duan G, Chang R, Chen Z, Zhang S, Dai M, Yang G. Catalase-peroxidase StKatG is a bacterial manganese oxidase from endophytic Salinicola tamaricis. Int J Biol Macromol 2022; 224:281-291. [DOI: 10.1016/j.ijbiomac.2022.10.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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2
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Tastan Bishop Ö, Mutemi Musyoka T, Barozi V. Allostery and missense mutations as intermittently linked promising aspects of modern computational drug discovery. J Mol Biol 2022; 434:167610. [DOI: 10.1016/j.jmb.2022.167610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
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3
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Püschmann J, Mahor D, de Geus DC, Strampraad MJF, Srour B, Hagen WR, Todorovic S, Hagedoorn PL. Unique Biradical Intermediate in the Mechanism of the Heme Enzyme Chlorite Dismutase. ACS Catal 2021; 11:14533-14544. [PMID: 34888122 PMCID: PMC8650003 DOI: 10.1021/acscatal.1c03432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/04/2021] [Indexed: 11/30/2022]
Abstract
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The heme enzyme chlorite
dismutase (Cld) catalyzes O–O bond
formation as part of the conversion of the toxic chlorite (ClO2–) to chloride (Cl–) and
molecular oxygen (O2). Enzymatic O–O bond formation
is rare in nature, and therefore, the reaction mechanism of Cld is
of great interest. Microsecond timescale pre-steady-state kinetic
experiments employing Cld from Azospira oryzae (AoCld), the natural substrate chlorite, and the
model substrate peracetic acid (PAA) reveal the formation of distinct
intermediates. AoCld forms a complex with PAA rapidly,
which is cleaved heterolytically to yield Compound I, which is sequentially
converted to Compound II. In the presence of chlorite, AoCld forms an initial intermediate with spectroscopic characteristics
of a 6-coordinate high-spin ferric substrate adduct, which subsequently
transforms at kobs = 2–5 ×
104 s–1 to an intermediate 5-coordinated
high-spin ferric species. Microsecond-timescale freeze-hyperquench
experiments uncovered the presence of a transient low-spin ferric
species and a triplet species attributed to two weakly coupled amino
acid cation radicals. The intermediates of the chlorite reaction were
not observed with the model substrate PAA. These findings demonstrate
the nature of physiologically relevant catalytic intermediates and
show that the commonly used model substrate may not behave as expected,
which demands a revision of the currently proposed mechanism of Clds.
The transient triplet-state biradical species that we designate as
Compound T is, to the best of our knowledge, unique in heme enzymology.
The results highlight electron paramagnetic resonance spectroscopic
evidence for transient intermediate formation during the reaction
of AoCld with its natural substrate chlorite. In
the proposed mechanism, the heme iron remains ferric throughout the
catalytic cycle, which may minimize the heme moiety’s reorganization
and thereby maximize the enzyme’s catalytic efficiency.
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Affiliation(s)
- Julia Püschmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Durga Mahor
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniël C. de Geus
- Janssen Vaccines & Prevention, Archimedesweg 4-6, 2333 CN Leiden, The Netherlands
| | - Marc J. F. Strampraad
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Batoul Srour
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wilfred R. Hagen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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4
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Shrestha R, Jia K, Khadka S, Eltis LD, Li P. Mechanistic Insights into DyPB from Rhodococcus jostii RHA1 Via Kinetic Characterization. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Samiksha Khadka
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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5
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Munir A, Wilson MT, Hardwick SW, Chirgadze DY, Worrall JAR, Blundell TL, Chaplin AK. Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis. Structure 2021; 29:899-912.e4. [PMID: 33444527 PMCID: PMC8355310 DOI: 10.1016/j.str.2020.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/27/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022]
Abstract
Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance. A cryo-EM structure to 2.7 Å resolution of M. tuberculosis KatG with isoniazid Cryo-EM is able to visualize multiple dynamic binding modes of isoniazid to KatG Structural disorder in isoniazid resistance mutations is observed Structural disorder of the resistance mutations results in the lack of heme retention
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Affiliation(s)
- Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Steven W Hardwick
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Dimitri Y Chirgadze
- CryoEM Facility, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
| | - Amanda K Chaplin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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6
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Lin YW. Structure and function of heme proteins regulated by diverse post-translational modifications. Arch Biochem Biophys 2018; 641:1-30. [DOI: 10.1016/j.abb.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 01/08/2023]
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7
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Njuma OJ, Davis I, Ndontsa EN, Krewall JR, Liu A, Goodwin DC. Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron hole-hopping within the enzyme. J Biol Chem 2017; 292:18408-18421. [PMID: 28972181 DOI: 10.1074/jbc.m117.791202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/22/2017] [Indexed: 11/06/2022] Open
Abstract
KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H2O2-induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H2O2 to O2 and H2O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H2O2 disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting (i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H2O2 Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates.
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Affiliation(s)
- Olive J Njuma
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Ian Davis
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Elizabeth N Ndontsa
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Jessica R Krewall
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312
| | - Aimin Liu
- the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249-0698, and
| | - Douglas C Goodwin
- From the Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312,
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8
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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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9
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Gasselhuber B, Carpena X, Graf MMH, Pirker KF, Nicolussi A, Sündermann A, Hofbauer S, Zamocky M, Furtmüller PG, Jakopitsch C, Oostenbrink C, Fita I, Obinger C. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation. Biochemistry 2015; 54:5425-38. [DOI: 10.1021/acs.biochem.5b00831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bernhard Gasselhuber
- Department
of Chemistry, Division of Biochemistry, 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
| | - 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
| | - Katharina F. Pirker
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Nicolussi
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Axel Sündermann
- 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
| | - Stefan Hofbauer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Biocenter 5, A-1030 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
| | - Paul G. Furtmüller
- Department
of Chemistry, Division of Biochemistry, 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
| | - 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
| | - Ignacio Fita
- 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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10
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Kruft BI, Magliozzo RS, Jarzęcki AA. Density Functional Theory Insights into the Role of the Methionine–Tyrosine–Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate. J Phys Chem A 2015; 119:6850-66. [DOI: 10.1021/jp511358p] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bonnie I. Kruft
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Andrzej A. Jarzęcki
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
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11
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Kudalkar SN, Njuma OJ, Li Y, Muldowney M, Fuanta NR, Goodwin DC. A role for catalase-peroxidase large loop 2 revealed by deletion mutagenesis: control of active site water and ferric enzyme reactivity. Biochemistry 2015; 54:1648-62. [PMID: 25674665 DOI: 10.1021/bi501221a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalase-peroxidases (KatGs), the only catalase-active members of their superfamily, all possess a 35-residue interhelical loop called large loop 2 (LL2). It is essential for catalase activity, but little is known about its contribution to KatG function. LL2 shows weak sequence conservation; however, its length is nearly identical across KatGs, and its apex invariably makes contact with the KatG-unique C-terminal domain. We used site-directed and deletion mutagenesis to interrogate the role of LL2 and its interaction with the C-terminal domain in KatG structure and catalysis. Single and double substitutions of the LL2 apex had little impact on the active site heme [by magnetic circular dichroism or electron paramagnetic resonance (EPR)] and activity (catalase or peroxidase). Conversely, deletion of a single amino acid from the LL2 apex reduced catalase activity by 80%. Deletion of two or more apex amino acids or all of LL2 diminished catalase activity by 300-fold. Peroxide-dependent but not electron donor-dependent kcat/KM values for deletion variant peroxidase activity were reduced 20-200-fold, and kon for cyanide binding diminished by 3 orders of magnitude. EPR spectra for deletion variants were all consistent with an increase in the level of pentacoordinate high-spin heme at the expense of hexacoordinate high-spin states. Together, these data suggest a shift in the distribution of active site waters, altering the reactivity of the ferric state, toward, among other things, compound I formation. These results identify the importance of LL2 length conservation for maintaining an intersubunit interaction that is essential for an active site water distribution that facilitates KatG catalytic activity.
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Affiliation(s)
- Shalley N Kudalkar
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
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12
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Zhao X, Hersleth HP, Zhu J, Andersson KK, Magliozzo RS. Access channel residues Ser315 and Asp137 in Mycobacterium tuberculosis catalase-peroxidase (KatG) control peroxidatic activation of the pro-drug isoniazid. Chem Commun (Camb) 2014; 49:11650-2. [PMID: 24185282 DOI: 10.1039/c3cc47022a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxidatic activation of the anti-tuberculosis pro-drug isoniazid by Mycobacterium tuberculosis catalase-peroxidase (KatG) is regulated by gating residues of a heme access channel. The steric restriction at the bottleneck of this channel is alleviated by replacement of residue Asp137 with Ser, according to crystallographic and kinetic studies.
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Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College and The Graduate Center of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA.
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13
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Njuma OJ, Ndontsa EN, Goodwin DC. Catalase in peroxidase clothing: Interdependent cooperation of two cofactors in the catalytic versatility of KatG. Arch Biochem Biophys 2013; 544:27-39. [PMID: 24280274 DOI: 10.1016/j.abb.2013.11.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/11/2013] [Accepted: 11/15/2013] [Indexed: 11/26/2022]
Abstract
Catalase-peroxidase (KatG) is found in eubacteria, archaea, and lower eukaryotae. The enzyme from Mycobacterium tuberculosis has received the greatest attention because of its role in activation of the antitubercular pro-drug isoniazid, and the high frequency with which drug resistance stems from mutations to the katG gene. Generally, the catalase activity of KatGs is striking. It rivals that of typical catalases, enzymes with which KatGs share no structural similarity. Instead, catalatic turnover is accomplished with an active site that bears a strong resemblance to a typical peroxidase (e.g., cytochrome c peroxidase). Yet, KatG is the only member of its superfamily with such capability. It does so using two mutually dependent cofactors: a heme and an entirely unique Met-Tyr-Trp (MYW) covalent adduct. Heme is required to generate the MYW cofactor. The MYW cofactor allows KatG to leverage heme intermediates toward a unique mechanism for H2O2 oxidation. This review evaluates the range of intermediates identified and their connection to the diverse catalytic processes KatG facilitates, including mechanisms of isoniazid activation.
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Affiliation(s)
- Olive J Njuma
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
| | - Elizabeth N Ndontsa
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
| | - Douglas C Goodwin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA.
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14
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Abstract
Methylamine dehydrogenase (MADH) requires the cofactor tryptophan tryptophylquinone (TTQ) for activity. TTQ is a posttranslational modification that results from an 8-electron oxidation of two specific tryptophans in the MADH β-subunit. The final 6-electron oxidation is catalyzed by an unusual c-type di-heme enzyme, MauG. The di-ferric enzyme can react with H(2)O(2), but atypically for c-type hemes the di-ferrous enzyme can react with O(2) as well. In both cases, an unprecedented bis-Fe(IV) redox state is formed, composed of a ferryl heme (Fe(IV)=O) with the second heme as Fe(IV) stabilized by His-Tyr axial ligation. Bis-Fe(IV) MauG acts as a potent 2-electron oxidant. Catalysis is long-range and requires a hole hopping electron transfer mechanism. This review highlights the current knowledge and focus of research into this fascinating system.
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Affiliation(s)
- Carrie M Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, Minnesota 55455, USA.
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15
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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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16
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Ndontsa EN, Moore RL, Goodwin DC. Stimulation of KatG catalase activity by peroxidatic electron donors. Arch Biochem Biophys 2012; 525:215-22. [DOI: 10.1016/j.abb.2012.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/25/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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17
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Zhao X, Khajo A, Jarrett S, Suarez J, Levitsky Y, Burger RM, Jarzecki AA, Magliozzo RS. Specific function of the Met-Tyr-Trp adduct radical and residues Arg-418 and Asp-137 in the atypical catalase reaction of catalase-peroxidase KatG. J Biol Chem 2012; 287:37057-65. [PMID: 22918833 DOI: 10.1074/jbc.m112.401208] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase activity of the dual-function heme enzyme catalase-peroxidase (KatG) depends on several structural elements, including a unique adduct formed from covalently linked side chains of three conserved amino acids (Met-255, Tyr-229, and Trp-107, Mycobacterium tuberculosis KatG numbering) (MYW). Mutagenesis, electron paramagnetic resonance, and optical stopped-flow experiments, along with calculations using density functional theory (DFT) methods revealed the basis of the requirement for a radical on the MYW-adduct, for oxyferrous heme, and for conserved residues Arg-418 and Asp-137 in the rapid catalase reaction. The participation of an oxyferrous heme intermediate (dioxyheme) throughout the pH range of catalase activity is suggested from our finding that carbon monoxide inhibits the activity at both acidic and alkaline pH. In the presence of H(2)O(2), the MYW-adduct radical is formed normally in KatG[D137S] but this mutant is defective in forming dioxyheme and lacks catalase activity. KatG[R418L] is also catalase deficient but exhibits normal formation of the adduct radical and dioxyheme. Both mutants exhibit a coincidence between MYW-adduct radical persistence and H(2)O(2) consumption as a function of time, and enhanced subunit oligomerization during turnover, suggesting that the two mutations disrupting catalase turnover allow increased migration of the MYW-adduct radical to protein surface residues. DFT calculations showed that an interaction between the side chain of residue Arg-418 and Tyr-229 in the MYW-adduct radical favors reaction of the radical with the adjacent dioxyheme intermediate present throughout turnover in WT KatG. Release of molecular oxygen and regeneration of resting enzyme are thereby catalyzed in the last step of a proposed catalase reaction.
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Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, USA
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18
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Enhancing the peroxidatic activity of KatG by deletion mutagenesis. J Inorg Biochem 2012; 116:106-15. [PMID: 23018273 DOI: 10.1016/j.jinorgbio.2012.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 11/23/2022]
Abstract
Catalase-peroxidase (KatG) enzymes use a peroxidase active site to facilitate robust catalase activity, an ability all other members of its superfamily lack. KatG's have a Met-Tyr-Trp covalent adduct that is essential for catalatic but not peroxidatic turnover. The tyrosine (Y226 in E. coli KatG) is supplied by a large loop (LL1) that is absent from all other plant peroxidases. Elimination of Y226 from the KatG structure, either by site directed mutagenesis (i.e., Y226F KatG) or by deletion of larger portions of LL1 invariably eliminates catalase activity, but deletion variants were substantially more active as peroxidases, up to an order of magnitude. Moreover, the deletion variants were more resistant to H(2)O(2)-dependent inactivation than Y226F KatG. Stopped-flow evaluation of reactions of H(2)O(2) with Y226F KatG and the most peroxidase active deletion variant (KatG[Δ209-228]) produced highly similar rate constants for formation of compounds I and II, and about a four-fold faster formation of compound III for the deletion variant as opposed to Y226F. Conversely, single turnover experiments showed a 60-fold slower return of Y226F KatG to its ferric state in the presence of the exogenous electron donor 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) than was determined for KatG(Δ209-228). Our data suggest that the peroxidatic output of KatG cannot be optimized simply by elimination of catalase activity alone, but also requires modifications that increase electron transfer between exogenous electron donors and the heme prosthetic group.
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Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MCY. Discovery and characterization of heme enzymes from unsequenced bacteria: application to microbial lignin degradation. J Am Chem Soc 2011; 133:18006-9. [PMID: 21671563 DOI: 10.1021/ja203972q] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria and other living organisms offer a potentially unlimited resource for the discovery of new chemical catalysts, but many interesting reaction phenotypes observed at the whole organism level remain difficult to elucidate down to the molecular level. A key challenge in the discovery process is the identification of discrete molecular players involved in complex biological transformations because multiple cryptic genetic components often work in concert to elicit an overall chemical phenotype. We now report a rapid pipeline for the discovery of new enzymes of interest from unsequenced bacterial hosts based on laboratory-scale methods for the de novo assembly of bacterial genome sequences using short reads. We have applied this approach to the biomass-degrading soil bacterium Amycolatopsis sp. 75iv2 ATCC 39116 (formerly Streptomyces setonii and S. griseus 75vi2) to discover and biochemically characterize two new heme proteins comprising the most abundant members of the extracellular oxidative system under lignin-reactive growth conditions.
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Affiliation(s)
- Margaret E Brown
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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20
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Zhao X, Suarez J, Khajo A, Yu S, Metlitsky L, Magliozzo RS. A radical on the Met-Tyr-Trp modification required for catalase activity in catalase-peroxidase is established by isotopic labeling and site-directed mutagenesis. J Am Chem Soc 2010; 132:8268-9. [PMID: 20507091 DOI: 10.1021/ja103311e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A transient tyrosyl-like radical with a narrow doublet X-band EPR signal is present during catalase turnover by Mycobacterium tuberculosis catalase-peroxidase (KatG). Labeling of KatG with beta-methylene-deuterated tyrosine causes a collapse of the doublet to a singlet, while for 3,5-ring-deuterated tyrosine-labeled enzyme, no changes occur in the EPR signal. Except for the replacement Tyr229Phe, all other single-tyrosine mutants of KatG exhibit the same narrow doublet EPR signal and catalase activity similar to that of the wild-type enzyme. These findings confirm that this catalytically competent radical is associated with Tyr229, whose 3' and 5' protons are replaced as a result of cross-links with neighboring Met255 and Trp107 side chains in the post-translationally modified enzyme containing a distal-side Met255-Tyr229-Trp107 adduct.
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Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, USA
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21
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Vlasits J, Jakopitsch C, Bernroitner M, Zamocky M, Furtmüller PG, Obinger C. Mechanisms of catalase activity of heme peroxidases. Arch Biochem Biophys 2010; 500:74-81. [DOI: 10.1016/j.abb.2010.04.018] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 04/23/2010] [Accepted: 04/24/2010] [Indexed: 11/15/2022]
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22
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Cade CE, Dlouhy AC, Medzihradszky KF, Salas-Castillo SP, Ghiladi RA. Isoniazid-resistance conferring mutations in Mycobacterium tuberculosis KatG: catalase, peroxidase, and INH-NADH adduct formation activities. Protein Sci 2010; 19:458-74. [PMID: 20054829 DOI: 10.1002/pro.324] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Mycobacterium tuberculosis catalase-peroxidase (KatG) is a bifunctional hemoprotein that has been shown to activate isoniazid (INH), a pro-drug that is integral to frontline antituberculosis treatments. The activated species, presumed to be an isonicotinoyl radical, couples to NAD(+)/NADH forming an isoniazid-NADH adduct that ultimately confers anti-tubercular activity. To better understand the mechanisms of isoniazid activation as well as the origins of KatG-derived INH-resistance, we have compared the catalytic properties (including the ability to form the INH-NADH adduct) of the wild-type enzyme to 23 KatG mutants which have been associated with isoniazid resistance in clinical M. tuberculosis isolates. Neither catalase nor peroxidase activities, the two inherent enzymatic functions of KatG, were found to correlate with isoniazid resistance. Furthermore, catalase function was lost in mutants which lacked the Met-Tyr-Trp crosslink, the biogenic cofactor in KatG which has been previously shown to be integral to this activity. The presence or absence of the crosslink itself, however, was also found to not correlate with INH resistance. The KatG resistance-conferring mutants were then assayed for their ability to generate the INH-NADH adduct in the presence of peroxide (t-BuOOH and H(2)O(2)), superoxide, and no exogenous oxidant (air-only background control). The results demonstrate that residue location plays a critical role in determining INH-resistance mechanisms associated with INH activation; however, different mutations at the same location can produce vastly different reactivities that are oxidant-specific. Furthermore, the data can be interpreted to suggest the presence of a second mechanism of INH-resistance that is not correlated with the formation of the INH-NADH adduct.
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Affiliation(s)
- Christine E Cade
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
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23
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Zhao X, Yu S, Ranguelova K, Suarez J, Metlitsky L, Schelvis JPM, Magliozzo RS. Role of the oxyferrous heme intermediate and distal side adduct radical in the catalase activity of Mycobacterium tuberculosis KatG revealed by the W107F mutant. J Biol Chem 2009; 284:7030-7. [PMID: 19139098 DOI: 10.1074/jbc.m808107200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidase (KatG) is essential in Mycobacterium tuberculosis for oxidative stress management and activation of the antitubercular pro-drug isoniazid. The role of a unique distal side adduct found in KatG enzymes, involving linked side chains of residues Met255, Tyr229, and Trp107 (MYW), in the unusual catalase activity of KatG is addressed here and in our companion paper (Suarez, J., Ranguelova, K., Jarzecki, A. A., Manzerova, J., Krymov, V., Zhao, X., Yu, S., Metlitsky, L., Gerfen, G. J., and Magliozzo, R. S. (2009) J. Biol. Chem. 284, in press). The KatG[W107F] mutant exhibited severely reduced catalase activity yet normal peroxidase activity, and as isolated contains more abundant 6-coordinate heme in high spin and low spin forms compared with the wild-type enzyme. Most interestingly, oxyferrous heme is also found in the purified enzyme. Oxyferrous KatG[W107F] was prepared by photolysis in air of the carbonyl enzyme or was generated using hydrogen peroxide decayed with a t1/2 of 2 days compared with 6 min for wild-type protein. The stability of oxyenyzme was modestly enhanced in KatG[Y229F] but was not affected in KatG[M255A]. Optical stopped-flow experiments showed rapid formation of Compound I in KatG[W107F] and facile formation of oxyferrous heme in the presence of micromolar hydrogen peroxide. An analysis of the relationships between catalase activity, stability of oxyferrous enzyme, and a proposed MYW adduct radical is presented. The loss of catalase function is assigned to the loss of the MYW adduct radical and structural changes that lead to greatly enhanced stability of oxyenzyme, an intermediate of the catalase cycle of native enzyme.
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Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, USA
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Suarez J, Ranguelova K, Jarzecki AA, Manzerova J, Krymov V, Zhao X, Yu S, Metlitsky L, Gerfen GJ, Magliozzo RS. An oxyferrous heme/protein-based radical intermediate is catalytically competent in the catalase reaction of Mycobacterium tuberculosis catalase-peroxidase (KatG). J Biol Chem 2009; 284:7017-29. [PMID: 19139099 DOI: 10.1074/jbc.m808106200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed.
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Affiliation(s)
- Javier Suarez
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, USA
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25
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Singh R, Wiseman B, Deemagarn T, Jha V, Switala J, Loewen PC. Comparative study of catalase-peroxidases (KatGs). Arch Biochem Biophys 2008; 471:207-14. [DOI: 10.1016/j.abb.2007.12.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 12/14/2007] [Accepted: 12/15/2007] [Indexed: 11/25/2022]
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26
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Ranguelova K, Girotto S, Gerfen GJ, Yu S, Suarez J, Metlitsky L, Magliozzo RS. Radical sites in Mycobacterium tuberculosis KatG identified using electron paramagnetic resonance spectroscopy, the three-dimensional crystal structure, and electron transfer couplings. J Biol Chem 2007; 282:6255-64. [PMID: 17204474 PMCID: PMC1885898 DOI: 10.1074/jbc.m607309200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidase (KatG) from Mycobacterium tuberculosis, a Class I peroxidase, exhibits high catalase activity and peroxidase activity with various substrates and is responsible for activation of the commonly used antitubercular drug, isoniazid (INH). KatG readily forms amino acid-based radicals during turnover with alkyl peroxides, and this work focuses on extending the identification and characterization of radicals forming on the millisecond to second time scale. Rapid freeze-quench electron paramagnetic resonance spectroscopy (RFQ-EPR) reveals a change in the structure of the initially formed radical in the presence of INH. Heme pocket binding of the drug and knowledge that KatG[Y229F] lacks this signal provides evidence for radical formation on residue Tyr(229). High field RFQ-EPR spectroscopy confirmed a tryptophanyl radical signal, and new analyses of X-band RFQ-EPR spectra also established its presence. High field EPR spectroscopy also confirmed that the majority radical species is a tyrosyl radical. Site-directed mutagenesis, along with simulations of EPR spectra based on x-ray structural data for particular tyrosine and tryptophan residues, enabled assignments based on predicted hyperfine coupling parameters. KatG mutants W107F, Y229F, and the double mutant W107F/Y229F showed alteration in type and yield of radical species. Results are consistent with formation of a tyrosyl radical reasonably assigned to residue Tyr(229) within the first few milliseconds of turnover. This is followed by a mixture of tyrosyl and tryptophanyl radical species and finally to only a tyrosyl radical on residue Tyr(353), which lies more distant from the heme. The radical processing of enzyme lacking the Trp(107)-Tyr(229)-Met(255) adduct (found as a unique structural feature of catalase-peroxidases) is suggested to be a reasonable assignment of the phenomena.
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Affiliation(s)
- Kalina Ranguelova
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Stefania Girotto
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Gary J. Gerfen
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Shengwei Yu
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Javier Suarez
- Department of Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
| | - Leonid Metlitsky
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, NY 11210 and The Graduate Center of the City University of New York, NY 10016, USA
- Department of Biochemistry, The Graduate Center of the City University of New York, NY 10016, USA
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27
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Kapetanaki SM, Zhao X, Yu S, Magliozzo RS, Schelvis JPM. Modification of the active site of Mycobacterium tuberculosis KatG after disruption of the Met-Tyr-Trp cross-linked adduct. J Inorg Biochem 2006; 101:422-33. [PMID: 17188362 PMCID: PMC1885897 DOI: 10.1016/j.jinorgbio.2006.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 11/01/2006] [Accepted: 11/02/2006] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis catalase-peroxidase (Mtb KatG) is a bifunctional enzyme that possesses both catalase and peroxidase activities and is responsible for the activation of the antituberculosis drug isoniazid. Mtb KatG contains an unusual adduct in its distal heme-pocket that consists of the covalently linked Trp107, Tyr229, and Met255. The KatG(Y229F) mutant lacks this adduct and has decreased steady-state catalase activity and enhanced peroxidase activity. In order to test a potential structural role of the adduct that supports catalase activity, we have used resonance Raman spectroscopy to probe the local heme environment of KatG(Y229F). In comparison to wild-type KatG, resting KatG(Y229F) contains a significant amount of 6-coordinate, low-spin heme and a more planar heme. Resonance Raman spectroscopy of the ferrous-CO complex of KatG(Y229F) suggest a non-linear Fe-CO binding geometry that is less tilted than in wild-type KatG. These data provide evidence that the Met-Tyr-Trp adduct imparts structural stability to the active site of KatG that seems to be important for sustaining catalase activity.
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Affiliation(s)
- Sofia M. Kapetanaki
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003
| | - Xiangbo Zhao
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210-2889
| | - Shengwei Yu
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210-2889
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College and the Graduate Center of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210-2889
| | - Johannes P. M. Schelvis
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003
- *Corresponding author. Tel.: +1 212 998 3597; fax: +1 212 260 7905. E-mail address:
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Sekiguchi JI, Miyoshi-Akiyama T, Augustynowicz-Kopeć E, Zwolska Z, Kirikae F, Toyota E, Kobayashi I, Morita K, Kudo K, Kato S, Kuratsuji T, Mori T, Kirikae T. Detection of multidrug resistance in Mycobacterium tuberculosis. J Clin Microbiol 2006; 45:179-92. [PMID: 17108078 PMCID: PMC1828975 DOI: 10.1128/jcm.00750-06] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a DNA sequencing-based method to detect mutations in the genome of drug-resistant Mycobacterium tuberculosis. Drug resistance in M. tuberculosis is caused by mutations in restricted regions of the genome. Eight genome regions associated with drug resistance, including rpoB for rifampin (RIF), katG and the mabA (fabG1)-inhA promoter for isoniazid (INH), embB for ethambutol (EMB), pncA for pyrazinamide (PZA), rpsL and rrs for streptomycin (STR), and gyrA for levofloxacin, were amplified simultaneously by PCR, and the DNA sequences were determined. It took 6.5 h to complete all procedures. Among the 138 clinical isolates tested, 55 were resistant to at least one drug. Thirty-four of 38 INH-resistant isolates (89.5%), 28 of 28 RIF-resistant isolates (100%), 15 of 18 EMB-resistant isolates (83.3%), 18 of 30 STR-resistant isolates (60%), and 17 of 17 PZA-resistant isolates (100%) had mutations related to specific drug resistance. Eighteen of these mutations had not been reported previously. These novel mutations include one in rpoB, eight in katG, one in the mabA-inhA regulatory region, two in embB, five in pncA, and one in rrs. Escherichia coli isolates expressing individually five of the eight katG mutations showed loss of catalase and INH oxidation activities, and isolates carrying any of the five pncA mutations showed no pyrazinamidase activity, indicating that these mutations are associated with INH and PZA resistance, respectively. Our sequencing-based method was also useful for testing sputa from tuberculosis patients and for screening of mutations in Mycobacterium bovis. In conclusion, our new method is useful for rapid detection of multiple-drug-resistant M. tuberculosis and for identifying novel mutations in drug-resistant M. tuberculosis.
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Affiliation(s)
- Jun-ichiro Sekiguchi
- International Medical Center of Japan, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
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Deemagarn T, Wiseman B, Carpena X, Ivancich A, Fita I, Loewen PC. Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei. Proteins 2006; 66:219-28. [PMID: 17063492 DOI: 10.1002/prot.21209] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Five residues in the multifunctional catalase-peroxidase KatG of Burkholderia pesudomallei are essential for catalase, but not peroxidase, activity. Asp141 is the only one of these catalase-specific residues not related with the covalent adduct found in KatGs that when replaced with a nonacidic residue reduces catalase activity to 5% of native levels. Replacing the nearby catalytic residue Arg108 causes a reduction in catalase activity to 35% of native levels, whereas a variant with both Asp141 and Arg108 replaced exhibits near normal catalase activity (82% of native), suggesting a synergism in the roles of the two residues in support of catalase activity in the enzyme. Among the Asp141 variants, D141E is unique in retaining normal catalase activity but with modified kinetics, suggesting more favorable compound I formation and less favorable compound I reduction. The crystal structure of the D141E variant has been determined at 1.8-A resolution, revealing that the carboxylate of Glu141 is moved only slightly compared with Asp141, but retains its hydrogen bond interaction with the main chain nitrogen of Ile237. In contrast, the low temperature ferric Electron Paramagnetic Resonance spectra of the D141A, R108A, and R108A/D141A variants are consistent with modifications of the water matrix and/or the relative positioning of the distal residue side chains. Such changes explain the reduction in catalase activity in all but the double variant R108A/D141A. Two pathways of hydrogen bonded solvent lead from the entrance channel into the heme active site, one running between Asp141 and Arg108 and the second between Asp141 and the main chain atoms of residues 237-239. It is proposed that binding of substrate H(2)O(2) to Asp141 and Arg108 controls H(2)O(2) access to the heme active site, thereby modulating the catalase reaction.
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Affiliation(s)
- Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Jakopitsch C, Obinger C, Un S, Ivancich A. Identification of Trp106 as the tryptophanyl radical intermediate in Synechocystis PCC6803 catalase-peroxidase by multifrequency Electron Paramagnetic Resonance spectroscopy. J Inorg Biochem 2006; 100:1091-9. [PMID: 16574230 DOI: 10.1016/j.jinorgbio.2006.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 02/14/2006] [Accepted: 02/14/2006] [Indexed: 11/28/2022]
Abstract
The reactive intermediates formed in the catalase-peroxidase from Synechocystis PCC6803 upon reaction with peroxyacetic acid, and in the absence of peroxidase substrates, are the oxoferryl-porphyrin radical and two subsequent protein-based radicals that we have previously assigned to a tyrosyl (Tyr()) and tryptophanyl (Trp()) radicals by using multifrequency Electron Paramagnetic Resonance (EPR) spectroscopy combined with deuterium labeling and site-directed mutagenesis. In this work, we have further investigated the Trp() in order to identify the site for the tryptophanyl radical formation, among the 26 Trp residues of the enzyme and to possibly understand the protein constraints that determine the selective formation of this radical. Based on our previous findings about the absence of the Trp() intermediate in four of the Synechocystis catalase-peroxidase variants on the heme distal side (W122F, W106A, H123Q, and R119A) we constructed new variants on Trp122 and Trp106 positions. Trp122 is very close to the iron on the heme distal side while Trp106 belongs to a short stretch (11 amino acid residues on the enzyme surface) that is highly conserved in catalase-peroxidases. We have used EPR spectroscopy to characterize the changes on the heme microenvironment induced by these mutations as well as the chemical nature of the radicals formed in each variant. Our findings identify Trp106 as the tryptophanyl radical site in Synechocystis catalase-peroxidase. The W122H and W106Y variants were specially designed to mimic the hydrogen-bond interactions of the naturally occurring Trp residues. These variants clearly demonstrated the important role of the extensive hydrogen-bonding network of the heme distal side, in the formation of the tryptophanyl radical. Moreover, the fact that W106Y is the only Synechocystis catalase-peroxidase variant of the distal heme side that recovers a catalase activity comparable to the WT enzyme, strongly indicates that the integrity of the extensive hydrogen-bonding network is also essential for the catalatic activity of the enzyme.
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Affiliation(s)
- Christa Jakopitsch
- Service de Bioénergétique, URA 2096 CNRS, Département de Biologie Joliot-Curie, CEA Saclay, Bat. 532, 91191 Gif-sur-Yvette, France
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Smulevich G, Jakopitsch C, Droghetti E, Obinger C. Probing the structure and bifunctionality of catalase-peroxidase (KatG). J Inorg Biochem 2006; 100:568-85. [PMID: 16516299 DOI: 10.1016/j.jinorgbio.2006.01.033] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 01/12/2006] [Accepted: 01/12/2006] [Indexed: 10/24/2022]
Abstract
Catalase-peroxidases (KatGs) exhibit peroxidase and substantial catalase activities similar to monofunctional catalases. Crystal structures of four different KatGs reveal the presence of a peroxidase-conserved proximal and distal heme pocket together with features unique to KatG. To gain insight into their structure-function properties, many variants were produced and very similar results were obtained irrespective of the origin of the KatG mutated. This review focuses mainly on the electronic absorption and resonance Raman results together with the combined analysis of pre-steady and steady-state kinetics of various mutants involving both the peroxidase-conserved and the KatG-specific residues of recombinant KatG from the cyanobacterium Synechocystis. Marked differences in the structural role of conserved amino acids and hydrogen-bond networks in KatG with respect to the other plant peroxidases were found. Typically, the catalatic but not the peroxidatic activity was very sensitive to mutations that disrupted the KatG-typical extensive hydrogen-bonding network. Moreover, the integrity of this network is crucial for the formation of distinct protein radicals formed upon incubation of KatG with peroxides in the absence of one-electron donors. The correlation between the structural architecture and the bifunctional activity is discussed and compared with data obtained for KatGs from other organisms.
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Affiliation(s)
- Giulietta Smulevich
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Florence, Italy.
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32
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Carpena X, Wiseman B, Deemagarn T, Singh R, Switala J, Ivancich A, Fita I, Loewen PC. A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases. EMBO Rep 2006; 6:1156-62. [PMID: 16211084 PMCID: PMC1369206 DOI: 10.1038/sj.embor.7400550] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/29/2005] [Accepted: 09/09/2005] [Indexed: 11/08/2022] Open
Abstract
The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidation and one that activates oxoferryl heme reduction by H(2)O(2), facilitating the catalatic pathway in a peroxidase. The influence of the arginine is imparted to the heme through its association with or dissociation from a tyrosinate that modulates reactivity through a Met-Tyr-Trp crosslinked adduct and a pi electron interaction of the heme with the adduct Trp.
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Affiliation(s)
- Xavier Carpena
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Ben Wiseman
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Rahul Singh
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
| | - Anabella Ivancich
- Service de Bioénergétique, URA 2096 CNRS, Département de Biologie Joliot-Curie, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Ignacio Fita
- Departament de Biologia Estructural (IBMB-CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
| | - Peter C Loewen
- Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada
- Tel: +1 204 474 8334; Fax: +1 204 474 7603; E-mail:
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Ardissone S, Laurenti E, Frendo P, Ghibaudi EM, Puppo A. Single-site mutations on the catalase–peroxidase from Sinorhizobium meliloti: role of the distal Gly and the three amino acids of the putative intrinsic cofactor. J Biol Inorg Chem 2005; 10:813-26. [PMID: 16217641 DOI: 10.1007/s00775-005-0032-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
KatB is the only catalase-peroxidase identified so far in Sinorhizobium meliloti. It plays a housekeeping role, as it is expressed throughout all the growth phases of the free-living bacterium and also during symbiosis. This paper describes the functional and structural characterization of the KatB mutants Gly303Ser, Trp95Ala, Trp95Phe, Tyr217Leu, Tyr217Phe and Met243Val carried out by optical and electron spin resonance spectroscopy. The aim of this work was to investigate the involvement of these residues in the catalatic and/or peroxidatic reaction and falls in the frame of the open dispute around the factors that influence the balance between catalatic and peroxidatic activity in heme enzymes. The Gly303 residue is not conserved in any other protein of this family, whereas the Trp95, Tyr217 and Met243 residues are thought to form an intrinsic cofactor that is likely to play a role in intramolecular electron transfer. Spectroscopic investigations show that the Gly303Ser mutant is almost similar to the wild-type KatB and should not be involved in substrate binding. Mutations on Trp95, Tyr217 and Met243 clear out the catalatic activity completely, whereas the peroxidatic activity is maintained or even increased with respect to that of the wild-type enzyme. The k (cat) values obtained for these mutants suggest that Trp95 and Tyr217 form a huge delocalized system that provides a pathway for electron transfer to the heme. Conversely, Met243 is likely to be placed close to the binding site of the organic molecules and plays a crucial role in substrate docking.
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Affiliation(s)
- Silvia Ardissone
- Dipartimento di Chimica I. F. M., Università di Torino, via Pietro Giuria 7, 10125, Turin, Italy
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34
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Ghiladi RA, Knudsen GM, Medzihradszky KF, Ortiz de Montellano PR. The Met-Tyr-Trp Cross-link in Mycobacterium tuberculosis Catalase-peroxidase (KatG). J Biol Chem 2005; 280:22651-63. [PMID: 15840564 DOI: 10.1074/jbc.m502486200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidases (KatG) are bifunctional enzymes possessing both catalase and peroxidase activities. Three crystal structures of different KatGs revealed the presence of a novel Met-Tyr-Trp cross-link that has been suggested to impart catalatic activity to the KatGs. High-performance liquid chromatographic separation of the peptide fragments resulting from tryptic digestion of recombinant Mycobacterium tuberculosis WT KatG identified a peptide with unusual UV-visible spectroscopic features attributable to the Met(255)-Tyr(229)-Trp(107) cross-link, whose structure was confirmed by mass spectrometry. WT KatG lacking the Met-Tyr-Trp cross-link was prepared, making possible studies of its formation under oxidizing conditions that generate either compound I (peroxyacetic acid, PAA) or compound II (2-methyl-1-phenyl-2-propyl hydroperoxide, MPPH). Incubation of this "cross-link-free" WT KatG with PAA revealed complete formation of the Met-Tyr-Trp structure after six equivalents of peracid were added, whereas MPPH was unable to promote cross-link formation. A mechanism for Met-Tyr-Trp autocatalytic formation by KatG compound I is proposed from these studies. Optical stopped-flow studies of WT KatG and KatG(Y229F), a mutant in which the cross-link cannot be formed, were performed with MPPH and revealed an unusual compound II spectrum for WT KatG, best described as (P.)Fe(III), where P. represents a protein-based radical. This contrasts with the oxoferryl compound II spectrum observed for KatG(Y229F) under identical conditions. The structure-function-spectroscopy relationship in KatG is discussed with relevance to the role that the Met-Tyr-Trp cross-link plays in the catalase-peroxidase mechanism.
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Affiliation(s)
- Reza A Ghiladi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94143, USA
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35
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Jakopitsch C, Wanasinghe A, Jantschko W, Furtmüller PG, Obinger C. Kinetics of Interconversion of Ferrous Enzymes, Compound II and Compound III, of Wild-type Synechocystis Catalase-peroxidase and Y249F. J Biol Chem 2005; 280:9037-42. [PMID: 15637065 DOI: 10.1074/jbc.m413317200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With the exception of catalase-peroxidases, heme peroxidases show no significant ability to oxidize hydrogen peroxide and are trapped and inactivated in the compound III form by H2O2 in the absence of one-electron donors. Interestingly, some KatG variants, which lost the catalatic activity, form compound III easily. Here, we compared the kinetics of interconversion of ferrous enzymes, compound II and compound III of wild-type Synechocystis KatG, the variant Y249F, and horseradish peroxidase (HRP). It is shown that dioxygen binding to ferrous KatG and Y249F is reversible and monophasic with apparent bimolecular rate constants of (1.2 +/- 0.3) x 10(5) M(-1) s(-1) and (1.6 +/- 0.2) x 10(5) M(-1) s(-1) (pH 7, 25 degrees C), similar to HRP. The dissociation constants (KD) of the ferrous-dioxygen were calculated to be 84 microm (wild-type KatG) and 129 microm (Y249F), higher than that in HRP (1.9 microm). Ferrous Y249F and HRP can also heterolytically cleave hydrogen peroxide, forming water and an oxoferryl-type compound II at similar rates ((2.4 +/- 0.3) x 10(5) M(-1) s(-1) and (1.1 +/- 0.2) x 10(5) M(-1) s(-1) (pH 7, 25 degrees C)). Significant differences were observed in the H2O2-mediated conversion of compound II to compound III as well as in the spectral features of compound II. When compared with HRP and other heme peroxidases, in Y249F, this reaction is significantly faster ((1.2 +/- 0.2) x 10(4) M(-1) s(-1))). Ferrous wild-type KatG was also rapidly converted by hydrogen peroxide in a two-phasic reaction via compound II to compound III (approximately 2.0 x 10(5) M(-1) s(-1)), the latter being also efficiently transformed to ferric KatG. These findings are discussed with respect to a proposed mechanism for the catalatic activity.
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Affiliation(s)
- Christa Jakopitsch
- Department of Chemistry, Division of Biochemistry, Metalloprotein Research Group, BOKU, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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36
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Deemagarn T, Carpena X, Singh R, Wiseman B, Fita I, Loewen PC. Structural Characterization of the Ser324Thr Variant of the Catalase-peroxidase (KatG) from Burkholderia pseudomallei. J Mol Biol 2005; 345:21-8. [PMID: 15567407 DOI: 10.1016/j.jmb.2004.10.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 09/27/2004] [Accepted: 10/11/2004] [Indexed: 11/18/2022]
Abstract
The Ser315Thr variant of the catalase-peroxidase KatG from Mycobacterium tuberculosis imparts resistance to the pro-drug isonicotinic acid hydrazide (isoniazid) through a failure to convert it to the active drug, isonicotinoyl-NAD. The equivalent variant in KatG from Burkholderia pseudomallei, Ser324Thr, has been constructed, revealing catalase and peroxidase activities that are similar to those of the native enzyme. The other activities of the variant protein, including the NADH oxidase, the isoniazid hydrazinolysis and isonicotinoyl-NAD synthase activities are reduced by 60-70%. The crystal structure of the variant differs from that of the native enzyme in having the methyl group of Thr324 situated in the entrance channel to the heme cavity, in a modified water matrix in the entrance channel and heme cavity, in lacking the putative perhydroxy modification on the heme, in the multiple locations of a few side-chains, and in the presence of an apparent perhydroxy modification on the indole nitrogen atom of the active-site Trp111. The position of the methyl group of Thr324 creates a constriction or narrowing of the channel leading to the heme cavity, providing an explanation for the lower reactivity towards isoniazid and the slower rate of isonicotinoyl-NAD synthesis.
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Affiliation(s)
- Taweewat Deemagarn
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
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37
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Bertrand T, Eady NAJ, Jones JN, Nagy JM, Jamart-Grégoire B, Raven EL, Brown KA. Crystal Structure of Mycobacterium tuberculosis Catalase-Peroxidase. J Biol Chem 2004; 279:38991-9. [PMID: 15231843 DOI: 10.1074/jbc.m402382200] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mycobacterium tuberculosis catalase-peroxidase is a multifunctional heme-dependent enzyme that activates the core anti-tuberculosis drug isoniazid. Numerous studies have been undertaken to elucidate the enzyme-dependent mechanism of isoniazid activation, and it is well documented that mutations that reduce activity or inactivate the catalase-peroxidase lead to increased levels of isoniazid resistance in M. tuberculosis. Interpretation of the catalytic activities and the effects of mutations upon the action of the enzyme to date have been limited due to the lack of a three-dimensional structure for this enzyme. In order to provide a more accurate model of the three-dimensional structure of the M. tuberculosis catalase-peroxidase, we have crystallized the enzyme and now report its crystal structure refined to 2.4-A resolution. The structure reveals new information about dimer assembly and provides information about the location of residues that may play a role in catalysis including candidates for protein-based radical formation. Modeling and computational studies suggest that the binding site for isoniazid is located near the delta-meso heme edge rather than in a surface loop structure as currently proposed. The availability of a crystal structure for the M. tuberculosis catalase-peroxidase also permits structural and functional effects of mutations implicated in causing elevated levels of isoniazid resistance in clinical isolates to be interpreted with improved confidence.
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Affiliation(s)
- Thomas Bertrand
- Department of Biological Sciences, Centre for Molecular Microbiology and Infection, Flowers Building, Imperial College London, London SW7 2AZ, United Kingdom
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38
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Jakopitsch C, Ivancich A, Schmuckenschlager F, Wanasinghe A, Pöltl G, Furtmüller PG, Rüker F, Obinger C. Influence of the unusual covalent adduct on the kinetics and formation of radical intermediates in synechocystis catalase peroxidase: a stopped-flow and EPR characterization of the MET275, TYR249, and ARG439 variants. J Biol Chem 2004; 279:46082-95. [PMID: 15326163 DOI: 10.1074/jbc.m408399200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidases (KatGs) are heme peroxidases with a catalatic activity comparable to monofunctional catalases. They contain an unusual covalent distal side adduct with the side chains of Trp(122), Tyr(249), and Met(275) (Synechocysis KatG numbering). The known crystal structures suggest that Tyr(249) and Met(275) could be within hydrogen-bonding distance to Arg(439). To investigate the role of this peculiar adduct, the variants Y249F, M275I, R439A, and R439N were investigated by electronic absorption, steady-state and transient-state kinetic techniques and EPR spectroscopy combined with deuterium labeling. Exchange of these conserved residues exhibited dramatic consequences on the bifunctional activity of this peroxidase. The turnover numbers of catalase activity of M275I, Y249F, R439A, and R439N are 0.6, 0.17, 4.9, and 3.14% of wild-type activity, respectively. By contrast, the peroxidase activity was unaffected or even enhanced, in particular for the M275I variant. As shown by mass spectrometry and EPR spectra, the KatG typical adduct is intact in both Arg(439) variants, as is the case of the wild-type enzyme, whereas in the M275I variant the covalent link exists only between Tyr(249) and Trp(122). In the Y249F variant, the link is absent. EPR studies showed that the radical species formed upon reaction of the Y249F and R439A/N variants with peroxoacetic acid are the oxoferryl-porphyrin radical, the tryptophanyl and the tyrosyl radicals, as in the wild-type enzyme. The dramatic loss in catalase activity of the Y249F variant allowed the comparison of the radical species formed with hydrogen peroxide and peroxoacetic acid. The EPR data strongly suggest that the sequence of intermediates formed in the absence of a one electron donor substrate, is por(.-)(+) --> Trp(.-) (or Trp(.-)(+)) --> Tyr(.-). The M275I variant did not form the Trp(.-) species because of the dramatic changes on the heme distal side, most probably induced by the repositioning of the remaining Trp(122)-Tyr(249) adduct. The results are discussed with respect to the bifunctional activity of catalase-peroxidases.
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Affiliation(s)
- Christa Jakopitsch
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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Cherepanov AV, De Vries S. Microsecond freeze-hyperquenching: development of a new ultrafast micro-mixing and sampling technology and application to enzyme catalysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1656:1-31. [PMID: 15136155 DOI: 10.1016/j.bbabio.2004.02.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Revised: 02/17/2004] [Accepted: 02/17/2004] [Indexed: 11/21/2022]
Abstract
A novel freeze-quench instrument with a characteristic <<dead-time>> of 137 +/- 18 micros is reported. The prototype has several key features that distinguish it from conventional freeze-quench devices and provide a significant improvement in time resolution: (a) high operating pressures (up to 400 bar) result in a sample flow with high linear rates (up to 200 m s(-1)); (b) tangential micro-mixer with an operating volume of approximately 1 nl yields short mixing times (up to 20 micros); (c) fast transport between the mixer and the cryomedium results in short reaction times: the ageing solution exits the mixer as a free-flowing jet, and the chemical reaction occurs "in-flight" on the way to the cryomedium; (d) a small jet diameter (approximately 20 microm) and a high jet velocity (approximately 200 m s(-1)) provide high sample-cooling rates, resulting in a short cryofixation time (up to 30 micros). The dynamic range of the freeze-quench device is between 130 micros and 15 ms. The novel tangential micro-mixer efficiently mixes viscous aqueous solutions, showing more than 95% mixing at eta < or = 4 (equivalent to protein concentrations up to 250 mg ml(-1)), which makes it an excellent tool for the preparation of pre-steady state samples of concentrated protein solutions for spectroscopic structure analysis. The novel freeze-quench device is characterized using the reaction of binding of azide to metmyoglobin from horse heart. Reaction samples are analyzed using 77 K optical absorbance spectroscopy, and X-band EPR spectroscopy. A simple procedure of spectral analysis is reported that allows (a) to perform a quantitative analysis of the reaction kinetics and (b) to identify and characterize novel reaction intermediates. The reduction of dioxygen by the bo3-type quinol oxidase from Escherichia coli is assayed using the MHQ technique. In these pilot experiments, low-temperature optical absorbance measurements show the rapid oxidation of heme o3 in the first 137 micros of the reaction, accompanied by the formation of an oxo-ferryl species. X-band EPR spectroscopy shows that a short-living radical intermediate is formed during the oxidation of heme o3. The radical decays within approximately 1 ms concomitant with the oxidation of heme b, and can be attributed to the PM reaction intermediate converting to the oxoferryl intermediate F. The general field of application of the freeze-quench methodology is discussed.
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Affiliation(s)
- Alexey V Cherepanov
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Singh R, Wiseman B, Deemagarn T, Donald LJ, Duckworth HW, Carpena X, Fita I, Loewen PC. Catalase-peroxidases (KatG) exhibit NADH oxidase activity. J Biol Chem 2004; 279:43098-106. [PMID: 15280362 DOI: 10.1074/jbc.m406374200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalase-peroxidases (KatG) produced by Burkholderia pseudomallei, Escherichia coli, and Mycobacterium tuberculosis catalyze the oxidation of NADH to form NAD+ and either H2O2 or superoxide radical depending on pH. The NADH oxidase reaction requires molecular oxygen, does not require hydrogen peroxide, is not inhibited by superoxide dismutase or catalase, and has a pH optimum of 8.75, clearly differentiating it from the peroxidase and catalase reactions with pH optima of 5.5 and 6.5, respectively, and from the NADH peroxidase-oxidase reaction of horseradish peroxidase. B. pseudomallei KatG has a relatively high affinity for NADH (Km=12 microm), but the oxidase reaction is slow (kcat=0.54 min(-1)) compared with the peroxidase and catalase reactions. The catalase-peroxidases also catalyze the hydrazinolysis of isonicotinic acid hydrazide (INH) in an oxygen- and H2O2-independent reaction, and KatG-dependent radical generation from a mixture of NADH and INH is two to three times faster than the combined rates of separate reactions with NADH and INH alone. The major products from the coupled reaction, identified by high pressure liquid chromatography fractionation and mass spectrometry, are NAD+ and isonicotinoyl-NAD, the activated form of isoniazid that inhibits mycolic acid synthesis in M. tuberculosis. Isonicotinoyl-NAD synthesis from a mixture of NAD+ and INH is KatG-dependent and is activated by manganese ion. M. tuberculosis KatG catalyzes isonicotinoyl-NAD formation from NAD+ and INH more efficiently than B. pseudomallei KatG.
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Affiliation(s)
- Rahul Singh
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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41
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Zhao X, Girotto S, Yu S, Magliozzo RS. Evidence for Radical Formation at Tyr-353 in Mycobacterium tuberculosis Catalase-Peroxidase (KatG). J Biol Chem 2004; 279:7606-12. [PMID: 14665627 DOI: 10.1074/jbc.m311884200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis KatG is a heme-containing catalase-peroxidase responsible for activation, through its peroxidase cycle, of the front line antituberculosis antibiotic isoniazid (isonicotinic acid hydrazide). Formation of Compound I (oxyferryl heme-porphyrin pi-cation radical), the classical peroxidase intermediate generated when the resting enzyme turns over with alkyl peroxides, is rapidly followed by production of a protein-centered tyrosyl radical in this enzyme. In our efforts to identify the residue at which this radical is formed, nitric oxide was used as a radical scavenging reagent. Quenching of the tyrosyl radical generated in the presence of NO was shown using electron paramagnetic resonance spectroscopy, and formation of nitrotyrosine was confirmed by proteolytic digestion followed by high performance liquid chromatography analysis of the NO-treated enzyme. These results are consistent with formation of nitrosyltyrosine by addition of NO to tyrosyl radical and oxidation of this intermediate to nitrotyrosine. Two predominant nitrotyrosine-containing peptides were identified that were purified and sequenced by Edman degradation. Both peptides were derived from the same M. tuberculosis KatG sequence spanning residues 346-356 with the amino acid sequence SPAGAWQYTAK, and both peptides contained nitrotyrosine at residue 353. Some modification of Trp-351 most probably into nitrosotryptophan was also found in one of the two peptides. Control experiments using denatured KatG or carried out in the absence of peroxide did not produce nitrotyrosine. In the mutant enzyme KatG(Y353F), which was constructed using site-directed mutagenesis, a tyrosyl radical was also formed upon turnover with peroxide but in poor yield compared with wild-type KatG. Residue Tyr-353 is unique to M. tuberculosis KatG and may play a special role in the function of this enzyme.
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Affiliation(s)
- Xiangbo Zhao
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA
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