1
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Schmidt D, Falb N, Serra I, Bellei M, Pfanzagl V, Hofbauer S, Van Doorslaer S, Battistuzzi G, Furtmüller PG, Obinger C. Compound I Formation and Reactivity in Dimeric Chlorite Dismutase: Impact of pH and the Dynamics of the Catalytic Arginine. Biochemistry 2023; 62:835-850. [PMID: 36706455 PMCID: PMC9910045 DOI: 10.1021/acs.biochem.2c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Indexed: 01/28/2023]
Abstract
The heme enzyme chlorite dismutase (Cld) catalyzes the degradation of chlorite to chloride and dioxygen. Many questions about the molecular reaction mechanism of this iron protein have remained unanswered, including the electronic nature of the catalytically relevant oxoiron(IV) intermediate and its interaction with the distal, flexible, and catalytically active arginine. Here, we have investigated the dimeric Cld from Cyanothece sp. PCC7425 (CCld) and two variants having the catalytic arginine R127 (i) hydrogen-bonded to glutamine Q74 (wild-type CCld), (ii) arrested in a salt bridge with a glutamate (Q74E), or (iii) being fully flexible (Q74V). Presented stopped-flow spectroscopic studies demonstrate the initial and transient appearance of Compound I in the reaction between CCld and chlorite at pH 5.0 and 7.0 and the dominance of spectral features of an oxoiron(IV) species (418, 528, and 551 nm) during most of the chlorite degradation period at neutral and alkaline pH. Arresting the R127 in a salt bridge delays chlorite decomposition, whereas increased flexibility accelerates the reaction. The dynamics of R127 does not affect the formation of Compound I mediated by hypochlorite but has an influence on Compound I stability, which decreases rapidly with increasing pH. The decrease in activity is accompanied by the formation of protein-based amino acid radicals. Compound I is demonstrated to oxidize iodide, chlorite, and serotonin but not hypochlorite. Serotonin is able to dampen oxidative damage and inactivation of CCld at neutral and alkaline pH. Presented data are discussed with respect to the molecular mechanism of Cld and the pronounced pH dependence of chlorite degradation.
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Affiliation(s)
- Daniel Schmidt
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Nikolaus Falb
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Ilenia Serra
- BIMEF
Laboratory, Department of Chemistry, University
of Antwerp, 2000Antwerp, Belgium
| | - Marzia Bellei
- Department
of Life Sciences, University of Modena and
Reggio Emilia, 41100Modena, Italy
| | - Vera Pfanzagl
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Stefan Hofbauer
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Sabine Van Doorslaer
- BIMEF
Laboratory, Department of Chemistry, University
of Antwerp, 2000Antwerp, Belgium
| | - Gianantonio Battistuzzi
- Department
of Chemistry and Geology, University of
Modena and Reggio Emilia, 41100Modena, Italy
| | - Paul G. Furtmüller
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
| | - Christian Obinger
- Institute
of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190Vienna, Austria
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2
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A genetically encoded system for oxygen generation in living cells. Proc Natl Acad Sci U S A 2022; 119:e2207955119. [PMID: 36215519 DOI: 10.1073/pnas.2207955119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oxygen plays a key role in supporting life on our planet. It is particularly important in higher eukaryotes where it boosts bioenergetics as a thermodynamically favorable terminal electron acceptor and has important roles in cell signaling and development. Many human diseases stem from either insufficient or excessive oxygen. Despite its fundamental importance, we lack methods with which to manipulate the supply of oxygen with high spatiotemporal resolution in cells and in organisms. Here, we introduce a genetic system, SupplemeNtal Oxygen Released from ChLorite (SNORCL), for on-demand local generation of molecular oxygen in living cells, by harnessing prokaryotic chlorite O2-lyase (Cld) enzymes that convert chlorite (ClO2-) into molecular oxygen (O2) and chloride (Cl-). We show that active Cld enzymes can be targeted to either the cytosol or mitochondria of human cells, and that coexpressing a chlorite transporter results in molecular oxygen production inside cells in response to externally added chlorite. This first-generation system allows fine temporal and spatial control of oxygen production, with immediate research applications. In the future, we anticipate that technologies based on SNORCL will have additional widespread applications in research, biotechnology, and medicine.
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3
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Geeraerts Z, Stiller OR, Lukat-Rodgers GS, Rodgers KR. Roles of High-Valent Hemes and pH Dependence in Halite Decomposition Catalyzed by Chlorite Dismutase from Dechloromonas aromatica. ACS Catal 2022; 12:8641-8657. [DOI: 10.1021/acscatal.2c01428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Olivia R. Stiller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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4
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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
![]()
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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5
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Schmidt D, Serra I, Mlynek G, Pfanzagl V, Hofbauer S, Furtmüller PG, Djinović-Carugo K, Van Doorslaer S, Obinger C. Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis. Biochemistry 2021; 60:621-634. [PMID: 33586945 PMCID: PMC7931450 DOI: 10.1021/acs.biochem.0c00910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Chlorite dismutases
(Clds) are heme b-containing
oxidoreductases that can decompose chlorite to chloride and molecular
oxygen. They are divided in two clades that differ in oligomerization,
subunit architecture, and the hydrogen-bonding network of the distal
catalytic arginine, which is proposed to switch between two conformations
during turnover. To understand the impact of the conformational dynamics
of this basic amino acid on heme coordination, structure, and catalysis,
Cld from Cyanothece sp. PCC7425 was used as a model
enzyme. As typical for a clade 2 Cld, its distal arginine 127 is hydrogen-bonded
to glutamine 74. The latter has been exchanged with either glutamate
(Q74E) to arrest R127 in a salt bridge or valine (Q74V) that mirrors
the setting in clade 1 Clds. We present the X-ray crystal structures
of Q74V and Q74E and demonstrate the pH-induced changes in the environment
and coordination of the heme iron by ultraviolet–visible, circular
dichroism, and electron paramagnetic resonance spectroscopies as well
as differential scanning calorimetry. The conformational dynamics
of R127 is shown to have a significant role in heme coordination during
the alkaline transition and in the thermal stability of the heme cavity,
whereas its impact on the catalytic efficiency of chlorite degradation
is relatively small. The findings are discussed with respect to (i)
the flexible loop connecting the N-terminal and C-terminal ferredoxin-like
domains, which differs in clade 1 and clade 2 Clds and carries Q74
in clade 2 proteins, and (ii) the proposed role(s) of the arginine
in catalysis.
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Affiliation(s)
- Daniel Schmidt
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Ilenia Serra
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria.,Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 5, SI-1000 Ljubljana, Slovenia
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
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6
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Mahor D, Püschmann J, Adema DR, Strampraad MJF, Hagedoorn PL. Unexpected photosensitivity of the well-characterized heme enzyme chlorite dismutase. J Biol Inorg Chem 2020; 25:1129-1138. [PMID: 33113038 PMCID: PMC7665973 DOI: 10.1007/s00775-020-01826-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022]
Abstract
Chlorite dismutase is a heme enzyme that catalyzes the conversion of the toxic compound ClO2- (chlorite) to innocuous Cl- and O2. The reaction is a very rare case of enzymatic O-O bond formation, which has sparked the interest to elucidate the reaction mechanism using pre-steady-state kinetics. During stopped-flow experiments, spectroscopic and structural changes of the enzyme were observed in the absence of a substrate in the time range from milliseconds to minutes. These effects are a consequence of illumination with UV-visible light during the stopped-flow experiment. The changes in the UV-visible spectrum in the initial 200 s of the reaction indicate a possible involvement of a ferric superoxide/ferrous oxo or ferric hydroxide intermediate during the photochemical inactivation. Observed EPR spectral changes after 30 min reaction time indicate the loss of the heme and release of iron during the process. During prolonged illumination, the oligomeric state of the enzyme changes from homo-pentameric to monomeric with subsequent protein precipitation. Understanding the effects of UV-visible light illumination induced changes of chlorite dismutase will help us to understand the nature and mechanism of photosensitivity of heme enzymes in general. Furthermore, previously reported stopped-flow data of chlorite dismutase and potentially other heme enzymes will need to be re-evaluated in the context of the photosensitivity. Illumination of recombinantly expressed Azospira oryzae Chlorite dismutase (AoCld) with a high-intensity light source, common in stopped-flow equipment, results in disruption of the bond between FeIII and the axial histidine. This leads to the enzyme losing its heme cofactor and changing its oligomeric state as shown by spectroscopic changes and loss of activity.
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Affiliation(s)
- Durga Mahor
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Julia Püschmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Diederik R Adema
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Marc J F Strampraad
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands.
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7
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Mahor D, Püschmann J, van den Haak M, Kooij PJ, van den Ouden DLJ, Strampraad MJF, Srour B, Hagedoorn PL. A traffic light enzyme: acetate binding reversibly switches chlorite dismutase from a red- to a green-colored heme protein. J Biol Inorg Chem 2020; 25:609-620. [PMID: 32246282 PMCID: PMC7239840 DOI: 10.1007/s00775-020-01784-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/22/2020] [Indexed: 11/28/2022]
Abstract
Abstract Chlorite dismutase is a unique heme enzyme that catalyzes the conversion of chlorite to chloride and molecular oxygen. The enzyme is highly specific for chlorite but has been known to bind several anionic and neutral ligands to the heme iron. In a pH study, the enzyme changed color from red to green in acetate buffer pH 5.0. The cause of this color change was uncovered using UV–visible and EPR spectroscopy. Chlorite dismutase in the presence of acetate showed a change of the UV–visible spectrum: a redshift and hyperchromicity of the Soret band from 391 to 404 nm and a blueshift of the charge transfer band CT1 from 647 to 626 nm. Equilibrium binding titrations with acetate resulted in a dissociation constant of circa 20 mM at pH 5.0 and 5.8. EPR spectroscopy showed that the acetate bound form of the enzyme remained high spin S = 5/2, however with an apparent change of the rhombicity and line broadening of the spectrum. Mutagenesis of the proximal arginine Arg183 to alanine resulted in the loss of the ability to bind acetate. Acetate was discovered as a novel ligand to chlorite dismutase, with evidence of direct binding to the heme iron. The green color is caused by a blueshift of the CT1 band that is characteristic of the high spin ferric state of the enzyme. Any weak field ligand that binds directly to the heme center may show the red to green color change, as was indeed the case for fluoride. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01784-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Durga Mahor
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Julia Püschmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Menno van den Haak
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Pepijn J Kooij
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - David L J van den Ouden
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Marc J F Strampraad
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Batoul Srour
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands.
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8
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Pfanzagl V, Nys K, Bellei M, Michlits H, Mlynek G, Battistuzzi G, Djinovic-Carugo K, Van Doorslaer S, Furtmüller PG, Hofbauer S, Obinger C. Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage. J Biol Chem 2018; 293:14823-14838. [PMID: 30072383 PMCID: PMC6153280 DOI: 10.1074/jbc.ra118.004773] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/26/2018] [Indexed: 11/06/2022] Open
Abstract
Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide-dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential, detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high-resolution crystal structures of WT B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp-143 and Arg-232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin cyanide complex, and (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H2O2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity, including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in KpDyP with absorbance maxima at 418, 527, and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.
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Affiliation(s)
- Vera Pfanzagl
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Kevin Nys
- the Department of Physics, University of Antwerp, 2610 Wilrijk, Belgium
| | | | - Hanna Michlits
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Georg Mlynek
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Gianantonio Battistuzzi
- Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and
| | - Kristina Djinovic-Carugo
- the Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | | | - Paul G Furtmüller
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Stefan Hofbauer
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Christian Obinger
- From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria,
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9
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Geeraerts Z, Celis AI, Mayfield JA, Lorenz M, Rodgers KR, DuBois JL, Lukat-Rodgers GS. Distinguishing Active Site Characteristics of Chlorite Dismutases with Their Cyanide Complexes. Biochemistry 2018; 57:1501-1516. [PMID: 29406727 PMCID: PMC5849076 DOI: 10.1021/acs.biochem.7b01278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
O2-evolving chlorite dismutases (Clds) efficiently convert chlorite (ClO2-) to O2 and Cl-. Dechloromonas aromatica Cld ( DaCld) is a highly active chlorite-decomposing homopentameric enzyme, typical of Clds found in perchlorate- and chlorate-respiring bacteria. The Gram-negative, human pathogen Klebsiella pneumoniae contains a homodimeric Cld ( KpCld) that also decomposes ClO2-, albeit with an activity 10-fold lower and a turnover number lower than those of DaCld. The interactions between the distal pocket and heme ligand of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their cyanide complexes for insight into active site characteristics that are deterministic for chlorite decomposition. At 4.7 × 10-9 M, the KD for the KpCld-CN- complex is 2 orders of magnitude smaller than that of DaCld-CN- and indicates an affinity for CN- that is greater than that of most heme proteins. The difference in CN- affinity between Kp- and DaClds is predominantly due to differences in koff. The kinetics of binding of cyanide to DaCld, DaCld(R183Q), and KpCld between pH 4 and 8.5 corroborate the importance of distal Arg183 and a p Ka of ∼7 in stabilizing complexes of anionic ligands, including the substrate. The Fe-C stretching and FeCN bending modes of the DaCld-CN- (νFe-C, 441 cm-1; δFeCN, 396 cm-1) and KpCld-CN- (νFe-C, 441 cm-1; δFeCN, 356 cm-1) complexes reveal differences in their FeCN angle, which suggest different distal pocket interactions with their bound cyanide. Conformational differences in their catalytic sites are also reported by the single ferrous KpCld carbonyl complex, which is in contrast to the two conformers observed for DaCld-CO.
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Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Jeffery A. Mayfield
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Megan Lorenz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, USA
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10
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Schaffner I, Mlynek G, Flego N, Pühringer D, Libiseller-Egger J, Coates L, Hofbauer S, Bellei M, Furtmüller PG, Battistuzzi G, Smulevich G, Djinović-Carugo K, Obinger C. Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies. ACS Catal 2017; 7:7962-7976. [PMID: 29142780 PMCID: PMC5678291 DOI: 10.1021/acscatal.7b01749] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 09/22/2017] [Indexed: 01/19/2023]
Abstract
![]()
The
heme enzyme chlorite dismutase (Cld) catalyzes the degradation
of chlorite to chloride and dioxygen. Although structure and steady-state
kinetics of Clds have been elucidated, many questions remain (e.g.,
the mechanism of chlorite cleavage and the pH dependence of the reaction).
Here, we present high-resolution X-ray crystal structures of a dimeric
Cld at pH 6.5 and 8.5, its fluoride and isothiocyanate complexes and
the neutron structure at pH 9.0 together with the pH dependence of
the Fe(III)/Fe(II) couple, and the UV–vis and resonance Raman
spectral features. We demonstrate that the distal Arg127 cannot act
as proton acceptor and is fully ionized even at pH 9.0 ruling out
its proposed role in dictating the pH dependence of chlorite degradation.
Stopped-flow studies show that (i) Compound I and hypochlorite do
not recombine and (ii) Compound II is the immediately formed redox
intermediate that dominates during turnover. Homolytic cleavage of
chlorite is proposed.
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Affiliation(s)
- Irene Schaffner
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Georg Mlynek
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Nicola Flego
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Dominic Pühringer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Julian Libiseller-Egger
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Leighton Coates
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Stefan Hofbauer
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Marzia Bellei
- Department
of Life Sciences, University of Modena and Reggio Emilia, Via Campi
103, 41125 Modena, Italy
| | - Paul G. Furtmüller
- Department
of Chemistry, Division of Biochemistry, BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Gianantonio Battistuzzi
- Department
of Chemistry and Geology, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Kristina Djinović-Carugo
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, A-1030 Vienna, Austria
- Department
of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - 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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11
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Geeraerts Z, Rodgers KR, DuBois JL, Lukat-Rodgers GS. Active Sites of O 2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron-Ligand Vibrational Correlations. Biochemistry 2017; 56:4509-4524. [PMID: 28758386 DOI: 10.1021/acs.biochem.7b00572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
O2-evolving chlorite dismutases (Clds) fall into two subfamilies, which efficiently convert ClO2- to O2 and Cl-. The Cld from Dechloromonas aromatica (DaCld) represents the chlorite-decomposing homopentameric enzymes found in perchlorate- and chlorate-respiring bacteria. The Cld from the Gram-negative human pathogen Klebsiella pneumoniae (KpCld) is representative of the second subfamily, comprising homodimeric enzymes having truncated N-termini. Here steric and nonbonding properties of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their fluorides, chlorides, and hydroxides. Cooperative binding of Cl- to KpCld drives formation of a hexacoordinate, high-spin aqua heme, whereas DaCld remains pentacoordinate and high-spin under analogous conditions. Fluoride coordinates to the heme iron in KpCld and DaCld, exhibiting ν(FeIII-F) bands at 385 and 390 cm-1, respectively. Correlation of these frequencies with their CT1 energies reveals strong H-bond donation to the F- ligand, indicating that atoms directly coordinated to heme iron are accessible to distal H-bond donation. New vibrational frequency correlations between either ν(FeIII-F) or ν(FeIII-OH) and ν(FeII-His) of Clds and other heme proteins are reported. These correlations orthogonalize proximal and distal effects on the bonding between iron and exogenous π-donor ligands. The axial Fe-X vibrations and the relationships between them illuminate both similarities and differences in the H-bonding and electrostatic properties of the distal and proximal heme environments in pentameric and dimeric Clds. Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety.
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Affiliation(s)
- Zachary Geeraerts
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Kenton R Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59715, United States
| | - Gudrun S Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58102, United States
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12
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From chlorite dismutase towards HemQ - the role of the proximal H-bonding network in haeme binding. Biosci Rep 2016; 36:BSR20150330. [PMID: 26858461 PMCID: PMC4793301 DOI: 10.1042/bsr20150330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Chlorite dismutase (Cld) and HemQ are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. Clds are able to convert chlorite into chloride and dioxygen, whereas HemQ is proposed to be involved in the haeme b synthesis of Gram-positive bacteria. A striking difference between these protein families concerns the proximal haeme cavity architecture. The pronounced H-bonding network in Cld, which includes the proximal ligand histidine and fully conserved glutamate and lysine residues, is missing in HemQ. In order to understand the functional consequences of this clearly evident difference, specific hydrogen bonds in Cld from 'Candidatus Nitrospira defluvii' (NdCld) were disrupted by mutagenesis. The resulting variants (E210A and K141E) were analysed by a broad set of spectroscopic (UV-vis, EPR and resonance Raman), calorimetric and kinetic methods. It is demonstrated that the haeme cavity architecture in these protein families is very susceptible to modification at the proximal site. The observed consequences of such structural variations include a significant decrease in thermal stability and also affinity between haeme b and the protein, a partial collapse of the distal cavity accompanied by an increased percentage of low-spin state for the E210A variant, lowered enzymatic activity concomitant with higher susceptibility to self-inactivation. The high-spin (HS) ligand fluoride is shown to exhibit a stabilizing effect and partially restore wild-type Cld structure and function. The data are discussed with respect to known structure-function relationships of Clds and the proposed function of HemQ as a coprohaeme decarboxylase in the last step of haeme biosynthesis in Firmicutes and Actinobacteria.
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13
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De Schutter A, Correia HD, Freire DM, Rivas MG, Rizzi A, Santos-Silva T, González PJ, Van Doorslaer S. Ligand Binding to Chlorite Dismutase from Magnetospirillum sp. J Phys Chem B 2015; 119:13859-69. [PMID: 26287794 DOI: 10.1021/acs.jpcb.5b04141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chlorite dismutase (Cld) catalyzes the reduction of chlorite to chloride and dioxygen. Here, the ligand binding to Cld of Magnetospirillum sp. (MaCld) is investigated with X-ray crystallography and electron paramagnetic resonance (EPR). EPR reveals a large heterogeneity in the structure of wild-type MaCld, showing a variety of low- and high-spin ferric heme forms. Addition of an axial ligand, such as azide or imidazole, removes this heterogeneity almost entirely. This is in line with the two high resolution crystal structures of MaCld obtained in the presence of azide and thiocyanate that show the coordination of the ligands to the heme iron. The crystal structure of the MaCld-azide complex reveals a single well-defined orientation of the azide molecule in the heme pocket. EPR shows, however, a pH-dependent heme structure, probably due to acid-base transitions of the surrounding amino-acid residues stabilizing azide. For the azide and imidazole complex of MaCld, the hyperfine and nuclear quadrupole interactions with the close-by (14)N and (1)H nuclei are determined using pulsed EPR. These values are compared to the corresponding data for the low-spin forms observed in the ferric wild-type MaCld and to existing EPR data on azide and imidazole complexes of other heme proteins.
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Affiliation(s)
- Amy De Schutter
- BIMEF Laboratory, Department of Physics, University of Antwerp , Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Hugo D Correia
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Diana M Freire
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - María G Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Alberto Rizzi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Teresa Santos-Silva
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Pablo J González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , Ciudad Universitaria, Paraje El Pozo, S3000ZAA Santa Fe, Argentina
| | - Sabine Van Doorslaer
- BIMEF Laboratory, Department of Physics, University of Antwerp , Universiteitsplein 1, B-2610 Wilrijk, Belgium
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