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Jackson LK, Dailey TA, Anderle B, Warren MJ, Bergonia HA, Dailey HA, Phillips JD. Exploiting Differences in Heme Biosynthesis between Bacterial Species to Screen for Novel Antimicrobials. Biomolecules 2023; 13:1485. [PMID: 37892169 PMCID: PMC10604556 DOI: 10.3390/biom13101485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The final three steps of heme biogenesis exhibit notable differences between di- and mono-derm bacteria. The former employs the protoporphyrin-dependent (PPD) pathway, while the latter utilizes the more recently uncovered coproporphyrin-dependent (CPD) pathway. In order to devise a rapid screen for potential inhibitors that differentiate the two pathways, the genes associated with the protoporphyrin pathway in an Escherichia coli YFP strain were replaced with those for the CPD pathway from Staphylococcus aureus (SA) through a sliding modular gene replacement recombineering strategy to generate the E. coli strain Sa-CPD-YFP. Potential inhibitors that differentially target the pathways were identified by screening compound libraries against the YFP-producing Sa-CPD-YFP strain in comparison to a CFP-producing E. coli strain. Using a mixed strain assay, inhibitors targeting either the CPD or PPD heme pathways were identified through a decrease in one fluorescent signal but not the other. An initial screen identified both azole and prodigiosin-derived compounds that were shown to specifically target the CPD pathway and which led to the accumulation of coproheme, indicating that the main target of inhibition would appear to be the coproheme decarboxylase (ChdC) enzyme. In silico modeling highlighted that these inhibitors are able to bind within the active site of ChdC.
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Affiliation(s)
- Laurie K. Jackson
- Department of Internal Medicine, Division of Hematology, University of Utah, Salt Lake City, UT 84112, USA; (L.K.J.); (H.A.B.)
| | - Tammy A. Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA (H.A.D.)
| | - Brenden Anderle
- WhiteTree Medical, 10437 S Jordan Gateway, South Jordan, UT 84095, USA;
| | - Martin J. Warren
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK;
| | - Hector A. Bergonia
- Department of Internal Medicine, Division of Hematology, University of Utah, Salt Lake City, UT 84112, USA; (L.K.J.); (H.A.B.)
| | - Harry A. Dailey
- Department of Microbiology, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA (H.A.D.)
| | - John D. Phillips
- Department of Internal Medicine, Division of Hematology, University of Utah, Salt Lake City, UT 84112, USA; (L.K.J.); (H.A.B.)
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2
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Postnikov EB, Wasiak M, Bartoszek M, Polak J, Zyubin A, Lavrova AI, Chora̧żewski M. Accessing Properties of Molecular Compounds Involved in Cellular Metabolic Processes with Electron Paramagnetic Resonance, Raman Spectroscopy, and Differential Scanning Calorimetry. Molecules 2023; 28:6417. [PMID: 37687246 PMCID: PMC10490169 DOI: 10.3390/molecules28176417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
In this work, we review some physical methods of macroscopic experiments, which have been recently argued to be promising for the acquisition of valuable characteristics of biomolecular structures and interactions. The methods we focused on are electron paramagnetic resonance spectroscopy, Raman spectroscopy, and differential scanning calorimetry. They were chosen since it can be shown that they are able to provide a mutually complementary picture of the composition of cellular envelopes (with special attention paid to mycobacteria), transitions between their molecular patterning, and the response to biologically active substances (reactive oxygen species and their antagonists-antioxidants-as considered in our case study).
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Affiliation(s)
- Eugene B. Postnikov
- Theoretical Physics Department, Kursk State University, Radishcheva St. 33, 305000 Kursk, Russia
| | - Michał Wasiak
- Department of Physical Chemistry, University of Lódź, ul. Pomorska 165, 90-236 Lódź, Poland;
| | - Mariola Bartoszek
- Institute of Chemistry, University of Silesia in Katowice, ul. Szkolna 9, 40-006 Katowice, Poland; (M.B.); (J.P.)
| | - Justyna Polak
- Institute of Chemistry, University of Silesia in Katowice, ul. Szkolna 9, 40-006 Katowice, Poland; (M.B.); (J.P.)
| | - Andrey Zyubin
- Sophya Kovalevskaya North-West Mathematical Research Center, Immanuel Kant Baltic Federal University, Nevskogo St. 14, 236041 Kaliningrad, Russia; (A.Z.); (A.I.L.)
| | - Anastasia I. Lavrova
- Sophya Kovalevskaya North-West Mathematical Research Center, Immanuel Kant Baltic Federal University, Nevskogo St. 14, 236041 Kaliningrad, Russia; (A.Z.); (A.I.L.)
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Ligovskiy Prospect 2-4, 194064 Saint Petersburg, Russia
| | - Mirosław Chora̧żewski
- Institute of Chemistry, University of Silesia in Katowice, ul. Szkolna 9, 40-006 Katowice, Poland; (M.B.); (J.P.)
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3
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Sebastiani F, Dali A, Alonso de Armiño DJ, Campagni L, Patil G, Becucci M, Hofbauer S, Estrin DA, Smulevich G. The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae. J Inorg Biochem 2023; 245:112243. [PMID: 37196412 DOI: 10.1016/j.jinorgbio.2023.112243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023]
Abstract
This work focuses on the carbon monoxide adducts of the wild-type and selected variants of the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae complexed with coproheme, monovinyl monopropionyl deuteroheme (MMD), and heme b. The UV - vis and resonance Raman spectroscopies together with the molecular dynamics simulations clearly show that the wild-type coproheme-CO adduct is characterized by two CO conformers, one hydrogen-bonded to the distal H118 residue and the other showing a weak polar interaction with the distal cavity. Instead, upon conversion to heme b, i.e. after decarboxylation of propionates 2 and 4 and rotation by 90o of the porphyrin ring inside the cavity, CO probes a less polar environment. In the absence of the H118 residue, both coproheme and heme b complexes form only the non-H-bonded CO species. The unrotated MMD-CO adduct as observed in the H118F variant, confirms that decarboxylation of propionate 2 only, does not affect the heme cavity. The rupture of both the H-bonds involving propionates 2 and 4 destabilizes the porphyrin inside the cavity with the subsequent formation of a CO adduct in an open conformation. In addition, in this work we present data on CO binding to reversed heme b, obtained by hemin reconstitution of the H118A variant, and to heme d, obtained by addition of an excess of hydrogen peroxide. The results will be discussed and compared with those reported for the representatives of the firmicute clade.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Diego Javier Alonso de Armiño
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Lorenzo Campagni
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, Vienna A-1190, Austria
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy.
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, Vienna A-1190, Austria.
| | - Dario A Estrin
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Universidad de Buenos Aires, Departamento de Quimica Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" DICUS, Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino (FI) I-50019, Italy; INSTM Research Unit of Firenze, via della Lastruccia 3, Sesto Fiorentino I-50019, Italy.
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4
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Falb N, Patil G, Furtmüller PG, Gabler T, Hofbauer S. Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis. Comput Struct Biotechnol J 2023; 21:3933-3945. [PMID: 37593721 PMCID: PMC10427985 DOI: 10.1016/j.csbj.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023] Open
Abstract
The coproporphyrin dependent heme biosynthesis pathway is almost exclusively utilized by Gram-positive bacteria. This fact makes it a worthwhile topic for basic research, since a fundamental understanding of a metabolic pathway is necessary to translate the focus towards medical biotechnology, which is very relevant in this specific case, considering the need for new antibiotic targets to counteract the pathogenicity of Gram-positive superbugs. Over the years a lot of structural data on the set of enzymes acting in Gram-positive heme biosynthesis has accumulated in the Protein Database (www.pdb.org). One major challenge is to filter and analyze all available structural information in sufficient detail in order to be helpful and to draw conclusions. Here we pursued to give a holistic overview of structural information on enzymes involved in the coproporphyrin dependent heme biosynthesis pathway. There are many aspects to be extracted from experimentally determined structures regarding the reaction mechanisms, where the smallest variation of the position of an amino acid residue might be important, but also on a larger level regarding protein-protein interactions, where the focus has to be on surface characteristics and subunit (secondary) structural elements and oligomerization. This review delivers a status quo, highlights still missing information, and formulates future research endeavors in order to better understand prokaryotic heme biosynthesis.
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Affiliation(s)
- Nikolaus Falb
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gaurav Patil
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
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5
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Patil G, Michlits H, Furtmüller PG, Hofbauer S. Reactivity of Coproheme Decarboxylase with Monovinyl, Monopropionate Deuteroheme. Biomolecules 2023; 13:946. [PMID: 37371526 PMCID: PMC10296651 DOI: 10.3390/biom13060946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Coproheme decarboxylases (ChdCs) are terminal enzymes of the coproporphyrin-dependent heme biosynthetic pathway. In this reaction, two propionate groups are cleaved from the redox-active iron-containing substrate, coproheme, to form vinyl groups of the heme b product. The two decarboxylation reactions proceed sequentially, and a redox-active three-propionate porphyrin, called monovinyl, monopropionate deuteroheme (MMD), is transiently formed as an intermediate. While the reaction mechanism for the first part of the redox reaction, which is initiated by hydrogen peroxide, has been elucidated in some detail, the second part of this reaction, starting from MMD, has not been studied. Here, we report the optimization of enzymatic MMD production by ChdC and purification by reversed-phase chromatography. With the obtained MMD, we were able to study the second part of heme b formation by actinobacterial ChdC from Corynebacterium diphtheriae, starting with Compound I formation upon the addition of hydrogen peroxide. The results indicate that the second part of the decarboxylation reaction is analogous to the first part, although somewhat slower, which is explained by differences in the active site architecture and its H-bonding network. The results are discussed in terms of known kinetic and structural data and help to fill some mechanistic gaps in the overall reaction catalyzed by ChdCs.
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Affiliation(s)
| | | | | | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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6
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Ushimaru R, Lyu J, Abe I. Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad016. [PMID: 37422437 PMCID: PMC10548856 DOI: 10.1093/jimb/kuad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
Tetrapyrroles represent a unique class of natural products that possess diverse chemical architectures and exhibit a broad range of biological functions. Accordingly, they attract keen attention from the natural product community. Many metal-chelating tetrapyrroles serve as enzyme cofactors essential for life, while certain organisms produce metal-free porphyrin metabolites with biological activities potentially beneficial for the producing organisms and for human use. The unique properties of tetrapyrrole natural products derive from their extensively modified and highly conjugated macrocyclic core structures. Most of these various tetrapyrrole natural products biosynthetically originate from a branching point precursor, uroporphyrinogen III, which contains propionate and acetate side chains on its macrocycle. Over the past few decades, many modification enzymes with unique catalytic activities, and the diverse enzymatic chemistries employed to cleave the propionate side chains from the macrocycles, have been identified. In this review, we highlight the tetrapyrrole biosynthetic enzymes required for the propionate side chain removal processes and discuss their various chemical mechanisms. ONE-SENTENCE SUMMARY This mini-review describes various enzymes involved in the propionate side chain cleavages during the biosynthesis of tetrapyrrole cofactors and secondary metabolites.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jiaqi Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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7
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An active site at work – the role of key residues in C. diphteriae coproheme decarboxylase. J Inorg Biochem 2022; 229:111718. [DOI: 10.1016/j.jinorgbio.2022.111718] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/14/2021] [Accepted: 01/01/2022] [Indexed: 12/12/2022]
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8
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Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase-A Computational Study. Int J Mol Sci 2022; 23:ijms23052564. [PMID: 35269706 PMCID: PMC8910490 DOI: 10.3390/ijms23052564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Coproheme decarboxylase (ChdC) is an important enzyme in the coproporphyrin-dependent pathway (CPD) of Gram-positive bacteria that decarboxylates coproheme on two propionates at position 2 and position 4 sequentially to generate heme b by using H2O2 as an oxidant. This work focused on the ChdC from Geobacillus stearothermophilus (GsChdC) to elucidate the mechanism of its sequential two-step decarboxylation of coproheme. The models of GsChdC in a complex with substrate and reaction intermediate were built to investigate the reorienting mechanism of harderoheme. Targeted molecular dynamics simulations on these models validated that harderoheme is able to rotate in the active site of GsChdC with a 19.06-kcal·mol-1 energy barrier after the first step of decarboxylation to bring the propionate at position 4 in proximity of Tyr145 to continue the second decarboxylation step. The harderoheme rotation mechanism is confirmed to be much easier than the release-rebinding mechanism. In the active site of GsChdC, Trp157 and Trp198 comprise a "gate" construction to regulate the clockwise rotation of the harderoheme. Lys149 plays a critical role in the rotation mechanism, which not only keeps the Trp157-Trp198 "gate" from being closed but also guides the propionate at position 4 through the gap between Trp157 and Trp198 through a salt bridge interaction.
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Layer G. Heme biosynthesis in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118861. [PMID: 32976912 DOI: 10.1016/j.bbamcr.2020.118861] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The cyclic tetrapyrrole heme is used as a prosthetic group in a broad variety of different proteins in almost all organisms. Often, it is essential for vital biochemical processes such as aerobic and anaerobic respiration as well as photosynthesis. In Nature, heme is made from the common tetrapyrrole precursor 5-aminolevulinic acid, and for a long time it was assumed that heme is biosynthesized by a single, common pathway in all organisms. However, although this is indeed the case in eukaryotes, heme biosynthesis is more diverse in the prokaryotic world, where two additional pathways exist. The final elucidation of the two 'alternative' heme biosynthesis routes operating in some bacteria and archaea was achieved within the last decade. This review summarizes the three different heme biosynthesis pathways with a special emphasis on the two 'new' prokaryotic routes.
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Affiliation(s)
- Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Wissenschaften, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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10
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Milazzo L, Gabler T, Pühringer D, Jandova Z, Maresch D, Michlits H, Pfanzagl V, Djinović-Carugo K, Oostenbrink C, Furtmüller PG, Obinger C, Smulevich G, Hofbauer S. Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b. ACS Catal 2019; 9:6766-6782. [PMID: 31423350 PMCID: PMC6691569 DOI: 10.1021/acscatal.9b00963] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/20/2019] [Indexed: 12/24/2022]
Abstract
Coproheme decarboxylase (ChdC) catalyzes the last step in the heme biosynthesis pathway of monoderm bacteria with coproheme acting both as redox cofactor and substrate. Hydrogen peroxide mediates the stepwise decarboxylation of propionates 2 and 4 of coproheme. Here we present the crystal structures of coproheme-loaded ChdC from Listeria monocytogenes (LmChdC) and the three-propionate intermediate, for which the propionate at position 2 (p2) has been converted to a vinyl group and is rotated by 90° compared to the coproheme complex structure. Single, double, and triple mutants of LmChdC, in which H-bonding interactions to propionates 2, 4, 6, and 7 were eliminated, allowed us to obtain the assignment of the coproheme propionates by resonance Raman spectroscopy and to follow the H2O2-mediated conversion of coproheme to heme b. Substitution of H2O2 by chlorite allowed us to monitor compound I formation in the inactive Y147H variant which lacks the catalytically essential Y147. This residue was demonstrated to be oxidized during turnover by using the spin-trap 2-methyl-2-nitrosopropane. Based on these findings and the data derived from molecular dynamics simulations of cofactor structures in distinct poses, we propose a reaction mechanism for the stepwise decarboxylation of coproheme that includes a 90° rotation of the intermediate three-propionate redox cofactor.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Dominic Pühringer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Zuzana Jandova
- Department
of Material Sciences and Process Engineering, Institute of Molecular
Modeling and Simulation, BOKU−University
of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Daniel Maresch
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Hanna Michlits
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Vera Pfanzagl
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
- Department
of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Chris Oostenbrink
- Department
of Material Sciences and Process Engineering, Institute of Molecular
Modeling and Simulation, BOKU−University
of Natural Resources and Life Sciences, 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
| | - Christian Obinger
- Department
of Chemistry, Division of Biochemistry, BOKU−University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università
di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Stefan Hofbauer
- 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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Simonova OR, Zaitseva SV, Tyulyaeva EY, Zdanovich SA, Koifman OI. Kinetics of β-Carotene Oxidation in the Presence of Highly Active Forms of µ-Carbido Diiron(IV) Tetraphenylporphyrinate. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418110390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Guengerich FP, Yoshimoto FK. Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions. Chem Rev 2018; 118:6573-6655. [PMID: 29932643 DOI: 10.1021/acs.chemrev.8b00031] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O2 in systems in which the binding of a substrate facilitates O2 activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
| | - Francis K Yoshimoto
- Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States.,Department of Chemistry , University of Texas-San Antonio , San Antonio , Texas 78249-0698 , United States
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13
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Milazzo L, Hofbauer S, Howes BD, Gabler T, Furtmüller PG, Obinger C, Smulevich G. Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes. Biochemistry 2018. [PMID: 29536725 PMCID: PMC5940323 DOI: 10.1021/acs.biochem.8b00186] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coproheme decarboxylases (ChdC) catalyze the hydrogen peroxide-mediated conversion of coproheme to heme b. This work compares the structure and function of wild-type (WT) coproheme decarboxylase from Listeria monocytogenes and its M149A, Q187A, and M149A/Q187A mutants. The UV-vis, resonance Raman, and electron paramagnetic resonance spectroscopies clearly show that the ferric form of the WT protein is a pentacoordinate quantum mechanically mixed-spin state, which is very unusual in biological systems. Exchange of the Met149 residue to Ala dramatically alters the heme coordination, which becomes a 6-coordinate low spin species with the amide nitrogen atom of the Q187 residue bound to the heme iron. The interaction between M149 and propionyl 2 is found to play an important role in keeping the Q187 residue correctly positioned for closure of the distal cavity. This is confirmed by the observation that in the M149A variant two CO conformers are present corresponding to open (A0) and closed (A1) conformations. The CO of the latter species, the only conformer observed in the WT protein, is H-bonded to Q187. In the absence of the Q187 residue or in the adducts of all the heme b forms of ChdC investigated herein (containing vinyls in positions 2 and 4), only the A0 conformer has been found. Moreover, M149 is shown to be involved in the formation of a covalent bond with a vinyl substituent of heme b at excess of hydrogen peroxide.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , Via della Lastruccia 3-13 , 50019 Sesto Fiorentino (Fi) , Italy
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18 , A-1190 Vienna , Austria
| | - Barry D Howes
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , Via della Lastruccia 3-13 , 50019 Sesto Fiorentino (Fi) , Italy
| | - Thomas Gabler
- 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
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18 , A-1190 Vienna , Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , Via della Lastruccia 3-13 , 50019 Sesto Fiorentino (Fi) , Italy
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14
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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15
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Streit BR, Celis AI, Moraski GC, Shisler KA, Shepard EM, Rodgers KR, Lukat-Rodgers GS, DuBois JL. Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b. J Biol Chem 2018; 293:3989-3999. [PMID: 29414780 DOI: 10.1074/jbc.ra117.000830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/01/2018] [Indexed: 01/02/2023] Open
Abstract
The H2O2-dependent oxidative decarboxylation of coproheme III is the final step in the biosynthesis of heme b in many microbes. However, the coproheme decarboxylase reaction mechanism is unclear. The structure of the decarboxylase in complex with coproheme III suggested that the substrate iron, reactive propionates, and an active-site tyrosine convey a net 2e-/2H+ from each propionate to an activated form of H2O2 Time-resolved EPR spectroscopy revealed that Tyr-145 formed a radical species within 30 s of the reaction of the enzyme-coproheme complex with H2O2 This radical disappeared over the next 270 s, consistent with a catalytic intermediate. Use of the harderoheme III intermediate as substrate or substitutions of redox-active side chains (W198F, W157F, or Y113S) did not strongly affect the appearance or intensity of the radical spectrum measured 30 s after initiating the reaction with H2O2, nor did it change the ∼270 s required for the radical signal to recede to ≤10% of its initial intensity. These results suggested Tyr-145 as the site of a catalytic radical involved in decarboxylating both propionates. Tyr-145• was accompanied by partial loss of the initially present Fe(III) EPR signal intensity, consistent with the possible formation of Fe(IV)=O. Site-specifically deuterated coproheme gave rise to a kinetic isotope effect of ∼2 on the decarboxylation rate constant, indicating that cleavage of the propionate Cβ-H bond was partly rate-limiting. The inferred mechanism requires two consecutive hydrogen atom transfers, first from Tyr-145 to the substrate Fe/H2O2 intermediate and then from the propionate Cβ-H to Tyr-145•.
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Affiliation(s)
- Bennett R Streit
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Arianna I Celis
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Garrett C Moraski
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Krista A Shisler
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Eric M Shepard
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
| | - Kenton R Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Gudrun S Lukat-Rodgers
- the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717-3400 and
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16
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Pfanzagl V, Holcik L, Maresch D, Gorgone G, Michlits H, Furtmüller PG, Hofbauer S. Coproheme decarboxylases - Phylogenetic prediction versus biochemical experiments. Arch Biochem Biophys 2018; 640:27-36. [PMID: 29331688 DOI: 10.1016/j.abb.2018.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 01/08/2023]
Abstract
Coproheme decarboxylases (ChdCs) are enzymes responsible for the catalysis of the terminal step in the coproporphyrin-dependent heme biosynthesis pathway. Phylogenetic analyses confirm that the gene encoding for ChdCs is widespread throughout the bacterial world. It is found in monoderm bacteria (Firmicutes, Actinobacteria), diderm bacteria (e. g. Nitrospirae) and also in Archaea. In order to test phylogenetic prediction ChdC representatives from all clades were expressed and examined for their coproheme decarboxylase activity. Based on available biochemical data and phylogenetic analyses a sequence motif (-Y-P-M/F-X-K/R-) is defined for ChdCs. We show for the first time that in diderm bacteria an active coproheme decarboxylase is present and that the archaeal ChdC homolog from Sulfolobus solfataricus is inactive and its physiological role remains elusive. This shows the limitation of phylogenetic prediction of an enzymatic activity, since the identified sequence motif is equally conserved across all previously defined clades.
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Affiliation(s)
- Vera Pfanzagl
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Laurenz Holcik
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulia Gorgone
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Hanna Michlits
- 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
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.
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17
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Celis AI, Gauss GH, Streit BR, Shisler K, Moraski GC, Rodgers KR, Lukat-Rodgers GS, Peters JW, DuBois JL. Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ). J Am Chem Soc 2017; 139:1900-1911. [PMID: 27936663 PMCID: PMC5348300 DOI: 10.1021/jacs.6b11324] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.
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Affiliation(s)
- Arianna I. Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - George H. Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Bennett R. Streit
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Krista Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Garrett C. Moraski
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - Gudrun S. Lukat-Rodgers
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050
| | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717-3400
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