1
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Yi K, Wang P, He C. Facile incorporation of non-canonical heme ligands in myoglobin through chemical protein synthesis. Bioorg Med Chem 2024; 112:117900. [PMID: 39217687 DOI: 10.1016/j.bmc.2024.117900] [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: 07/17/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
The incorporation of non-canonical amino acids (ncAAs) into the metal coordination environments of proteins has endowed metalloproteins with enhanced properties and novel activities, particularly in hemoproteins. In this work, we disclose a scalable synthetic strategy that enables the production of myoglobin (Mb) variants with non-canonical heme ligands, i.e., HoCys and f4Tyr. The ncAA-containing Mb* variants (with H64V/V68A mutations) were obtained through two consecutive native chemical ligations and a subsequent desulfurization step, with overall isolated yield up to 28.6 % in over 10-milligram scales. After refolding and heme b cofactor reconstitution, the synthetic Mb* variants showed typical electronic absorption bands. When subjected to the catalysis of the cyclopropanation of styrene, both synthetic variants, however, were not as competent as the His-ligated Mb*. We envisioned that the synthetic method reported herein would be useful for incorporating a variety of ncAAs with diverse structures and properties into Mb for varied purposes.
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Affiliation(s)
- Kewei Yi
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Peng Wang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China.
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2
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Hargrove T, Lamb DC, Wawrzak Z, Hull M, Kelly SL, Guengerich FP, Lepesheva GI. Identification of Potent and Selective Inhibitors of Acanthamoeba: Structural Insights into Sterol 14α-Demethylase as a Key Drug Target. J Med Chem 2024; 67:7443-7457. [PMID: 38683753 PMCID: PMC11089504 DOI: 10.1021/acs.jmedchem.4c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii. The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.
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Affiliation(s)
- Tatiana
Y. Hargrove
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - David C. Lamb
- Faculty
of Medicine, Health and Life Science, Swansea
University, Swansea SA2 8PP, U.K.
| | - Zdzislaw Wawrzak
- Synchrotron
Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Marcus Hull
- Faculty
of Medicine, Health and Life Science, Swansea
University, Swansea SA2 8PP, U.K.
| | - Steven L. Kelly
- Faculty
of Medicine, Health and Life Science, Swansea
University, Swansea SA2 8PP, U.K.
| | - F. Peter Guengerich
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Galina I. Lepesheva
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Vanderbilt
Institute of Chemical Biology, Nashville, Tennessee 37232, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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3
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Schroeder L, Diepold N, Gäfe S, Niemann HH, Kottke T. Coupling and regulation mechanisms of the flavin-dependent halogenase PyrH observed by infrared difference spectroscopy. J Biol Chem 2024; 300:107210. [PMID: 38519030 PMCID: PMC11021962 DOI: 10.1016/j.jbc.2024.107210] [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: 12/18/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024] Open
Abstract
Flavin-dependent halogenases are central enzymes in the production of halogenated secondary metabolites in various organisms and they constitute highly promising biocatalysts for regioselective halogenation. The mechanism of these monooxygenases includes formation of hypohalous acid from a reaction of fully reduced flavin with oxygen and halide. The hypohalous acid then diffuses via a tunnel to the substrate-binding site for halogenation of tryptophan and other substrates. Oxidized flavin needs to be reduced for regeneration of the enzyme, which can be performed in vitro by a photoreduction with blue light. Here, we employed this photoreduction to study characteristic structural changes associated with the transition from oxidized to fully reduced flavin in PyrH from Streptomyces rugosporus as a model for tryptophan-5-halogenases. The effect of the presence of bromide and chloride or the absence of any halides on the UV-vis spectrum of the enzyme demonstrated a halide-dependent structure of the flavin-binding pocket. Light-induced FTIR difference spectroscopy was applied and the signals assigned by selective isotope labeling of the protein moiety. The identified structural changes in α-helix and β-sheet elements were strongly dependent on the presence of bromide, chloride, the substrate tryptophan, and the product 5-chloro-tryptophan, respectively. We identified a clear allosteric coupling in solution at ambient conditions between cofactor-binding site and substrate-binding site that is active in both directions, despite their separation by a tunnel. We suggest that this coupling constitutes a fine-tuned mechanism for the promotion of the enzymatic reaction of flavin-dependent halogenases in dependence of halide and substrate availability.
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Affiliation(s)
- Lea Schroeder
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Niklas Diepold
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany; Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Simon Gäfe
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Hartmut H Niemann
- Structural Biochemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Biophysical Chemistry and Diagnostics, Department of Chemistry, Bielefeld University, Bielefeld, Germany; Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany.
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4
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Jordan S, Li B, Traore E, Wu Y, Usai R, Liu A, Xie ZR, Wang Y. Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis. J Biol Chem 2023; 299:105049. [PMID: 37451485 PMCID: PMC10424215 DOI: 10.1016/j.jbc.2023.105049] [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: 05/23/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting a novel drug target. Several nonproteinogenic amino acids are integrated into rufomycins, including a conserved 3-nitro-tyrosine. RufO, a cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation of 3-nitro-tyrosine in the presence of O2 and NO. To define its biological function, the interaction between RufO and the proposed substrate tyrosine is investigated using various spectroscopic methods that are sensitive to the structural change of a heme center. However, a low- to high-spin state transition and a dramatic increase in the redox potential that are commonly found in CYPs upon ligand binding have not been observed. Furthermore, a 1.89-Å crystal structure of RufO shows that the enzyme has flexible surface regions, a wide-open substrate access tunnel, and the heme center is largely exposed to solvent. Comparison with a closely related nitrating CYP reveals a spacious and hydrophobic distal pocket in RufO, which is incapable of stabilizing a free amino acid. Molecular docking validates the experimental data and proposes a possible substrate. Collectively, our results disfavor tyrosine as the substrate of RufO and point to the possibility that the nitration occurs during or after the assembly of the peptides. This study indicates a new function of the unique nitrating enzyme and provides insights into the biosynthesis of nonribosomal peptides.
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Affiliation(s)
- Stephanie Jordan
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Bingnan Li
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Ephrahime Traore
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Yifei Wu
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Remigio Usai
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Zhong-Ru Xie
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia, USA
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, Georgia, USA.
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5
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Tong Y, Rozeboom HJ, Loonstra MR, Wijma HJ, Fraaije MW. Characterization of two bacterial multi-flavinylated proteins harboring multiple covalent flavin cofactors. BBA ADVANCES 2023; 4:100097. [PMID: 37455753 PMCID: PMC10339131 DOI: 10.1016/j.bbadva.2023.100097] [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: 05/24/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
In recent years, studies have shown that a large number of bacteria secrete multi-flavinylated proteins. The exact roles and properties, of these extracellular flavoproteins that contain multiple covalently anchored FMN cofactors, are still largely unknown. Herein, we describe the biochemical and structural characterization of two multi-FMN-containing covalent flavoproteins, SaFMN3 from Streptomyces azureus and CbFMN4 from Clostridiaceae bacterium. Based on their primary structure, these proteins were predicted to contain three and four covalently tethered FMN cofactors, respectively. The genes encoding SaFMN3 and CbFMN4 were heterologously coexpressed with a flavin transferase (ApbE) in Escherichia coli, and could be purified by affinity chromatography in good yields. Both proteins were found to be soluble and to contain covalently bound FMN molecules. The SaFMN3 protein was studied in more detail and found to display a single redox potential (-184 mV) while harboring three covalently attached flavins. This is in line with the high sequence similarity when the domains of each flavoprotein are compared. The fully reduced form of SaFMN3 is able to use dioxygen as electron acceptor. Single domains from both proteins were expressed, purified and crystallized. The crystal structures were elucidated, which confirmed that the flavin cofactor is covalently attached to a threonine. Comparison of both crystal structures revealed a high similarity, even in the flavin binding pocket. Based on the crystal structure, mutants of the SaFMN3-D2 domain were designed to improve its fluorescence quantum yield by changing the microenvironment of the isoalloxazine moiety of the flavin cofactor. Residues that quench the flavin fluorescence were successfully identified. Our study reveals biochemical details of multi-FMN-containing proteins, contributing to a better understanding of their role in bacteria and providing leads to future utilization of these flavoprotein in biotechnology.
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6
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Nolan K, Wang Y. Combined spectroscopic and structural approaches to explore the mechanism of histidine-ligated heme-dependent aromatic oxygenases. Methods Enzymol 2023; 685:405-432. [PMID: 37245909 PMCID: PMC11057917 DOI: 10.1016/bs.mie.2023.03.008] [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] [Indexed: 05/30/2023]
Abstract
The emergence of histidine-ligated heme-dependent aromatic oxygenases (HDAOs) has greatly enriched heme chemistry, and more studies are required to appreciate the diversity found in His-ligated heme proteins. This chapter describes recent methods in probing the HDAO mechanisms in detail, along with the discussion on how they can benefit structure-function studies of other heme systems. The experimental details are centered on studies of TyrHs, followed by explanation of how the results obtained would advance the understanding of the specific enzyme and also HDAOs. Spectroscopic methods, namely, electronic absorption and EPR spectroscopies, and X-ray crystallography are valuable techniques commonly used to characterize the properties of the heme center and the nature of heme-based intermediate. Herein, we show that the combination of these tools are extremely powerful, not only because one can acquire electronic, magnetic, and conformational information from different phases, but also because of the advantages brought by spectroscopic characterization on crystal samples.
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Affiliation(s)
- Katie Nolan
- Department of Chemistry, University of Georgia, Athens, GA, United States
| | - Yifan Wang
- Department of Chemistry, University of Georgia, Athens, GA, United States.
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7
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Siriboe MG, Vargas DA, Fasan R. Dehaloperoxidase Catalyzed Stereoselective Synthesis of Cyclopropanol Esters. J Org Chem 2022. [PMID: 36542602 DOI: 10.1021/acs.joc.2c02030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chiral cyclopropanols are highly desirable building blocks for medicinal chemistry, but the stereoselective synthesis of these molecules remains challenging. Here, a novel strategy is reported for the diastereo- and enantioselective synthesis of cyclopropanol derivatives via the biocatalytic asymmetric cyclopropanation of vinyl esters with ethyl diazoacetate (EDA). A dehaloperoxidase enzyme from Amphitrite ornata was repurposed to catalyze this challenging cyclopropanation reaction, and its activity and stereoselectivity were optimized via protein engineering. Using this system, a broad range of electron-deficient vinyl esters were efficiently converted to the desired cyclopropanation products with up to 99.5:0.5 diastereomeric and enantiomeric ratios. In addition, the engineered dehaloperoxidase-based biocatalyst is able to catalyze a variety of other abiological carbene transfer reactions, including N-H/S-H carbene insertion with EDA as well as cyclopropanation with diazoacetonitrile, thus adding to the multifunctionality of this enzyme and defining it as a valuable new scaffold for the development of novel carbene transferases.
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Affiliation(s)
- Mary G Siriboe
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York14627, United States
| | - David A Vargas
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York14627, United States
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8
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Maschmann ZA, Chua TK, Chandrasekaran S, Ibáñez H, Crane BR. Redox properties and PAS domain structure of the Escherichia coli energy sensor Aer indicate a multistate sensing mechanism. J Biol Chem 2022; 298:102598. [PMID: 36252616 PMCID: PMC9668731 DOI: 10.1016/j.jbc.2022.102598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
The Per-Arnt-Sim (PAS; named for the representative proteins: Period, Aryl hydrocarbon receptor nuclear translocator protein and Single-minded) domain of the dimeric Escherichia coli aerotaxis receptor Aer monitors cellular respiration through a redox-sensitive flavin adenine dinucleotide (FAD) cofactor. Conformational shifts in the PAS domain instigated by the oxidized FAD (FADOX)/FAD anionic semiquinone (FADASQ) redox couple traverse the HAMP (histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and kinase control domains of the Aer dimer to regulate CheA kinase activity. The PAS domain of Aer is unstable and has not been previously purified. Here, residue substitutions that rescue FAD binding in an FAD binding-deficient full-length Aer variant were used in combination to stabilize the Aer PAS domain. We solved the 2.4 Å resolution crystal structure of this variant, Aer-PAS-GVV, and revealed a PAS fold that contains distinct features associated with FAD-based redox sensing, such as a close contact between the Arg115 side chain and N5 of the isoalloxazine ring and interactions of the flavin with the side chains of His53 and Asn85 that are poised to convey conformational signals from the cofactor to the protein surface. In addition, we determined the FADox/FADASQ formal potentials of Aer-PAS-GVV and full-length Aer reconstituted into nanodiscs. The Aer redox couple is remarkably low at -289.6 ± 0.4 mV. In conclusion, we propose a model for Aer energy sensing based on the low potential of Aer-PAS-FADox/FADASQ couple and the inability of Aer-PAS to bind to the fully reduced FAD hydroquinone.
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Affiliation(s)
- Zachary A Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | | | - Héctor Ibáñez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
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9
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Monteiro T, Moreira M, Gaspar SBR, Almeida MG. Bilirubin oxidase as a single enzymatic oxygen scavenger for the development of reductase-based biosensors in the open air and its application on a nitrite biosensor. Biosens Bioelectron 2022; 217:114720. [PMID: 36148736 DOI: 10.1016/j.bios.2022.114720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022]
Abstract
The commercialization of amperometric or voltammetric biosensors that operate at potentials lower than -0.2 V vs SHE has been hindered by the need for anoxic working conditions due to the interference of molecular oxygen, whose electrochemical reduction can potentially mask other redox processes and generate reactive oxygen species (ROS). A deoxygenation step must be thus integrated into the analytical process. To this end, several (bio)chemical oxygen scavenging systems have been proposed, such as the bi-enzyme system, glucose oxidase/catalase. Still, a few issues persist owing to enzyme impurities and the formation of oxygen reactive species. Here in, we propose a new mono-enzymatic oxygen scavenging system composed of a multicopper oxidase as a single biocatalytic oxygen reducer. As a model, we used bilirubin oxidase (BOD), which catalyzes the direct reduction of oxygen to water in the presence of an electron donor substrate, without releasing hydrogen peroxide. Both the direct electron transfer and mediated electrochemical approach using different co-substrates were screened for the ability to promote the enzymatic reduction of oxygen. An optimal combination of BOD with sodium ascorbate proved to be quick (5 min) and effective. It was subsequently employed, as a proof-of-concept, in a voltammetric biosensor based on a multiheme cytochrome c nitrite reductase, which performs the reduction of nitrite to ammonia at potentials below -0.3 V vs SHE. The nitrite biosensor performed well under ambient air, with no need for a second enzyme to account for the build-up of oxygen reactive intermediaries.
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Affiliation(s)
- Tiago Monteiro
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Miguel Moreira
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Sara B R Gaspar
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Maria Gabriela Almeida
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry / Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; Centro de investigação interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511, Caparica, Portugal.
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10
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Competition between intra-protein charge recombination and electron transfer outside photosystem I complexes used for photovoltaic applications. Photochem Photobiol Sci 2022; 21:319-336. [PMID: 35119621 DOI: 10.1007/s43630-022-00170-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/07/2022] [Indexed: 02/01/2023]
Abstract
Photosystem I (PSI) complexes isolated from three different species were electrodeposited on FTO conducting glass, forming a photoactive multilayer of the photo-electrode, for investigation of intricate electron transfer (ET) properties in such green hybrid nanosystems. The internal quantum efficiency of photo-electrochemical cells (PEC) containing the PSI-based photo-electrodes did not exceed ~ 0.5%. To reveal the reason for such a low efficiency of photocurrent generation, the temporal evolution of the transient concentration of the photo-oxidized primary electron donor, P+, was studied in aqueous suspensions of the PSI complexes by time-resolved absorption spectroscopy. The results of these measurements provided the information on: (1) completeness of charge separation in PSI reaction centers (RCs), (2) dynamics of internal charge recombination, and (3) efficiency of electron transfer from PSI to the electrolyte, which is the reaction competing with the internal charge recombination in the PSI RC. The efficiency of the full charge separation in the PSI complexes used for functionalization of the electrodes was ~ 90%, indicating that incomplete charge separation was not the main reason for the small yield of photocurrents. For the PSI particles isolated from a green alga Chlamydomonas reinhardtii, the probability of ET outside PSI was ~ 30-40%, whereas for their counterparts isolated from a cyanobacterium Synechocystis sp. PCC 6803 and a red alga Cyanidioschyzon merolae, it represented a mere ~ 4%. We conclude from the transient absorption data for the PSI biocatalysts in solution that the observed small photocurrent efficiency of ~ 0.5% for all the PECs analyzed in this study is likely due to: (1) limited efficiency of ET outside PSI, particularly in the case of PECs based on PSI from Synechocystis and C. merolae, and (2) the electrolyte-mediated electric short-circuiting in PSI particles forming the photoactive layer, particularly in the case of the C. reinhardtii PEC.
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11
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Nam D, Tinoco A, Shen Z, Adukure RD, Sreenilayam G, Khare SD, Fasan R. Enantioselective Synthesis of α-Trifluoromethyl Amines via Biocatalytic N-H Bond Insertion with Acceptor-Acceptor Carbene Donors. J Am Chem Soc 2022; 144:2590-2602. [PMID: 35107997 PMCID: PMC8855427 DOI: 10.1021/jacs.1c10750] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The biocatalytic
toolbox has recently been expanded to include
enzyme-catalyzed carbene transfer reactions not occurring in Nature.
Herein, we report the development of a biocatalytic strategy for the
synthesis of enantioenriched α-trifluoromethyl amines through
an asymmetric N–H carbene insertion reaction catalyzed by engineered
variants of cytochrome c552 from Hydrogenobacter thermophilus. Using a combination of protein and substrate engineering, this
metalloprotein scaffold was redesigned to enable the synthesis of
chiral α-trifluoromethyl amino esters with up to >99% yield
and 95:5 er using benzyl 2-diazotrifluoropropanoate as the carbene
donor. When the diazo reagent was varied, the enantioselectivity of
the enzyme could be inverted to produce the opposite enantiomers of
these products with up to 99.5:0.5 er. This methodology is applicable
to a broad range of aryl amine substrates, and it can be leveraged
to obtain chemoenzymatic access to enantioenriched β-trifluoromethyl-β-amino
alcohols and halides. Computational analyses provide insights into
the interplay of protein- and reagent-mediated control on the enantioselectivity
of this reaction. This work introduces the first example of a biocatalytic
N–H carbenoid insertion with an acceptor–acceptor carbene
donor, and it offers a biocatalytic solution for the enantioselective
synthesis of α-trifluoromethylated amines as valuable synthons
for medicinal chemistry and the synthesis of bioactive molecules.
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Affiliation(s)
- Donggeon Nam
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Antonio Tinoco
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Zhuofan Shen
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Ronald D Adukure
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | | | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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12
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Samuelian JS, Gremminger TJ, Song Z, Poudyal RR, Li J, Zhou Y, Staller SA, Carballo JA, Roychowdhury-Saha M, Chen SJ, Burke DH, Heng X, Baum DA. An RNA aptamer that shifts the reduction potential of metabolic cofactors. Nat Chem Biol 2022; 18:1263-1269. [PMID: 36097297 PMCID: PMC9596375 DOI: 10.1038/s41589-022-01121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/25/2022] [Indexed: 01/19/2023]
Abstract
The discovery of ribozymes has inspired exploration of RNA's potential to serve as primordial catalysts in a hypothesized RNA world. Modern oxidoreductase enzymes employ differential binding between reduced and oxidized forms of redox cofactors to alter cofactor reduction potential and enhance the enzyme's catalytic capabilities. The utility of differential affinity has been underexplored as a chemical strategy for RNA. Here we show an RNA aptamer that preferentially binds oxidized forms of flavin over reduced forms and markedly shifts flavin reduction potential by -40 mV, similar to shifts for oxidoreductases. Nuclear magnetic resonance structural analysis revealed π-π and donor atom-π interactions between the aptamer and flavin that cause unfavorable contacts with the electron-rich reduced form, suggesting a mechanism by which the local environment of the RNA-binding pocket drives the observed shift in cofactor reduction potential. It seems likely that primordial RNAs could have used similar strategies in RNA world metabolisms.
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Affiliation(s)
- John S. Samuelian
- grid.262962.b0000 0004 1936 9342Department of Chemistry, Saint Louis University, St. Louis, MO USA
| | - Thomas J. Gremminger
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,Present Address: KCAS, LLC, Shawnee, KS USA
| | - Zhenwei Song
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA
| | - Raghav R. Poudyal
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Bond Life Sciences Center, University of Missouri, Columbia, MO USA ,grid.410513.20000 0000 8800 7493Present Address: Pfizer, Biomedicine Design, Cambridge, MA USA
| | - Jun Li
- grid.134936.a0000 0001 2162 3504Department of Physics, University of Missouri, Columbia, MO USA
| | - Yuanzhe Zhou
- grid.134936.a0000 0001 2162 3504Department of Physics, University of Missouri, Columbia, MO USA
| | - Seth A. Staller
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,Present Address: Laronde, Inc., Cambridge, MA USA
| | - Johan A. Carballo
- grid.262962.b0000 0004 1936 9342Department of Chemistry, Saint Louis University, St. Louis, MO USA
| | - Manami Roychowdhury-Saha
- grid.411377.70000 0001 0790 959XDepartment of Chemistry, Indiana University, Bloomington, IN USA ,grid.505809.10000 0004 5998 7997Present Address: GRAIL, Menlo Park, CA USA
| | - Shi-Jie Chen
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Physics, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Institute for Data Science and Informatics, University of Missouri, Columbia, MO USA
| | - Donald H. Burke
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Bond Life Sciences Center, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Biological Engineering, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO USA
| | - Xiao Heng
- grid.134936.a0000 0001 2162 3504Department of Biochemistry, University of Missouri, Columbia, MO USA
| | - Dana A. Baum
- grid.262962.b0000 0004 1936 9342Department of Chemistry, Saint Louis University, St. Louis, MO USA
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13
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Abstract
Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.
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15
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Pott M, Tinzl M, Hayashi T, Ota Y, Dunkelmann D, Mittl PRE, Hilvert D. Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme*. Angew Chem Int Ed Engl 2021; 60:15063-15068. [PMID: 33880851 DOI: 10.1002/anie.202103437] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 11/06/2022]
Abstract
Changing the primary metal coordination sphere is a powerful strategy for tuning metalloprotein properties. Here we used amber stop codon suppression with engineered pyrrolysyl-tRNA synthetases, including two newly evolved enzymes, to replace the proximal histidine in myoglobin with Nδ -methylhistidine, 5-thiazoylalanine, 4-thiazoylalanine and 3-(3-thienyl)alanine. In addition to tuning the heme redox potential over a >200 mV range, these noncanonical ligands modulate the protein's carbene transfer activity with ethyl diazoacetate. Variants with increased reduction potential proved superior for cyclopropanation and N-H insertion, whereas variants with reduced Eo values gave higher S-H insertion activity. Given the functional importance of histidine in many enzymes, these genetically encoded analogues could be valuable tools for probing mechanism and enabling new chemistries.
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Affiliation(s)
- Moritz Pott
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Takahiro Hayashi
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Yusuke Ota
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Daniel Dunkelmann
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, 8057, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
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16
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Pott M, Tinzl M, Hayashi T, Ota Y, Dunkelmann D, Mittl PRE, Hilvert D. Noncanonical Heme Ligands Steer Carbene Transfer Reactivity in an Artificial Metalloenzyme**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Moritz Pott
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Matthias Tinzl
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Takahiro Hayashi
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Yusuke Ota
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | | | - Peer R. E. Mittl
- Department of Biochemistry University of Zürich 8057 Zürich Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
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17
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Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbß by coupling gas binding to electron transfer. Proc Natl Acad Sci U S A 2021; 118:2016717118. [PMID: 33436410 DOI: 10.1073/pnas.2016717118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rev-Erbβ is a nuclear receptor that couples circadian rhythm, metabolism, and inflammation. Heme binding to the protein modulates its function as a repressor, its stability, its ability to bind other proteins, and its activity in gas sensing. Rev-Erbβ binds Fe3+-heme more tightly than Fe2+-heme, suggesting its activities may be regulated by the heme redox state. Yet, this critical role of heme redox chemistry in defining the protein's resting state and function is unknown. We demonstrate by electrochemical and whole-cell electron paramagnetic resonance experiments that Rev-Erbβ exists in the Fe3+ form within the cell allowing the protein to be heme replete even at low concentrations of labile heme in the nucleus. However, being in the Fe3+ redox state contradicts Rev-Erb's known function as a gas sensor, which dogma asserts must be Fe2+ This paper explains why the resting Fe3+ state is congruent both with heme binding and cellular gas sensing. We show that the binding of CO/NO elicits a striking increase in the redox potential of the Fe3+/Fe2+ couple, characteristic of an EC mechanism in which the unfavorable Electrochemical reduction of heme is coupled to the highly favorable Chemical reaction of gas binding, making the reduction spontaneous. Thus, Fe3+-Rev-Erbβ remains heme-loaded, crucial for its repressor activity, and undergoes reduction when diatomic gases are present. This work has broad implications for proteins in which ligand-triggered redox changes cause conformational changes influencing its function or interprotein interactions (e.g., between NCoR1 and Rev-Erbβ). This study opens up the possibility of CO/NO-mediated regulation of the circadian rhythm through redox changes in Rev-Erbβ.
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18
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Featherston ER, Mattocks JA, Tirsch JL, Cotruvo JA. Heterologous expression, purification, and characterization of proteins in the lanthanome. Methods Enzymol 2021; 650:119-157. [PMID: 33867019 DOI: 10.1016/bs.mie.2021.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent work has revealed that certain lanthanides-in particular, the more earth-abundant, lighter lanthanides-play essential roles in pyrroloquinoline quinone (PQQ) dependent alcohol dehydrogenases from methylotrophic and non-methylotrophic bacteria. More recently, efforts of several laboratories have begun to identify the molecular players (the lanthanome) involved in selective uptake, recognition, and utilization of lanthanides within the cell. In this chapter, we present protocols for the heterologous expression in Escherichia coli, purification, and characterization of many of the currently known proteins that comprise the lanthanome of the model facultative methylotroph, Methylorubrum extorquens AM1. In addition to the methanol dehydrogenase XoxF, these proteins include the associated c-type cytochrome, XoxG, and solute binding protein, XoxJ. We also present new, streamlined protocols for purification of the highly selective lanthanide-binding protein, lanmodulin, and a solute binding protein for PQQ, PqqT. Finally, we discuss simple, spectroscopic methods for determining lanthanide- and PQQ-binding stoichiometry of proteins. We envision that these protocols will be useful to investigators identifying and characterizing novel members of the lanthanome in many organisms.
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Affiliation(s)
- Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Jonathan L Tirsch
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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19
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Maklashina E, Cecchini G. Determination of Flavin Potential in Proteins by Xanthine/Xanthine Oxidase Method. Bio Protoc 2020; 10:e3571. [PMID: 33659541 DOI: 10.21769/bioprotoc.3571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/02/2022] Open
Abstract
This protocol describes a simple xanthine/xanthine oxidase enzymatic equilibration method for determination of the redox potential of a flavin. As an example of the use of this method, we determine the reduction potential of the covalently bound FAD cofactor ( Em = -55 mV) in the SdhA flavoprotein subunit of succinate dehydrogenase from Escherichia coli. In principle, this method can be used routinely to determine the redox potential of flavin cofactors in any simple flavoprotein from equilibrium concentrations with an appropriate reference dye of known Em without the use of sophisticated electrochemical equipment.
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Affiliation(s)
- Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, USA.,Department of Biochemistry & Biophysics, University of California, San Francisco, Ca 95158, USA
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121, USA.,Department of Biochemistry & Biophysics, University of California, San Francisco, Ca 95158, USA
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20
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Bertsova YV, Kulik LV, Mamedov MD, Baykov AA, Bogachev AV. Flavodoxin with an air-stable flavin semiquinone in a green sulfur bacterium. PHOTOSYNTHESIS RESEARCH 2019; 142:127-136. [PMID: 31302833 DOI: 10.1007/s11120-019-00658-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Flavodoxins are small proteins with a non-covalently bound FMN that can accept two electrons and accordingly adopt three redox states: oxidized (quinone), one-electron reduced (semiquinone), and two-electron reduced (quinol). In iron-deficient cyanobacteria and algae, flavodoxin can substitute for ferredoxin as the electron carrier in the photosynthetic electron transport chain. Here, we demonstrate a similar function for flavodoxin from the green sulfur bacterium Chlorobium phaeovibrioides (cp-Fld). The expression of the cp-Fld gene, found in a close proximity with the genes for other proteins associated with iron transport and storage, increased in a low-iron medium. cp-Fld produced in Escherichia coli exhibited the optical, ERP, and electron-nuclear double resonance spectra that were similar to those of known flavodoxins. However, unlike all other flavodoxins, cp-Fld exhibited unprecedented stability of FMN semiquinone to oxidation by air and difference in midpoint redox potentials for the quinone-semiquinone and semiquinone-quinol couples (- 110 and - 530 mV, respectively). cp-Fld could be reduced by pyruvate:ferredoxin oxidoreductase found in the membrane-free extract of Chl. phaeovibrioides cells and photo-reduced by the photosynthetic reaction center found in membrane vesicles from these cells. The green sulfur bacterium Chl. phaeovibrioides appears thus to be a new type of the photosynthetic organisms that can use flavodoxin as an alternative electron carrier to cope with iron deficiency.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Leonid V Kulik
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk, Russia, 630090
- Novosibirsk State University, Novosibirsk, Russia, 630090
| | - Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119234.
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21
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Carminati DM, Fasan R. Stereoselective Cyclopropanation of Electron-Deficient Olefins with a Cofactor Redesigned Carbene Transferase Featuring Radical Reactivity. ACS Catal 2019; 9:9683-9697. [PMID: 32257582 DOI: 10.1021/acscatal.9b02272] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Engineered myoglobins and other hemoproteins have recently emerged as promising catalysts for asymmetric olefin cyclopropanation reactions via carbene transfer chemistry. Despite this progress, the transformation of electron-poor alkenes has proven very challenging using these systems. Here, we describe the design of a myoglobin-based carbene transferase incorporating a non-native iron-porphyrin cofactor and axial ligand, as an efficient catalyst for the asymmetric cyclopropanation of electron-deficient alkenes. Using this metalloenzyme, a broad range of both electron-rich and electron-deficient alkenes are cyclopropanated with high efficiency and high diastereo- and enantioselectivity (up to >99% de and ee). Mechanistic studies revealed that the expanded reaction scope of this carbene transferase is dependent upon the acquisition of metallocarbene radical reactivity as a result of the reconfigured coordination environment around the metal center. The radical-based reactivity of this system diverges from the electrophilic reactivity of myoglobin and most of known organometallic carbene transfer catalysts. This work showcases the value of cofactor redesign toward tuning and expanding the reactivity of metalloproteins in abiological reactions and it provides a biocatalytic solution to the asymmetric cyclopropanation of electrodeficient alkenes. The metallocarbene radical reactivity exhibited by this biocatalyst is anticipated to prove useful in the context of a variety of other synthetic transformations.
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Affiliation(s)
- Daniela M. Carminati
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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22
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Freeman SL, Kwon H, Portolano N, Parkin G, Venkatraman Girija U, Basran J, Fielding AJ, Fairall L, Svistunenko DA, Moody PCE, Schwabe JWR, Kyriacou CP, Raven EL. Heme binding to human CLOCK affects interactions with the E-box. Proc Natl Acad Sci U S A 2019; 116:19911-19916. [PMID: 31527239 PMCID: PMC6778266 DOI: 10.1073/pnas.1905216116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The circadian clock is an endogenous time-keeping system that is ubiquitous in animals and plants as well as some bacteria. In mammals, the clock regulates the sleep-wake cycle via 2 basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain proteins-CLOCK and BMAL1. There is emerging evidence to suggest that heme affects circadian control, through binding of heme to various circadian proteins, but the mechanisms of regulation are largely unknown. In this work we examine the interaction of heme with human CLOCK (hCLOCK). We present a crystal structure for the PAS-A domain of hCLOCK, and we examine heme binding to the PAS-A and PAS-B domains. UV-visible and electron paramagnetic resonance spectroscopies are consistent with a bis-histidine ligated heme species in solution in the oxidized (ferric) PAS-A protein, and by mutagenesis we identify His144 as a ligand to the heme. There is evidence for flexibility in the heme pocket, which may give rise to an additional Cys axial ligand at 20K (His/Cys coordination). Using DNA binding assays, we demonstrate that heme disrupts binding of CLOCK to its E-box DNA target. Evidence is presented for a conformationally mobile protein framework, which is linked to changes in heme ligation and which has the capacity to affect binding to the E-box. Within the hCLOCK structural framework, this would provide a mechanism for heme-dependent transcriptional regulation.
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Affiliation(s)
- Samuel L Freeman
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom
| | - Hanna Kwon
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom
| | - Nicola Portolano
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Gary Parkin
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Umakhanth Venkatraman Girija
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Jaswir Basran
- Department of Chemistry, University of Leicester, LE1 7RH Leicester, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Alistair J Fielding
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, United Kingdom
| | - Peter C E Moody
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Charalambos P Kyriacou
- Department of Genetics and Genome Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, BS8 1TS Bristol, United Kingdom;
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23
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Featherston ER, Rose HR, McBride MJ, Taylor EM, Boal AK, Cotruvo JA. Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity. Chembiochem 2019; 20:2360-2372. [PMID: 31017712 PMCID: PMC6814260 DOI: 10.1002/cbic.201900184] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 12/31/2022]
Abstract
Lanthanide (Ln)-dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems contain two other proteins, XoxG (a c-type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. In this work, we have biochemically and structurally characterized these proteins from the methyltroph Methylobacterium extorquens AM1. In contrast to results obtained in an artificial assay system, assays of XoxFs metallated with LaIII , CeIII , and NdIII using their physiological electron acceptor, XoxG, display Ln-independent activities, but the Km for XoxG markedly increases from La to Nd. This result suggests that XoxG's redox properties are tuned specifically for lighter Lns in XoxF, an interpretation supported by the unusually low reduction potential of XoxG (+172 mV). The X-ray crystal structure of XoxG provides a structural basis for this reduction potential and insight into the XoxG-XoxF interaction. Finally, the X-ray crystal structure of XoxJ reveals a large hydrophobic cleft and suggests a role in the activation of XoxF. These studies enrich our understanding of the underlying chemical principles that enable the activity of XoxF with multiple lanthanides in vitro and in vivo.
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Affiliation(s)
- Emily R. Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hannah R. Rose
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elle M. Taylor
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph A. Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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24
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Amdahl MB, Petersen EE, Bocian K, Kaliszuk SJ, DeMartino AW, Tiwari S, Sparacino-Watkins CE, Corti P, Rose JJ, Gladwin MT, Fago A, Tejero J. The Zebrafish Cytochrome b5/Cytochrome b5 Reductase/NADH System Efficiently Reduces Cytoglobins 1 and 2: Conserved Activity of Cytochrome b5/Cytochrome b5 Reductases during Vertebrate Evolution. Biochemistry 2019; 58:3212-3223. [PMID: 31257865 DOI: 10.1021/acs.biochem.9b00406] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cytoglobin is a heme protein evolutionarily related to hemoglobin and myoglobin. Cytoglobin is expressed ubiquitously in mammalian tissues; however, its physiological functions are yet unclear. Phylogenetic analyses indicate that the cytoglobin gene is highly conserved in vertebrate clades, from fish to reptiles, amphibians, birds, and mammals. Most proposed roles for cytoglobin require the maintenance of a pool of reduced cytoglobin (FeII). We have shown previously that the human cytochrome b5/cytochrome b5 reductase system, considered a quintessential hemoglobin/myoglobin reductant, can reduce human and zebrafish cytoglobins ≤250-fold faster than human hemoglobin or myoglobin. It was unclear whether this reduction of zebrafish cytoglobins by mammalian proteins indicates a conserved pathway through vertebrate evolution. Here, we report the reduction of zebrafish cytoglobins 1 and 2 by the zebrafish cytochrome b5 reductase and the two zebrafish cytochrome b5 isoforms. In addition, the reducing system also supports reduction of Globin X, a conserved globin in fish and amphibians. Indeed, the zebrafish reducing system can maintain a fully reduced pool for both cytoglobins, and both cytochrome b5 isoforms can support this process. We determined the P50 for oxygen to be 0.5 Torr for cytoglobin 1 and 4.4 Torr for cytoglobin 2 at 25 °C. Thus, even at low oxygen tensions, the reduced cytoglobins may exist in a predominant oxygen-bound form. Under these conditions, the cytochrome b5/cytochrome b5 reductase system can support a conserved role for cytoglobins through evolution, providing electrons for redox signaling reactions such as nitric oxide dioxygenation, nitrite reduction, and phospholipid oxidation.
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Affiliation(s)
- Matthew B Amdahl
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Elin E Petersen
- Department of Bioscience , Aarhus University , DK-8000 Aarhus C, Denmark
| | - Kaitlin Bocian
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Stefan J Kaliszuk
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Anthony W DeMartino
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Sagarika Tiwari
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Courtney E Sparacino-Watkins
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Jason J Rose
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Division of Pulmonary, Allergy and Critical Care Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Mark T Gladwin
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Division of Pulmonary, Allergy and Critical Care Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Angela Fago
- Department of Bioscience , Aarhus University , DK-8000 Aarhus C, Denmark
| | - Jesús Tejero
- Heart, Lung, Blood, and Vascular Medicine Institute , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Bioengineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Division of Pulmonary, Allergy and Critical Care Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States.,Department of Pharmacology and Chemical Biology , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
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25
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A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species. Proc Natl Acad Sci U S A 2019; 116:14955-14960. [PMID: 31270241 DOI: 10.1073/pnas.1904234116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Many bacteria contain cytoplasmic chemoreceptors that lack sensor domains. Here, we demonstrate that such cytoplasmic receptors found in 8 different bacterial and archaeal phyla genetically couple to metalloproteins related to β-lactamases and nitric oxide reductases. We show that this oxygen-binding di-iron protein (ODP) acts as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable μ-peroxo adduct. Crystal structures of ODP from Td and the thermophile Thermotoga maritima (Tm) in the Fe[III]2-O2 2-, Zn[II], and apo states display differences in subunit association, conformation, and metal coordination that indicate potential mechanisms for sensing. In reconstituted systems, iron-peroxo ODP destabilizes the phosphorylated form of the receptor-coupled histidine kinase CheA, thereby providing a biochemical link between oxygen sensing and chemotaxis in diverse prokaryotes, including anaerobes of ancient origin.
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Wang Y, Davis I, Shin I, Wherritt DJ, Griffith WP, Dornevil K, Colabroy KL, Liu A. Biocatalytic Carbon-Hydrogen and Carbon-Fluorine Bond Cleavage through Hydroxylation Promoted by a Histidyl-Ligated Heme Enzyme. ACS Catal 2019; 9:4764-4776. [PMID: 31355048 DOI: 10.1021/acscatal.9b00231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
LmbB2 is a peroxygenase-like enzyme that hydroxylates L-tyrosine to L-3,4-dihydroxyphenylalanine (DOPA) in the presence of hydrogen peroxide. However, its heme cofactor is ligated by a proximal histidine, not cysteine. We show that LmbB2 can oxidize L-tyrosine analogs with ring-deactivated substituents such as 3-nitro-, fluoro-, chloro-, iodo-L-tyrosine. We also found that the 4-hydroxyl group of the substrate is essential for reacting with the heme-based oxidant and activating the aromatic C-H bond. The most interesting observation of this study was obtained with 3-fluoro-L-tyrosine as a substrate and mechanistic probe. The LmbB2-mediated catalytic reaction yielded two hydroxylated products with comparable populations, i.e., oxidative C-H bond cleavage at C5 to generate 3-fluoro-5-hydroxyl-L-tyrosine and oxygenation at C3 concomitant with a carbon-fluorine bond cleavage to yield DOPA and fluoride. An iron protein-mediated hydroxylation on both C-H and C-F bonds with multiple turnovers is unprecedented. Thus, this finding reveals a significant potential of biocatalysis in C-H/C-X bond (X = halogen) cleavage. Further 18O-labeling results suggest that the source of oxygen for hydroxylation is a peroxide, and that a commonly expected oxidation by a high-valent iron intermediate followed by hydrolysis is not supported for the C-F bond cleavage. Instead, the C-F bond cleavage is proposed to be initiated by a nucleophilic aromatic substitution mediated by the iron-hydroperoxo species. Based on the experimental results, two mechanisms are proposed to explain how LmbB2 hydroxylates the substrate and cleaves C-H/C-F bond. This study broadens the understanding of heme enzyme catalysis and sheds light on enzymatic applications in medicinal and environmental fields.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Inchul Shin
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Daniel J. Wherritt
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Wendell P. Griffith
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Keri L. Colabroy
- Department of Chemistry, Muhlenberg College, Allentown, Pennsylvania 18104, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
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27
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Miller AF, Duan HD, Varner TA, Mohamed Raseek N. Reduction midpoint potentials of bifurcating electron transfer flavoproteins. Methods Enzymol 2019; 620:365-398. [PMID: 31072494 DOI: 10.1016/bs.mie.2019.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recently, a variety of enzymes have been found to accept electrons from NAD(P)H yet reduce lower-potential carriers such as ferredoxin and flavodoxin semiquinone, in apparent violation of thermodynamics. The reaction is favorable overall, however, because these enzymes couple the foregoing endergonic one-electron transfer to exergonic transfer of the other electron from each NAD(P)H, in a process called "flavin-based electron bifurcation." The reduction midpoint potentials (E°s) of the multiple flavins in these enzymes are critical to their mechanisms. We describe methods we have found to be useful for measuring each of the E°s of each of the flavins in bifurcating electron transfer flavoproteins.
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Affiliation(s)
- A-F Miller
- Department of Chemistry, University of Kentucky, Lexington, KY, United States.
| | - H D Duan
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
| | - T A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
| | - N Mohamed Raseek
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
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28
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Schut GJ, Mohamed-Raseek N, Tokmina-Lukaszewska M, Mulder DW, Nguyen DMN, Lipscomb GL, Hoben JP, Patterson A, Lubner CE, King PW, Peters JW, Bothner B, Miller AF, Adams MWW. The catalytic mechanism of electron-bifurcating electron transfer flavoproteins (ETFs) involves an intermediary complex with NAD<sup/>. J Biol Chem 2019; 294:3271-3283. [PMID: 30567738 PMCID: PMC6398123 DOI: 10.1074/jbc.ra118.005653] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/11/2018] [Indexed: 12/20/2022] Open
Abstract
Electron bifurcation plays a key role in anaerobic energy metabolism, but it is a relatively new discovery, and only limited mechanistic information is available on the diverse enzymes that employ it. Herein, we focused on the bifurcating electron transfer flavoprotein (ETF) from the hyperthermophilic archaeon Pyrobaculum aerophilum The EtfABCX enzyme complex couples NADH oxidation to the endergonic reduction of ferredoxin and exergonic reduction of menaquinone. We developed a model for the enzyme structure by using nondenaturing MS, cross-linking, and homology modeling in which EtfA, -B, and -C each contained FAD, whereas EtfX contained two [4Fe-4S] clusters. On the basis of analyses using transient absorption, EPR, and optical titrations with NADH or inorganic reductants with and without NAD+, we propose a catalytic cycle involving formation of an intermediary NAD+-bound complex. A charge transfer signal revealed an intriguing interplay of flavin semiquinones and a protein conformational change that gated electron transfer between the low- and high-potential pathways. We found that despite a common bifurcating flavin site, the proposed EtfABCX catalytic cycle is distinct from that of the genetically unrelated bifurcating NADH-dependent ferredoxin NADP+ oxidoreductase (NfnI). The two enzymes particularly differed in the role of NAD+, the resting and bifurcating-ready states of the enzymes, how electron flow is gated, and the two two-electron cycles constituting the overall four-electron reaction. We conclude that P. aerophilum EtfABCX provides a model catalytic mechanism that builds on and extends previous studies of related bifurcating ETFs and can be applied to the large bifurcating ETF family.
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Affiliation(s)
- Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | | | | | - David W Mulder
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Diep M N Nguyen
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229
| | - John P Hoben
- the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Angela Patterson
- the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Carolyn E Lubner
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - Paul W King
- the Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, and
| | - John W Peters
- the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164
| | - Brian Bothner
- the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Anne-Frances Miller
- the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Michael W W Adams
- From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229,
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Monteiro T, Gomes S, Jubete E, Añorga L, Silveira CM, Almeida MG. A quasi-reagentless point-of-care test for nitrite and unaffected by oxygen and cyanide. Sci Rep 2019; 9:2622. [PMID: 30796298 PMCID: PMC6385495 DOI: 10.1038/s41598-019-39209-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 12/17/2022] Open
Abstract
The ubiquitous nitrite is a major analyte in the management of human health and environmental risks. The current analytical methods are complex techniques that do not fulfil the need for simple, robust and low-cost tools for on-site monitoring. Electrochemical reductase-based biosensors are presented as a powerful alternative, due to their good analytical performance and miniaturization potential. However, their real-world application is limited by the need of anoxic working conditions, and the standard oxygen removal strategies are incompatible with point-of-care measurements. Instead, a bienzymatic oxygen scavenger system comprising glucose oxidase and catalase can be used to promote anoxic conditions in aired environments. Herein, carbon screen-printed electrodes were modified with cytochrome c nitrite reductase together with glucose oxidase and catalase, so that nitrite cathodic detection could be performed by cyclic voltammetry under ambient air. The resulting biosensor displayed good linear response to the analyte (2–200 µM, sensitivity of 326 ± 5 mA M−1 cm−2 at −0.8 V; 0.8–150 µM, sensitivity of 511 ± 11 mA M−1 cm−2 at −0.5 V), while being free from oxygen interference and stable up to 1 month. Furthermore, the biosensor’s catalytic response was unaffected by the presence of cyanide, a well-known inhibitor of heme-enzymes.
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Affiliation(s)
- Tiago Monteiro
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Monte de Caparica, Portugal
| | - Sara Gomes
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Monte de Caparica, Portugal
| | - Elena Jubete
- CIDETEC, Sensors Unit, Parque Científico y Tecnológico de San Sebastián, P° Miramón 196, 2014 Donostia, San Sebastián, Spain
| | - Larraitz Añorga
- CIDETEC, Sensors Unit, Parque Científico y Tecnológico de San Sebastián, P° Miramón 196, 2014 Donostia, San Sebastián, Spain
| | - Célia M Silveira
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Monte de Caparica, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Maria Gabriela Almeida
- UCIBIO, REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Monte de Caparica, Portugal. .,Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511, Caparica, Portugal.
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Lim YJ, Foo TC, Yeung AWS, Tu X, Ma Y, Hawkins CL, Witting PK, Jameson GNL, Terentis AC, Thomas SR. Human Indoleamine 2,3-Dioxygenase 1 Is an Efficient Mammalian Nitrite Reductase. Biochemistry 2019; 58:974-986. [PMID: 30585477 DOI: 10.1021/acs.biochem.8b01231] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The heme enzyme indoleamine 2,3-dioxygenase-1 (IDO1) catalyzes the first reaction of l-tryptophan oxidation along the kynurenine pathway. IDO1 is a central immunoregulatory enzyme with important implications for inflammation, infectious disease, autoimmune disorders, and cancer. Here we demonstrate that IDO1 is a mammalian nitrite reductase capable of chemically reducing nitrite to nitric oxide (NO) under hypoxia. Ultraviolet-visible absorption and resonance Raman spectroscopy showed that incubation of dithionite-reduced, ferrous-IDO1 protein (FeII-IDO1) with nitrite under anaerobic conditions resulted in the time-dependent formation of an FeII-nitrosyl IDO1 species, which was inhibited by substrate l-tryptophan, dependent on the concentration of nitrite or IDO1, and independent of the concentration of the reductant, dithionite. The bimolecular rate constant for IDO1 nitrite reductase activity was determined as 5.4 M-1 s-1 (pH 7.4, 23 °C), which was comparable to that measured for myoglobin (3.6 M-1 s-1; pH 7.4, 23 °C), an efficient and biologically important mammalian heme-based nitrite reductase. IDO1 nitrite reductase activity was pH-dependent but differed with myoglobin in that it showed a reduced proton dependency at pH >7. Electron paramagnetic resonance studies measuring NO production showed that the conventional IDO1 dioxygenase reducing cofactors, ascorbate and methylene blue, enhanced IDO1's nitrite reductase activity and the time- and IDO1 concentration-dependent release of NO in a manner inhibited by l-tryptophan or the IDO inhibitor 1-methyl-l-tryptophan. These data identify IDO1 as an efficient mammalian nitrite reductase that is capable of generating NO under anaerobic conditions. IDO1's nitrite reductase activity may have important implications for the enzyme's biological actions when expressed within hypoxic tissues.
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Affiliation(s)
| | - Timothy C Foo
- Department of Chemistry and Biochemistry , Florida Atlantic University , Boca Raton , Florida 33431 , United States
| | | | | | | | - Clare L Hawkins
- Department of Biomedical Sciences , University of Copenhagen , Copenhagen N DK-2200 , Denmark
| | - Paul K Witting
- Discipline of Pathology, Charles Perkins Centre, Faculty of Medicine and Health , University of Sydney , Sydney , NSW 2006 , Australia
| | - Guy N L Jameson
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , VIC 3010 , Australia
| | - Andrew C Terentis
- Department of Chemistry and Biochemistry , Florida Atlantic University , Boca Raton , Florida 33431 , United States
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Abstract
The movement or trafficking of heme is critical for cellular functions (e.g., oxygen transport and energy production); however, intracellular heme is tightly regulated due to its inherent cytotoxicity. These factors, combined with the transient nature of transport, have resulted in a lack of direct knowledge on the mechanisms of heme binding and trafficking. Here, we used the cytochrome c biogenesis system II pathway as a model to study heme trafficking. System II is composed of two integral membrane proteins (CcsBA) which function to transport heme across the membrane and stereospecifically position it for covalent attachment to apocytochrome c. We mapped two heme binding domains in CcsBA and suggest a path for heme trafficking. These data, in combination with metagenomic coevolution data, are used to determine a structural model of CcsBA, leading to increased understanding of the mechanisms for heme transport and the cytochrome c synthetase function of CcsBA. Although intracellular heme trafficking must occur for heme protein assembly, only a few heme transporters have been unequivocally discovered and nothing is known about their structure or mechanisms. Cytochrome c biogenesis in prokaryotes requires the transport of heme from inside to outside for stereospecific attachment to cytochrome c via two thioether bonds (at CXXCH). The CcsBA integral membrane protein was shown to transport and attach heme (and thus is a cytochrome c synthetase), but the structure and mechanisms underlying these two activities are poorly understood. We employed a new cysteine/heme crosslinking tool that traps endogenous heme in heme binding sites. We combined these data with a comprehensive imidazole correction approach (for heme ligand interrogation) to map heme binding sites. Results illuminate the process of heme transfer through the membrane to an external binding site (called the WWD domain). Using meta-genomic data (GREMLIN) and Rosetta modeling programs, a structural model of the transmembrane (TM) regions in CcsBA were determined. The heme mapping data were then incorporated to model the TM heme binding site (with TM-His1 and TM-His2 as ligands) and the external heme binding WWD domain (with P-His1 and P-His2 as ligands). Other periplasmic structure/function studies facilitated modeling of the full CcsBA protein as a framework for understanding the mechanisms. Mechanisms are proposed for heme transport from TM-His to WWD/P-His and subsequent stereospecific attachment of heme. A ligand exchange of the P-His1 for histidine of CXXCH at the synthetase active site is suggested.
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Sarma MK, Quadir MGA, Bhaduri R, Kaushik S, Goswami P. Composite polymer coated magnetic nanoparticles based anode enhances dye degradation and power production in microbial fuel cells. Biosens Bioelectron 2018; 119:94-102. [DOI: 10.1016/j.bios.2018.07.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 12/25/2022]
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Bacon BA, Liu Y, Kincaid JR, Boon EM. Spectral Characterization of a Novel NO Sensing Protein in Bacteria: NosP. Biochemistry 2018; 57:6187-6200. [PMID: 30272959 DOI: 10.1021/acs.biochem.8b00451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A novel family of bacterial hemoproteins named NosP has been discovered recently; its members are proposed to function as nitric oxide (NO) responsive proteins involved in bacterial group behaviors such as quorum sensing and biofilm growth and dispersal. Currently, little is known about molecular activation mechanisms in NosP. Here, functional studies were performed utilizing the distinct spectroscopic characteristics associated with the NosP heme cofactor. NosPs from Pseudomonas aeruginosa ( Pa), Vibrio cholerae ( Vc), and Legionella pneumophila ( Lpg) were studied in their ferrous unligated forms as well as their ferrous CO, ferrous NO, and ferric CN adducts. The resonance Raman (rR) data collected on the ferric forms strongly support the existence of a distorted heme cofactor, which is a common feature in NO sensors. The ferrous spectra exhibit a 213 cm-1 feature, which is assigned to the Fe-Nhis stretching mode. The Fe-C and C-O frequencies in the spectra of ferrous CO NosP complexes are inversely correlated with relatively similar frequencies, consistent with a proximal histidine ligand and a relatively hydrophobic environment. The rR spectra obtained for isotopically labeled ferrous NO adducts provide evidence of formation of a 5-coordinate NO complex, resulting from proximal Fe-Nhis cleavage, which is believed to play a role in biological heme-NO signal transduction. Additionally, we found that of the three NosPs studied, Lpg NosP contains the most electropositive ligand binding pocket, while Pa NosP has the most electronegative ligand binding pocket. This pattern is also observed in the measured heme reduction potentials for these three proteins, which may indicate distinct functions for each.
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Affiliation(s)
- Bezalel A Bacon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States
| | - Yilin Liu
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - James R Kincaid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Elizabeth M Boon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States.,Department of Chemistry and Institute of Chemical Biology and Drug Discovery , Stony Brook University , Stony Brook , New York 11794-3400 , United States
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35
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Johnson EA, Russo MM, Nye DB, Schlessman JL, Lecomte JTJ. Lysine as a heme iron ligand: A property common to three truncated hemoglobins from Chlamydomonas reinhardtii. Biochim Biophys Acta Gen Subj 2018; 1862:2660-2673. [PMID: 30251657 DOI: 10.1016/j.bbagen.2018.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND The nuclear genome of Chlamydomonas reinhardtii encodes a dozen hemoglobins of the truncated lineage. Four of these, named THB1-4, contain a single ~130-residue globin unit. THB1, which is cytoplasmic and capable of nitric oxide dioxygenation activity, uses a histidine and a lysine as axial ligands to the heme iron. In the present report, we compared THB2, THB3, and THB4 to THB1 to gain structural and functional insights into algal globins. METHODS We inspected properties of the globin domains prepared by recombinant means through site-directed mutagenesis, electronic absorption, CD, and NMR spectroscopies, and X-ray crystallography. RESULTS Recombinant THB3, which lacks the proximal histidine but has a distal histidine, binds heme weakly. NMR data demonstrate that the recombinant domains of THB2 and THB4 coordinate the ferrous heme iron with the proximal histidine and a lysine from the distal helix. An X-ray structure of ferric THB4 confirms lysine coordination. THB1, THB2, and THB4 have reduction potentials between -65 and -100 mV, are capable of nitric oxide dioxygenation, are reduced at different rates by the diaphorase domain of C. reinhardtii nitrate reductase, and show different response to peroxide treatment. CONCLUSIONS Three single-domain C. reinhardtii hemoglobins use lysine as a distal heme ligand in both Fe(III) and Fe(II) oxidation states. This common feature is likely related to enzymatic activity in the management of reactive oxygen species. GENERAL SIGNIFICANCE Primary structure analysis of hemoglobins has limited power in the prediction of heme ligation. Experimental determination reveals variations in this essential property across the superfamily.
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Affiliation(s)
- Eric A Johnson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Miranda M Russo
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Jamie L Schlessman
- Chemistry Department, U.S. Naval Academy, Annapolis, MD 21402, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
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36
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Capture and characterization of a reactive haem–carbenoid complex in an artificial metalloenzyme. Nat Catal 2018. [DOI: 10.1038/s41929-018-0105-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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37
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Maklashina E, Rajagukguk S, Iverson TM, Cecchini G. The unassembled flavoprotein subunits of human and bacterial complex II have impaired catalytic activity and generate only minor amounts of ROS. J Biol Chem 2018; 293:7754-7765. [PMID: 29610278 PMCID: PMC5961047 DOI: 10.1074/jbc.ra118.001977] [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: 01/17/2018] [Revised: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
Complex II (SdhABCD) is a membrane-bound component of mitochondrial and bacterial electron transport chains, as well as of the TCA cycle. In this capacity, it catalyzes the reversible oxidation of succinate. SdhABCD contains the SDHA protein harboring a covalently bound FAD redox center and the iron-sulfur protein SDHB, containing three distinct iron-sulfur centers. When assembly of this complex is compromised, the flavoprotein SDHA may accumulate in the mitochondrial matrix or bacterial cytoplasm. Whether the unassembled SDHA has any catalytic activity, for example in succinate oxidation, fumarate reduction, reactive oxygen species (ROS) generation, or other off-pathway reactions, is not known. Therefore, here we investigated whether unassembled Escherichia coli SdhA flavoprotein, its homolog fumarate reductase (FrdA), and the human SDHA protein have succinate oxidase or fumarate reductase activity and can produce ROS. Using recombinant expression in E. coli, we found that the free flavoproteins from these divergent biological sources have inherently low catalytic activity and generate little ROS. These results suggest that the iron-sulfur protein SDHB in complex II is necessary for robust catalytic activity. Our findings are consistent with those reported for single-subunit flavoprotein homologs that are not associated with iron-sulfur or heme partner proteins.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and
| | - Sany Rajagukguk
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121
| | - T. M. Iverson
- the Departments of Pharmacology and ,Biochemistry, ,the Center for Structural Biology, and ,the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and , Recipient of Senior Research Career Scientist Award IK6BX004215 from the Department of Veterans Affairs. To whom correspondence should be addressed:
Molecular Biology Division (151-S), San Francisco Veterans Affairs Healthcare System, 4150 Clement St., San Francisco, CA 94121. Tel.:
415-221-4810, Ext. 24416; E-mail:
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Duan HD, Lubner CE, Tokmina-Lukaszewska M, Gauss GH, Bothner B, King PW, Peters JW, Miller AF. Distinct properties underlie flavin-based electron bifurcation in a novel electron transfer flavoprotein FixAB from Rhodopseudomonas palustris. J Biol Chem 2018; 293:4688-4701. [PMID: 29462786 DOI: 10.1074/jbc.ra117.000707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/08/2018] [Indexed: 11/06/2022] Open
Abstract
A newly recognized third fundamental mechanism of energy conservation in biology, electron bifurcation, uses free energy from exergonic redox reactions to drive endergonic redox reactions. Flavin-based electron bifurcation furnishes low-potential electrons to demanding chemical reactions, such as reduction of dinitrogen to ammonia. We employed the heterodimeric flavoenzyme FixAB from the diazotrophic bacterium Rhodopseudomonas palustris to elucidate unique properties that underpin flavin-based electron bifurcation. FixAB is distinguished from canonical electron transfer flavoproteins (ETFs) by a second FAD that replaces the AMP of canonical ETF. We exploited near-UV-visible CD spectroscopy to resolve signals from the different flavin sites in FixAB and to interrogate the putative bifurcating FAD. CD aided in assigning the measured reduction midpoint potentials (E° values) to individual flavins, and the E° values tested the accepted model regarding the redox properties required for bifurcation. We found that the higher-E° flavin displays sequential one-electron (1-e-) reductions to anionic semiquinone and then to hydroquinone, consistent with the reactivity seen in canonical ETFs. In contrast, the lower-E° flavin displayed a single two-electron (2-e-) reduction without detectable accumulation of semiquinone, consistent with unstable semiquinone states, as required for bifurcation. This is the first demonstration that a FixAB protein possesses the thermodynamic prerequisites for bifurcating activity, and the separation of distinct optical signatures for the two flavins lays a foundation for mechanistic studies to learn how electron flow can be directed in a protein environment. We propose that a novel optical signal observed at long wavelength may reflect electron delocalization between the two flavins.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - George H Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
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Pott M, Hayashi T, Mori T, Mittl PRE, Green AP, Hilvert D. A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold. J Am Chem Soc 2018; 140:1535-1543. [DOI: 10.1021/jacs.7b12621] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Moritz Pott
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Takahiro Hayashi
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Takahiro Mori
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Peer R. E. Mittl
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Anthony P. Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
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40
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Allhorn M, Arve S, Brüggemann H, Lood R. A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes. Sci Rep 2016; 6:36412. [PMID: 27805044 PMCID: PMC5090349 DOI: 10.1038/srep36412] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/10/2016] [Indexed: 12/14/2022] Open
Abstract
The role of the skin microbiota in human health is poorly understood. Here, we identified and characterized a novel antioxidant enzyme produced by the skin microbiota, designated RoxP for radical oxygenase of Propionibacterium acnes. RoxP is uniquely produced by the predominant skin bacterium P. acnes, with no homologs in other bacteria; it is highly expressed and strongly secreted into culture supernatants. We show that RoxP binds heme, reduces free radicals, and can protect molecules from oxidation. Strikingly, RoxP is crucial for the survival of P. acnes in oxic conditions and for skin colonization of P. acnes ex vivo. Taken together, our study strongly suggests that RoxP facilitates P. acnes’ survival on human skin, and is an important beneficial factor for the host-commensal interaction. Thus, RoxP is the first described skin microbiota-derived mutualistic factor that potentially can be exploited for human skin protection.
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Affiliation(s)
- Maria Allhorn
- Department of Clinical Sciences Lund, Division of Infection Medicine, Biomedical Center B14, Lund University, Lund, Sweden
| | - Sabine Arve
- Department of Clinical Sciences Lund, Division of Infection Medicine, Biomedical Center B14, Lund University, Lund, Sweden
| | | | - Rolf Lood
- Department of Clinical Sciences Lund, Division of Infection Medicine, Biomedical Center B14, Lund University, Lund, Sweden
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41
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Fernando JFS, Shortell MP, Noble CJ, Harmer JR, Jaatinen EA, Waclawik ER. Controlling Au Photodeposition on Large ZnO Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2016; 8:14271-83. [PMID: 27196721 DOI: 10.1021/acsami.6b03128] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This study investigated how to control the rate of photoreduction of metastable AuCl2(-) at the solid-solution interface of large ZnO nanoparticles (NPs) (50-100 nm size). Band-gap photoexcitation of electronic charge in ZnO by 370 nm UV light yielded Au NP deposition and the formation of ZnO-Au NP hybrids. Au NP growth was observed to be nonepitaxial, and the patterns of Au photodeposition onto ZnO NPs observed by high-resolution transmission electron microscopy were consistent with reduction of AuCl2(-) at ZnO facet edges and corner sites. Au NP photodeposition was effective in the presence of labile oleylamine ligands attached to the ZnO surface; however, when a strong-binding dodecanethiol ligand coated the surface, photodeposition was quenched. Rates of interfacial electron transfer at the ZnO-solution interface were adjusted by changing the solvent, and these rates were observed to strongly depend on the solvent's permittivity (ε) and viscosity. From measurements of electron transfer from ZnO to the organic dye toluidine blue at the ZnO-solution interface, it was confirmed that low ε solvent mixtures (ε ≈ 9.5) possessed markedly higher rates of photocatalytic interfacial electron transfer (∼3.2 × 10(4) electrons·particle(-1)·s(-1)) compared to solvent mixtures with high ε (ε = 29.9, ∼1.9 × 10(4) electrons·particle(-1)·s(-1)). Dissolved oxygen content in the solvent and the exposure time of ZnO to band-gap, near-UV photoexcitation were also identified as factors that strongly affected Au photodeposition behavior. Production of Au clusters was favored under conditions that caused electron accumulation in the ZnO-Au NP hybrid. Under conditions where electron discharge was rapid (such as in low ε solvents), AuCl2(-) precursor ions photoreduced at ZnO surfaces in less than 5 s, leading to deposition of several small, isolated ∼6 nm Au NP on the ZnO host instead.
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Affiliation(s)
- Joseph F S Fernando
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology , Brisbane, Queensland 4000, Australia
| | - Matthew P Shortell
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology , Brisbane, Queensland 4000, Australia
| | - Christopher J Noble
- Centre for Advanced Imaging, University of Queensland , Brisbane, Queensland 4072, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland , Brisbane, Queensland 4072, Australia
| | - Esa A Jaatinen
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology , Brisbane, Queensland 4000, Australia
| | - Eric R Waclawik
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology , Brisbane, Queensland 4000, Australia
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42
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Sutherland MC, Rankin JA, Kranz RG. Heme Trafficking and Modifications during System I Cytochrome c Biogenesis: Insights from Heme Redox Potentials of Ccm Proteins. Biochemistry 2016; 55:3150-6. [PMID: 27198710 DOI: 10.1021/acs.biochem.6b00427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochromes c require covalent attachment of heme via two thioether bonds at conserved CXXCH motifs, a process accomplished in prokaryotes by eight integral membrane proteins (CcmABCDEFGH), termed System I. Heme is trafficked from inside the cell to outside (via CcmABCD) and chaperoned (holoCcmE) to the cytochrome c synthetase (CcmF/H). Purification of key System I pathway intermediates allowed the determination of heme redox potentials. The data support a model whereby heme is oxidized to form holoCcmE and subsequently reduced by CcmF/H for thioether formation, with Fe(2+) being required for attachment to CXXCH. Results provide insight into mechanisms for the oxidation and reduction of heme in vivo.
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Affiliation(s)
- Molly C Sutherland
- Department of Biology, Washington University , St. Louis, Missouri 63130, United States
| | - Joel A Rankin
- Department of Biology, Washington University , St. Louis, Missouri 63130, United States
| | - Robert G Kranz
- Department of Biology, Washington University , St. Louis, Missouri 63130, United States
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Nnamchi CI, Parkin G, Efimov I, Basran J, Kwon H, Svistunenko DA, Agirre J, Okolo BN, Moneke A, Nwanguma BC, Moody PCE, Raven EL. Structural and spectroscopic characterisation of a heme peroxidase from sorghum. J Biol Inorg Chem 2015; 21:63-70. [PMID: 26666777 PMCID: PMC4771821 DOI: 10.1007/s00775-015-1313-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 10/28/2022]
Abstract
A cationic class III peroxidase from Sorghum bicolor was purified to homogeneity. The enzyme contains a high-spin heme, as evidenced by UV-visible spectroscopy and EPR. Steady state oxidation of guaiacol was demonstrated and the enzyme was shown to have higher activity in the presence of calcium ions. A Fe(III)/Fe(II) reduction potential of -266 mV vs NHE was determined. Stopped-flow experiments with H2O2 showed formation of a typical peroxidase Compound I species, which converts to Compound II in the presence of calcium. A crystal structure of the enzyme is reported, the first for a sorghum peroxidase. The structure reveals an active site that is analogous to those for other class I heme peroxidase, and a substrate binding site (assigned as arising from binding of indole-3-acetic acid) at the γ-heme edge. Metal binding sites are observed in the structure on the distal (assigned as a Na(+) ion) and proximal (assigned as a Ca(2+)) sides of the heme, which is consistent with the Ca(2+)-dependence of the steady state and pre-steady state kinetics. It is probably the case that the structural integrity (and, thus, the catalytic activity) of the sorghum enzyme is dependent on metal ion incorporation at these positions.
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Affiliation(s)
| | - Gary Parkin
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Igor Efimov
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Jaswir Basran
- Department of Molecular and Cell Biology, Henry Wellcome Laboratory for Structural Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK
| | - Hanna Kwon
- Department of Molecular and Cell Biology, Henry Wellcome Laboratory for Structural Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK
| | - Dimitri A Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK
| | | | - Anene Moneke
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | | | - Peter C E Moody
- Department of Molecular and Cell Biology, Henry Wellcome Laboratory for Structural Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK
| | - Emma L Raven
- Department of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Hargrove TY, Wawrzak Z, Lamb DC, Guengerich FP, Lepesheva GI. Structure-Functional Characterization of Cytochrome P450 Sterol 14α-Demethylase (CYP51B) from Aspergillus fumigatus and Molecular Basis for the Development of Antifungal Drugs. J Biol Chem 2015; 290:23916-34. [PMID: 26269599 DOI: 10.1074/jbc.m115.677310] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/18/2023] Open
Abstract
Aspergillus fumigatus is the opportunistic fungal pathogen that predominantly affects the immunocompromised population and causes 600,000 deaths/year. The cytochrome P450 51 (CYP51) inhibitor voriconazole is currently the drug of choice, yet the treatment efficiency remains low, calling for rational development of more efficient agents. A. fumigatus has two CYP51 genes, CYP51A and CYP51B, which share 59% amino acid sequence identity. CYP51B is expressed constitutively, whereas gene CYP51A is reported to be inducible. We expressed, purified, and characterized A. fumigatus CYP51B, including determination of its substrate preferences, catalytic parameters, inhibition, and x-ray structure in complexes with voriconazole and the experimental inhibitor (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide (VNI). The enzyme demethylated its natural substrate eburicol and the plant CYP51 substrate obtusifoliol at steady-state rates of 17 and 16 min(-1), respectively, but did not metabolize lanosterol, and the topical antifungal drug miconazole was the strongest inhibitor that we identified. The x-ray crystal structures displayed high overall similarity of A. fumigatus CYP51B to CYP51 orthologs from other biological kingdoms but revealed phylum-specific differences relevant to enzyme catalysis and inhibition. The complex with voriconazole provides an explanation for the potency of this relatively small molecule, whereas the complex with VNI outlines a direction for further enhancement of the efficiency of this new inhibitory scaffold to treat humans afflicted with filamentous fungal infections.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zdzislaw Wawrzak
- the Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439
| | - David C Lamb
- Swansea University, Swansea, Wales SA2 8PP, United Kingdom, and
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Galina I Lepesheva
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
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