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Sgammato R, Van Brempt N, Aerts R, Van Doorslaer S, Dewilde S, Herrebout W, Johannessen C. Interaction of nitrite with ferric protoglobin from Methanosarcina acetivorans - an interesting model for spectroscopic studies of the haem-ligand interaction. Dalton Trans 2023; 52:2976-2987. [PMID: 36651272 DOI: 10.1039/d2dt03252j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin belonging to the same lineage of the globin superfamily as globin-coupled sensors. A putative role in the scavenging of reactive nitrogen and oxygen species has been suggested as a possible adaptation mechanism of the host organism to different gaseous environments in the course of evolution. A combination of optical absorption, electronic circular dichroism (ECD), resonance Raman (rRaman), and electron paramagnetic resonance (EPR) reveal the unusual in vitro reaction of ferric MaPgb with nitrite. In contrast to other globins, a large excess of nitrite did not induce the formation of a nitriglobin form in MaPgb. Surprisingly, the addition of nitrite in mildly acidic pH led to the formation of a stable nitric-oxide ligated ferric form of the protein (MaPgb-NO). Furthermore, the 300-700 nm ECD spectrum of ferric MaPgb is for the first time reported and discussed, showing strong differences in the Soret and Q ellipticity compared to ferric myoglobin, in line with the unusually strongly ruffled haem group of MaPgb and the related quantum-mechanical admixture of the S = 5/2 and S = 3/2 state of its ferric form. The Soret and Q ellipticity change strongly upon formation of MaPgb-NO, revealing a significant effect of the nitric-oxide ligation on the haem group and pocket. The related changes in the asymmetric pyrrole half-ring stretching vibration modes observed in the rRaman spectra give experimental support to earlier theoretical models, in which an important role of the in-plane breathing modes of the haem was predicted for the stabilization of the binding of diatomic gases to MaPgb.
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Affiliation(s)
- Roberta Sgammato
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Niels Van Brempt
- Laboratory of Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.,Laboratory of Protein Sciences, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Roy Aerts
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Sabine Van Doorslaer
- Laboratory of Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Sylvia Dewilde
- Laboratory of Protein Sciences, Proteomics and Epigenetic Signaling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Wouter Herrebout
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Christian Johannessen
- Laboratory of Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
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Hammerschmid D, Germani F, Drusin SI, Fagnen C, Schuster CD, Hoogewijs D, Marti MA, Venien-Bryan C, Moens L, Van Doorslaer S, Sobott F, Dewilde S. Structural modeling of a novel membrane-bound globin-coupled sensor in Geobacter sulfurreducens. Comput Struct Biotechnol J 2021; 19:1874-1888. [PMID: 33995893 PMCID: PMC8076648 DOI: 10.1016/j.csbj.2021.03.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Globin-coupled sensors (GCS) usually consist of three domains: a sensor/globin, a linker, and a transmitter domain. The globin domain (GD), activated by ligand binding and/or redox change, induces an intramolecular signal transduction resulting in a response of the transmitter domain. Depending on the nature of the transmitter domain, GCSs can have different activities and functions, including adenylate and di-guanylate cyclase, histidine kinase activity, aerotaxis and/or oxygen sensing function. The gram-negative delta-proteobacterium Geobacter sulfurreducens expresses a protein with a GD covalently linked to a four transmembrane domain, classified, by sequence similarity, as GCS (GsGCS). While its GD is fully characterized, not so its transmembrane domain, which is rarely found in the globin superfamily. In the present work, GsGCS was characterized spectroscopically and by native ion mobility-mass spectrometry in combination with cryo-electron microscopy. Although lacking high resolution, the oligomeric state and the electron density map were valuable for further rational modeling of the full-length GsGCS structure. This model demonstrates that GsGCS forms a transmembrane domain-driven tetramer with minimal contact between the GDs and with the heme groups oriented outward. This organization makes an intramolecular signal transduction less likely. Our results, including the auto-oxidation rate and redox potential, suggest a potential role for GsGCS as redox sensor or in a membrane-bound e-/H+ transfer. As such, GsGCS might act as a player in connecting energy production to the oxidation of organic compounds and metal reduction. Database searches indicate that GDs linked to a four or seven helices transmembrane domain occur more frequently than expected.
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Key Words
- AfGcHK, Anaeromyxobacter sp. Fw109-5 GcHK
- AsFRMF, Ascaris suum FRMF-amide receptor
- AvGReg, Azotobacter vinilandii Greg
- BpGReg, Bordetella pertussis Greg
- BsHemAT, Bacillus subtilis HemAT
- CCS, collision cross section
- CIU, collision-induced unfolding
- CMC, critical micelle concentration
- CV, cyclic voltammetry
- CeGLB26, Caenorhabditis elegans globin 26
- CeGLB33, Caenorhabditis elegans globin 33
- CeGLB6, Caenorhabditis elegans globin 6
- DDM, n-dodecyl-β-d-maltoside
- DPV, differential pulse voltammetry
- EcDosC, Escherichia coli Dos with DGC activity
- FMRF, H-Phe-Met-Arg-Phe-NH2 neuropeptide
- GCS, globin-coupled sensor
- GD, globin domain
- GGDEF, Gly-Gly-Asp-Glu-Phe motive
- Gb, globin
- Geobacter sulfurreducens
- GintHb, hemoglobin from Gasterophilus intestinalis
- Globin-coupled sensor
- GsGCS, Geobacter sulfurreducens GCS
- GsGCS162, GD of GsGCS
- IM-MS, ion mobility-mass spectrometry
- LmHemAC, Leishmania major HemAC
- MaPgb, Methanosarcina acetivorans protoglobin
- MtTrHbO, Mycobacterium tuberculosis truncated hemoglobin O
- NH4OAc, ammonium acetate
- OG, n-octyl-β-d-glucopyranoside
- PDE, phosphodiesterase
- PcMb, Physether catodon myoglobin
- PccGCS, Pectobacterium carotivorum GCS
- PsiE, phosphate-starvation-inducible E
- RR, resonance Raman
- SCE, saturated calomel electrode
- SHE, standard hydrogen electrode
- SaktrHb, Streptomyces avermitilis truncated hemoglobin-antibiotic monooxygenase
- SwMb, myoglobin from sperm whale
- TD, Transmitter domain
- TmD, Transmembrane domain
- Transmembrane domain
- Transmembrane-coupled globins
- mNgb, mouse neuroglobin
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Affiliation(s)
- Dietmar Hammerschmid
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Francesca Germani
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Salvador I. Drusin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - David Hoogewijs
- Section of Medicine, Department of Endocrinology, Metabolism and Cardiovascular System, University of Fribourg, Switzerland
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Catherine Venien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 75005 Paris, France
| | - Luc Moens
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Sabine Van Doorslaer
- Biophysics and Biomedical Physics, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Sylvia Dewilde
- Proteinchemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Chiura T, Mak PJ. Investigation of Cyanide Ligand as an Active Site Probe of Human Heme Oxygenase. Inorg Chem 2021; 60:4633-4645. [PMID: 33754715 DOI: 10.1021/acs.inorgchem.0c03611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human heme oxygenase (hHO-1) is a physiologically important enzyme responsible for free heme catabolism. The enzyme's high regiospecificity is controlled by the distal site hydrogen bond network that involves water molecules and the D140 amino acid residue. In this work, we probe the active site environment of the wild-type (WT) hHO-1 and its D140 mutants using resonance Raman (rR) spectroscopy. Cyanide ligands are more stable than dioxygen adducts and are an effective probe of active site environment of heme proteins. The inherently linear geometry of the Fe-C-N fragment can be altered by the steric, electrostatic, and H-bonding interactions imposed by the amino acid residues present in the heme distal site, resulting in a tilted or bent configuration. The WT hHO-1 and its D140A, D140N, and D140E mutants were studied in the presence of natural abundance CN- and its isotopic analogues (13CN-, C15N-, and 13C15N-). Deconvolution of spectral data revealed that the ν(Fe-CN) stretching and δ(Fe-CN) bending modes are present at 454 and 376 cm-1, respectively. The rR spectral patterns of the CN- adducts of WT revealed that the Fe-C-N fragment adopts a tilted conformation, with a larger bending contribution for the D140A, D140N, and D140E mutants. These studies suggest that the FeCN fragment in hHO-1 is tilted more strongly toward the porphyrin macrocycle compared to other histidine-ligated proteins, reflecting the propensity of the exogenous hHO-l ligands to position toward the α-meso-carbon, which is crucial for the HO reactivity and essential for regioselectivity.
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Affiliation(s)
- Tapiwa Chiura
- Chemistry Department, Saint Louis University, Saint Louis, Missouri 63103, United States
| | - Piotr J Mak
- Chemistry Department, Saint Louis University, Saint Louis, Missouri 63103, United States
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4
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Nys K, Cuypers B, Berghmans H, Hammerschmid D, Moens L, Dewilde S, Van Doorslaer S. Surprising differences in the respiratory protein of insects: A spectroscopic study of haemoglobin from the European honeybee and the malaria mosquito. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140413. [PMID: 32179182 DOI: 10.1016/j.bbapap.2020.140413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
Only recently it was discovered that haemoglobin (Hb) belongs to the standard gene repertoire of insects, although their tracheal system is used for respiration. A classical oxygen-carrying function of Hb is only obvious for hexapods living in hypoxic environments. In other insect species, including the common fruit fly Drosophila melanogaster, the physiological role of Hb is yet unclear. Here, we study recombinant haemoglobin from the European honeybee Apis mellifera (Ame) and the malaria mosquito Anopheles gambiae (Aga). Spectroscopic evidence shows that both proteins can be classified as hexacoordinate Hbs with a strong affinity for the distal histidine. AgaHb1 is proposed to play a role in oxygen transport or sensing based on its multimeric state, slow autoxidation, and small but significant amount of five-coordinated haem in the deoxy ferrous form. AmeHb appears to behave more like vertebrate neuroglobin with a complex function given its diversified distribution in the genome.
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Affiliation(s)
- Kevin Nys
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium.
| | - Bert Cuypers
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Herald Berghmans
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | - Dietmar Hammerschmid
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | - Luc Moens
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
| | - Sylvia Dewilde
- PPES Laboratory, Department of Biomedical Sciences, University of Antwerp, Belgium.
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5
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Uchida T, Dojun N, Ota K, Sekine Y, Nakamura Y, Umetsu S, Ishimori K. Role of conserved arginine in the heme distal site of HutZ from Vibrio cholerae in the heme degradation reaction. Arch Biochem Biophys 2019; 677:108165. [PMID: 31689379 DOI: 10.1016/j.abb.2019.108165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
HutZ from Vibrio cholerae is a dimeric enzyme that catalyzes degradation of heme. The highly conserved Arg92 residue in the HutZ family is proposed to interact with an iron-bound water molecule in the distal heme pocket. To clarify the specific role of Arg92 in the heme degradation reaction, the residue was substituted with alanine, leucine, histidine or lysine to modulate electrostatic interactions with iron-bound ligand. All four Arg92 mutants reacted with hydrogen peroxide to form verdoheme, a prominent intermediate in the heme degradation process. However, when ascorbic acid was used as an electron source, iron was not released even at pH 6.0 despite a decrease in the Soret band, indicating that non-enzymatic heme degradation occurred. Comparison of the rates of heme reduction, ligand binding and verdoheme formation suggested that proton transfer to the reduced oxyferrous heme, a potential rate-limiting step of heme degradation in HutZ, is hampered by mutation. In our previous study, we found that the increase in the distance between heme and Trp109 from 16 to 18 Å upon lowering the pH from 8.0 to 6.0 leads to activation of ascorbic acid-assisted heme degradation by HutZ. The distance in Arg92 mutants was >19 Å at pH 6.0, suggesting that subunit-subunit interactions at this pH are not suitable for heme degradation, similar to Asp132 and His63 mutants. These results suggest that interactions of Arg92 with heme-bound ligand induce alterations in the distance between subunits, which plays a key role in controlling the heme degradation activity of HutZ.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan.
| | - Nobuhiko Dojun
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Ota
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yukari Sekine
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuina Nakamura
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Sayaka Umetsu
- Division of Chemistry, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
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6
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Emerging role of carbon monoxide in regulation of cellular pathways and in the maintenance of gastric mucosal integrity. Pharmacol Res 2018; 129:56-64. [DOI: 10.1016/j.phrs.2018.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/12/2018] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
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7
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Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme. Sci Rep 2018; 8:3637. [PMID: 29483528 PMCID: PMC5826923 DOI: 10.1038/s41598-018-21804-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/09/2018] [Indexed: 12/01/2022] Open
Abstract
Bacterial nitric oxide reductases (NORs) catalyse the reduction of NO to N2O and H2O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the immune defense of the host. Although NORs belong to the heme-copper oxidase superfamily, comprising proton-pumping O2-reducing enzymes, the best studied NORs, cNORs (cytochrome c-dependent), are non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). Recombinant qNOR from Neisseria meningitidis, a human pathogen, purified from Escherichia coli, showed high catalytic activity and spectroscopic properties largely similar to cNORs. However, in contrast to cNOR, liposome-reconstituted qNOR showed respiratory control ratios above two, indicating that NO reduction by qNOR was electrogenic. Further, we determined a 4.5 Å crystal structure of the N. meningitidis qNOR, allowing exploration of a potential proton transfer pathway from the cytoplasm by mutagenesis. Most mutations had little effect on the activity, however the E-498 variants were largely inactive, while the corresponding substitution in cNOR was previously shown not to induce significant effects. We thus suggest that, contrary to cNOR, the N. meningitidis qNOR uses cytoplasmic protons for NO reduction. Our results allow possible routes for protons to be discussed.
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8
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Uchida T, Dojun N, Sekine Y, Ishimori K. Heme Proximal Hydrogen Bonding between His170 and Asp132 Plays an Essential Role in the Heme Degradation Reaction of HutZ from Vibrio cholerae. Biochemistry 2017; 56:2723-2734. [DOI: 10.1021/acs.biochem.7b00152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takeshi Uchida
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Nobuhiko Dojun
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yukari Sekine
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
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9
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Uchida T, Kobayashi N, Muneta S, Ishimori K. The Iron Chaperone Protein CyaY from Vibrio cholerae Is a Heme-Binding Protein. Biochemistry 2017; 56:2425-2434. [DOI: 10.1021/acs.biochem.6b01304] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Takeshi Uchida
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Noriyuki Kobayashi
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Souichiro Muneta
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
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10
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Hu B, He M, Yao Z, Schulz CE, Li J. Unique Axial Imidazole Geometries of Fully Halogenated Iron(II) Porphyrin Complexes: Crystal Structures and Mössbauer Spectroscopic Studies. Inorg Chem 2016; 55:9632-9643. [DOI: 10.1021/acs.inorgchem.6b01364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Bin Hu
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Mingrui He
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Zhen Yao
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Charles E. Schulz
- Department
of Physics, Knox College, Galesburg, Illinois 61401, United States
| | - Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
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11
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He M, Li X, Liu Y, Li J. Axial Mn–CCN Bonds of Cyano Manganese(II) Porphyrin Complexes: Flexible and Weak? Inorg Chem 2016; 55:5871-9. [PMID: 27228473 DOI: 10.1021/acs.inorgchem.6b00173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingrui He
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District,
Beijing 101408, China
| | - Xiangjun Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District,
Beijing 101408, China
| | - Yanhong Liu
- Technical
Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianfeng Li
- College
of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District,
Beijing 101408, China
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12
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Sekine Y, Tanzawa T, Tanaka Y, Ishimori K, Uchida T. Cytoplasmic Heme-Binding Protein (HutX) from Vibrio cholerae Is an Intracellular Heme Transport Protein for the Heme-Degrading Enzyme, HutZ. Biochemistry 2016; 55:884-93. [DOI: 10.1021/acs.biochem.5b01273] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yukari Sekine
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Takehito Tanzawa
- Graduate
School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yoshikazu Tanaka
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- PRESTO, Japan Science and Technology Agency, Sapporo 060-0810, Japan
| | - Koichiro Ishimori
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takeshi Uchida
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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13
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Tilleman L, Abbruzzetti S, Ciaccio C, De Sanctis G, Nardini M, Pesce A, Desmet F, Moens L, Van Doorslaer S, Bruno S, Bolognesi M, Ascenzi P, Coletta M, Viappiani C, Dewilde S. Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans. PLoS One 2015; 10:e0125959. [PMID: 26047471 PMCID: PMC4457829 DOI: 10.1371/journal.pone.0125959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 03/28/2015] [Indexed: 12/02/2022] Open
Abstract
Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20)101 was mutated to Ser). The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the “more reactive” and “less reactive” conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60)B9, Tyr(61)B10, and Phe(93)E11. Trp(60)B9 and Tyr(61)B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93)E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60)B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60)B9, Tyr(61)B10, and Phe(93)E11 play a role in regulating heme/ligand affinity.
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Affiliation(s)
- Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Giampiero De Sanctis
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | | | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Stefano Bruno
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Cristiano Viappiani
- Department of Physics and Earth Sciences, University of Parma, Parma, Italy
- * E-mail: (SD); (CV)
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- * E-mail: (SD); (CV)
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14
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Tsai AL, Martin E, Berka V, Olson JS. How do heme-protein sensors exclude oxygen? Lessons learned from cytochrome c', Nostoc puntiforme heme nitric oxide/oxygen-binding domain, and soluble guanylyl cyclase. Antioxid Redox Signal 2012; 17:1246-63. [PMID: 22356101 PMCID: PMC3430480 DOI: 10.1089/ars.2012.4564] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ligand selectivity for dioxygen (O(2)), carbon monoxide (CO), and nitric oxide (NO) is critical for signal transduction and is tailored specifically for each heme-protein sensor. Key NO sensors, such as soluble guanylyl cyclase (sGC), specifically recognized low levels of NO and achieve a total O(2) exclusion. Several mechanisms have been proposed to explain the O(2) insensitivity, including lack of a hydrogen bond donor and negative electrostatic fields to selectively destabilize bound O(2), distal steric hindrance of all bound ligands to the heme iron, and restriction of in-plane movements of the iron atom. RECENT ADVANCES Crystallographic structures of the gas sensors, Thermoanaerobacter tengcongensis heme-nitric oxide/oxygen-binding domain (Tt H-NOX(1)) or Nostoc puntiforme (Ns) H-NOX, and measurements of O(2) binding to site-specific mutants of Tt H-NOX and the truncated β subunit of sGC suggest the need for a H-bonding donor to facilitate O(2) binding. CRITICAL ISSUES However, the O(2) insensitivity of full length sGC with a site-specific replacement of isoleucine by a tyrosine on residue 145 and the very slow autooxidation of Ns H-NOX and cytochrome c' suggest that more complex mechanisms have evolved to exclude O(2) but retain high affinity NO binding. A combined graphical analysis of ligand binding data for libraries of heme sensors, globins, and model heme shows that the NO sensors dramatically inhibit the formation of six-coordinated NO, CO, and O(2) complexes by direct distal steric hindrance (cyt c'), proximal constraints of in-plane iron movement (sGC), or combinations of both following a sliding scale rule. High affinity NO binding in H-NOX proteins is achieved by multiple NO binding steps that produce a high affinity five-coordinate NO complex, a mechanism that also prevents NO dioxygenation. FUTURE DIRECTIONS Knowledge advanced by further extensive test of this "sliding scale rule" hypothesis should be valuable in guiding novel designs for heme based sensors.
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Affiliation(s)
- Ah-Lim Tsai
- Division of Hematology, University of Texas Health Science Center at Houston, Houston, Texas 77225, USA.
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15
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Hannibal L, Collins D, Brassard J, Chakravarti R, Vempati R, Dorlet P, Santolini J, Dawson JH, Stuehr DJ. Heme binding properties of glyceraldehyde-3-phosphate dehydrogenase. Biochemistry 2012; 51:8514-29. [PMID: 22957700 DOI: 10.1021/bi300863a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that also functions in transcriptional regulation, oxidative stress, vesicular trafficking, and apoptosis. Because GAPDH is required for the insertion of cellular heme into inducible nitric oxide synthase [Chakravarti, R., et al. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 18004-18009], we extensively characterized the heme binding properties of GAPDH. Substoichiometric amounts of ferric heme bound to GAPDH (one heme per GAPDH tetramer) to form a low-spin complex with UV-visible maxima at 362, 418, and 537 nm and when reduced to ferrous gave maxima at 424, 527, and 559 nm. Ferric heme association and dissociation rate constants at 10 °C were as follows: k(on) = 17800 M(-1) s(-1), k(off1) = 7.0 × 10(-3) s(-1), and k(off2) = 3.3 × 10(-4) s(-1) (giving approximate affinities of 19-390 nM). Ferrous heme bound more poorly to GAPDH and dissociated with a k(off) of 4.2 × 10(-3) s(-1). Magnetic circular dichroism, resonance Raman, and electron paramagnetic resonance spectroscopic data on the ferric, ferrous, and ferrous-CO complexes of GAPDH showed that the heme is bis-ligated with His as the proximal ligand. The distal ligand in the ferric complex was not displaced by CN(-) or N(3)(-) but in the ferrous complex could be displaced by CO at a rate of 1.75 s(-1) (for >0.2 mM CO). Studies with heme analogues revealed selectivity toward the coordinating metal and porphyrin ring structure. The GAPDH-heme complex was isolated from bacteria induced to express rabbit GAPDH in the presence of δ-aminolevulinic acid. Our finding of heme binding to GAPDH expands the protein's potential roles. The strength, selectivity, reversibility, and redox sensitivity of heme binding to GAPDH are consistent with it performing heme sensing or heme chaperone-like functions in cells.
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Affiliation(s)
- Luciana Hannibal
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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16
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Abbruzzetti S, Tilleman L, Bruno S, Viappiani C, Desmet F, Van Doorslaer S, Coletta M, Ciaccio C, Ascenzi P, Nardini M, Bolognesi M, Moens L, Dewilde S. Ligation tunes protein reactivity in an ancient haemoglobin: kinetic evidence for an allosteric mechanism in Methanosarcina acetivorans protoglobin. PLoS One 2012; 7:e33614. [PMID: 22479420 PMCID: PMC3313925 DOI: 10.1371/journal.pone.0033614] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/13/2012] [Indexed: 11/19/2022] Open
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | | | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Paolo Ascenzi
- Dipartimento di Biologia, Università Roma Tre, Roma, Italy
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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17
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Bérczi A, Desmet F, Van Doorslaer S, Asard H. Spectral characterization of the recombinant mouse tumor suppressor 101F6 protein. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:1129-42. [PMID: 19943161 DOI: 10.1007/s00249-009-0564-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 10/29/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Tumor suppressor protein 101F6, a gene product of the 3p21.3 (human) and 9F1 (mouse) chromosomal region, has recently been identified as a member of the cytochrome b561 (Cyt-b561) protein family by sequence homology. The His(6)-tagged recombinant mouse tumor suppressor Cyt-b561 protein (TSCytb) was recently expressed in yeast and purified, and the ascorbate reducibility was determined. TSCytb is auto-oxidizable and has two distinct heme b centers with redox potentials of approximately 40 and approximately 140 mV. Its split alpha-band in the dithionite-reduced spectrum at both 295 and 77 K is well resolved, and the separation between the two alpha-peaks is approximately 7 nm (approximately 222 cm(-1)). Singular value decomposition analysis of the split alpha-band in the ascorbate-reduced spectra revealed the presence of two major spectral components, each of them with split alpha-band but with different peak separations (6 and 8 nm). Similar minor differences in peak separation were obtained when the split alpha-bands in ascorbate-reduced difference spectra at low (<1 mM) and high (>10 mM) ascorbate concentrations were analysed. According to low-temperature electron paramagnetic resonance (EPR) spectroscopy, the two heme b centers are in the low-spin ferric state with maximum principal g values of 3.61 and 2.96, respectively. These values differ from the ones observed for other members of the Cyt-b561 family. According to resonance Raman spectroscopy, the porphyrin rings are in a relaxed state. The spectroscopic results are only partially in agreement with those obtained earlier for the native chromaffin granule Cyt-b561.
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Affiliation(s)
- Alajos Bérczi
- Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, Temesvári krt. 62, P.O. Box 521, 6701, Szeged, Hungary.
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18
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Vetter SW, Terentis AC, Osborne RL, Dawson JH, Goodin DB. Replacement of the axial histidine heme ligand with cysteine in nitrophorin 1: spectroscopic and crystallographic characterization. J Biol Inorg Chem 2009; 14:179-91. [PMID: 18923851 PMCID: PMC2635096 DOI: 10.1007/s00775-008-0436-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
To evaluate the potential of using heme-containing lipocalin nitrophorin 1 (NP1) as a template for protein engineering, we have replaced the native axial heme-coordinating histidine residue with glycine, alanine, and cysteine. We report here the characterization of the cysteine mutant H60C_NP1 by spectroscopic and crystallographic methods. The UV/vis, resonance Raman, and magnetic circular dichroism spectra suggest weak thiolate coordination of the ferric heme in the H60C_NP1 mutant. Reduction to the ferrous state resulted in loss of cysteine coordination, while addition of exogenous imidazole ligands gave coordination changes that varied with the ligand. Depending on the substitution of the imidazole, we could distinguish three heme coordination states: five-coordinate monoimidazole, six-coordinate bisimidazole, and six-coordinate imidazole/thiolate. Ligand binding affinities were measured and found to be generally 2-3 orders of magnitude lower for the H60C mutant relative to NP1. Two crystal structures of the H60C_NP1 in complex with imidazole and histamine were solved to 1.7- and 1.96-A resolution, respectively. Both structures show that the H60C mutation is well tolerated by the protein scaffold and suggest that heme-thiolate coordination in H60C_NP1 requires some movement of the heme within its binding cavity. This adjustment may be responsible for the ease with which the engineered heme-thiolate coordination can be displaced by exogenous ligands.
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Affiliation(s)
- Stefan W Vetter
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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Pesce A, Thijs L, Nardini M, Desmet F, Sisinni L, Gourlay L, Bolli A, Coletta M, Van Doorslaer S, Wan X, Alam M, Ascenzi P, Moens L, Bolognesi M, Dewilde S. HisE11 and HisF8 provide bis-histidyl heme hexa-coordination in the globin domain of Geobacter sulfurreducens globin-coupled sensor. J Mol Biol 2008; 386:246-60. [PMID: 19109973 DOI: 10.1016/j.jmb.2008.12.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/05/2008] [Accepted: 12/09/2008] [Indexed: 02/08/2023]
Abstract
Among heme-based sensors, recent phylogenomic and sequence analyses have identified 34 globin coupled sensors (GCS), to which an aerotactic or gene-regulating function has been tentatively ascribed. Here, the structural and biochemical characterization of the globin domain of the GCS from Geobacter sulfurreducens (GsGCS(162)) is reported. A combination of X-ray crystallography (crystal structure at 1.5 A resolution), UV-vis and resonance Raman spectroscopy reveals the ferric GsGCS(162) as an example of bis-histidyl hexa-coordinated GCS. In contrast to the known hexa-coordinated globins, the distal heme-coordination in ferric GsGCS(162) is provided by a His residue unexpectedly located at the E11 topological site. Furthermore, UV-vis and resonance Raman spectroscopy indicated that ferrous deoxygenated GsGCS(162) is a penta-/hexa-coordinated mixture, and the heme hexa-to-penta-coordination transition does not represent a rate-limiting step for carbonylation kinetics. Lastly, electron paramagnetic resonance indicates that ferrous nitrosylated GsGCS(162) is a penta-coordinated species, where the proximal HisF8-Fe bond is severed.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, CNISM and Center for Excellence in Biomedical Research, University of Genova, Via Dodecaneso, 33, I-16146 Genova, Italy
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20
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Ichimura S, Uchida T, Taniguchi S, Hira S, Tosha T, Morishima I, Kitagawa T, Ishimori K. Unique peroxidase reaction mechanism in prostaglandin endoperoxide H synthase-2: compound I in prostaglandin endoperoxide H synthase-2 can be formed without assistance by distal glutamine residue. J Biol Chem 2007; 282:16681-90. [PMID: 17403665 DOI: 10.1074/jbc.m610785200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prostaglandin-endoperoxide H synthase-2 (PGHS-2) shows peroxidase activity to promote the cyclooxygenase reaction for prostaglandin H2, but one of the highly conserved amino acid residues in peroxidases, distal Arg, stabilizing the developing negative charge on the peroxide through a hydrogen-bonding interaction, is replaced with a neutral amino acid residue, Gln. To characterize the peroxidase reaction in PGHS-2, we prepared three distal glutamine (Gln-189) mutants, Arg (Gln-->Arg), Asn (Gln-->Asn), and Val (Gln-->Val) mutants, and examined their peroxidase activity together with their structural characterization by absorption and resonance Raman spectra. Although a previous study (Landino, L. M., Crews, B. C., Gierse, J. K., Hauser, S. D., and Marnett, L. (1997) J. Biol. Chem. 272, 21565-21574) suggested that the Gln residue might serve as a functionally equivalent residue to Arg, our current results clearly showed that the peroxidase activity of the Val and Asn mutants was comparable with that of the wild-type enzyme. In addition, the Fe-C and C-O stretching modes in the CO adduct were almost unperturbed by the mutation, implying that Gln-189 might not directly interact with the heme-ligated peroxide. Rather, the peroxidase activity of the Arg mutant was depressed, concomitant with the heme environmental change from a six-coordinate to a five-coordinate structure. Introduction of the bulky amino acid residue, Arg, would interfere with the ligation of a water molecule to the heme iron, suggesting that the side chain volume, and not the amide group, at position 189 is essential for the peroxidase activity of PGHS-2. Thus, we can conclude that the O-O bond cleavage in PGHS-2 is promoted without interactions with charged side chains at the peroxide binding site, which is significantly different from that in typical plant peroxidases.
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Affiliation(s)
- Shizuo Ichimura
- Division of Chemistry, Graduate School of Science, Hokkaido University, Hokkaido 060-0810, Japan
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21
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Kobayashi K, Pal B, Yoshioka S, Kato Y, Asano Y, Kitagawa T, Aono S. Spectroscopic and substrate binding properties of heme-containing aldoxime dehydratases, OxdB and OxdRE. J Inorg Biochem 2006; 100:1069-74. [PMID: 16414119 DOI: 10.1016/j.jinorgbio.2005.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 12/05/2005] [Accepted: 12/06/2005] [Indexed: 11/15/2022]
Abstract
Aldoxime dehydratase (Oxd) is a novel hemeprotein that catalyzes the dehydration reaction of aldoxime to produce nitrile. In this study, we studied the spectroscopic and substrate binding properties of two Oxds, OxdB from Bacillus sp. strain OxB-1 and OxdRE from Rhodococcus sp. N-771, that show different quaternary structures and relatively low amino acid sequence identity. Electronic absorption and resonance Raman spectroscopy revealed that ferric OxdRE contained a six-coordinate low-spin heme, while ferric OxdB contained a six-coordinate high-spin heme. Both ferrous OxdRE and OxdB included a five-coordinate high-spin heme to which the substrate was bound via its nitrogen atom for the reaction to occur. Although the ferric Oxds were inactive for catalysis, the substrate was bound to the ferric heme via its oxygen atom in both OxdB and OxdRE. Electronic paramagnetic resonance (EPR) and rapid scanning spectroscopy revealed that the flexibility of the heme pocket was different between OxdB and OxdRE, which might affect their substrate specificity.
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Affiliation(s)
- Katsuaki Kobayashi
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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22
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Wu L, Wang R. Carbon Monoxide: Endogenous Production, Physiological Functions, and Pharmacological Applications. Pharmacol Rev 2005; 57:585-630. [PMID: 16382109 DOI: 10.1124/pr.57.4.3] [Citation(s) in RCA: 648] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Over the last decade, studies have unraveled many aspects of endogenous production and physiological functions of carbon monoxide (CO). The majority of endogenous CO is produced in a reaction catalyzed by the enzyme heme oxygenase (HO). Inducible HO (HO-1) and constitutive HO (HO-2) are mostly recognized for their roles in the oxidation of heme and production of CO and biliverdin, whereas the biological function of the third HO isoform, HO-3, is still unclear. The tissue type-specific distribution of these HO isoforms is largely linked to the specific biological actions of CO on different systems. CO functions as a signaling molecule in the neuronal system, involving the regulation of neurotransmitters and neuropeptide release, learning and memory, and odor response adaptation and many other neuronal activities. The vasorelaxant property and cardiac protection effect of CO have been documented. A plethora of studies have also shown the importance of the roles of CO in the immune, respiratory, reproductive, gastrointestinal, kidney, and liver systems. Our understanding of the cellular and molecular mechanisms that regulate the production and mediate the physiological actions of CO has greatly advanced. Many diseases, including neurodegenerations, hypertension, heart failure, and inflammation, have been linked to the abnormality in CO metabolism and function. Enhancement of endogenous CO production and direct delivery of exogenous CO have found their applications in many health research fields and clinical settings. Future studies will further clarify the gasotransmitter role of CO, provide insight into the pathogenic mechanisms of many CO abnormality-related diseases, and pave the way for innovative preventive and therapeutic strategies based on the physiologic effects of CO.
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Affiliation(s)
- Lingyun Wu
- Department of Biology, Lakehead University, 955 Oliver Rd., Thunder Bay, Ontario, Canada P7B 5E1
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23
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Gupta K, Selinsky BS, Kaub CJ, Katz AK, Loll PJ. The 2.0 A resolution crystal structure of prostaglandin H2 synthase-1: structural insights into an unusual peroxidase. J Mol Biol 2004; 335:503-18. [PMID: 14672659 DOI: 10.1016/j.jmb.2003.10.073] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prostaglandin H2 synthase (EC 1.14.99.1) is an integral membrane enzyme containing a cyclooxygenase site, which is the target for the non-steroidal anti-inflammatory drugs, and a spatially distinct peroxidase site. Previous crystallographic studies of this clinically important drug target have been hindered by low resolution. We present here the 2.0 A resolution X-ray crystal structure of ovine prostaglandin H2 synthase-1 in complex with alpha-methyl-4-biphenylacetic acid, a defluorinated analog of the non-steroidal anti-inflammatory drug flurbiprofen. Detergent molecules are seen to bind to the protein's membrane-binding domain, and their positions suggest the depth to which this domain is likely to penetrate into the lipid bilayer. The relation of the enzyme's proximal heme ligand His388 to the heme iron is atypical for a peroxidase; the iron-histidine bond is unusually long and a substantial tilt angle is observed between the heme and imidazole planes. A molecule of glycerol, used as a cryoprotectant during diffraction experiments, is seen to bind in the peroxidase site, offering the first view of any ligand in this active site. Insights gained from glycerol binding may prove useful in the design of a peroxidase-specific ligand.
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Affiliation(s)
- Kushol Gupta
- Department of Biochemistry, Drexel University College of Medicine, 245 N 15th Street, Mailstop 497, Philadelphia, PA 19102-1192, USA
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24
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Abbott LC, Feilden CJ, Anderton CL, Moore JN. Resonance Raman spectroscopy of photolabile transition metal carbonyls: controlled photoalteration with continuous wave lasers to record spectra of reactants or transient species. APPLIED SPECTROSCOPY 2003; 57:960-969. [PMID: 14661839 DOI: 10.1366/000370203322258922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A method has been developed that enables resonance Raman spectra of photolabile species in solution to be recorded under conditions where the level of photoalteration is controlled: a low level enables reactant spectra to be recorded, whereas a high level enables the spectra of short-lived transient species to be recorded in real time using continuous-wave (CW) lasers and standard Raman detection equipment. The design includes a sealed flow system, enabling air-sensitive species to be studied under an inert atmosphere. A simple theoretical model has been developed to aid the interpretation of experimental results, and its applicability is demonstrated. Controlled photoalteration and its theory are demonstrated with 413.1-nm excitation of carbonmonoxymyoglobin (MbCO), which generates deoxymyoglobin (deoxy-Mb) on photolysis, and for which the spectra of both species are well established. The methods have also been applied to two air-sensitive, photolabile transition metal carbonyls using 514.5-nm wavelength excitation: for Cp2Mo2(CO)6 (Cp = eta5-C5H5), increasing levels of photoalteration result only in a decrease in the parent band intensities, relative to the solvent bands; for Cp2Fe2(CO)4, increasing levels of photoalteration result in the appearance of additional bands that are assigned to the transient species CpFe(mu-CO)3FeCp, formed following the loss of a CO ligand.
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Affiliation(s)
- Laurence C Abbott
- Department of Chemistry, The University of York, Heslington, York YO10 5DD, UK
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25
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Rouzer CA, Marnett LJ. Mechanism of free radical oxygenation of polyunsaturated fatty acids by cyclooxygenases. Chem Rev 2003; 103:2239-304. [PMID: 12797830 DOI: 10.1021/cr000068x] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Carol A Rouzer
- A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Department of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Ingram Comprehensive Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Cukier RI, Seibold SA. Molecular Dynamics Simulations of Prostaglandin Endoperoxide H Synthase-1. Role of Water and the Mechanism of Compound I Formation from Hydrogen Peroxide. J Phys Chem B 2002. [DOI: 10.1021/jp021232i] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. I. Cukier
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
| | - S. A. Seibold
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322
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Pinakoulaki E, Pfitzner U, Ludwig B, Varotsis C. The role of the cross-link His-Tyr in the functional properties of the binuclear center in cytochrome c oxidase. J Biol Chem 2002; 277:13563-8. [PMID: 11825904 DOI: 10.1074/jbc.m112200200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Resonance Raman and Fourier transform infrared spectroscopies have been used to study the aa(3)-type cytochrome c oxidase and the Y280H mutant from Paracoccus denitrificans. The stability of the binuclear center in the absence of the Tyr(280)-His(276) cross-link is not compromised since heme a(3) retains the same proximal environment, spin, and coordination state as in the wild type enzyme in both the oxidized and reduced states. We observe two C-O modes in the Y280H mutant at 1966 and 1975 cm(-1). The 1975 cm(-1) mode is assigned to a gamma-form and represents a structure of the active site in which Cu(B) exerts a steric effect on the heme a(3)-bound CO. Therefore, the role of the cross-link is to fix Cu(B) in a certain configuration and distance from heme a(3), and not to allow histidine ligands to coordinate to Cu(B) rather than to heme a(3), rendering the enzyme inactive, as proposed recently (Das, T. K., Pecoraro, C., Tomson, F. L., Gennis, R. B., and Rousseau, D. L. (1998) Biochemistry 37, 14471-14476). The results provide solid evidence that in the Y280H mutant the catalytic site retains its active configuration that allows O(2) binding to heme a(3). Oxygenated intermediates are formed by mixing oxygen with the CO-bound mixed-valence wild type and Y280H enzymes with similar Soret maxima at 438 nm.
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