1
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Timm J, Pike DH, Mancini JA, Tyryshkin AM, Poudel S, Siess JA, Molinaro PM, McCann JJ, Waldie KM, Koder RL, Falkowski PG, Nanda V. Design of a minimal di-nickel hydrogenase peptide. SCIENCE ADVANCES 2023; 9:eabq1990. [PMID: 36897954 PMCID: PMC10005181 DOI: 10.1126/sciadv.abq1990] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/07/2023] [Indexed: 06/07/2023]
Abstract
Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.
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Affiliation(s)
- Jennifer Timm
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Douglas H. Pike
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Joshua A. Mancini
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Alexei M. Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Saroj Poudel
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Jan A. Siess
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Paul M. Molinaro
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - James J. McCann
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - Kate M. Waldie
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY 10016, USA
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences and Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
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2
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Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y. Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat Commun 2022; 13:7591. [PMID: 36481732 PMCID: PMC9731990 DOI: 10.1038/s41467-022-34771-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health problem. Despite the enormous efforts made in the last decade, threats from some species, including drug-resistant Neisseria gonorrhoeae, continue to rise and would become untreatable. The development of antibiotics with a different mechanism of action is seriously required. Here, we identified an allosteric inhibitory site buried inside eukaryotic mitochondrial heme-copper oxidases (HCOs), the essential respiratory enzymes for life. The steric conformation around the binding pocket of HCOs is highly conserved among bacteria and eukaryotes, yet the latter has an extra helix. This structural difference in the conserved allostery enabled us to rationally identify bacterial HCO-specific inhibitors: an antibiotic compound against ceftriaxone-resistant Neisseria gonorrhoeae. Molecular dynamics combined with resonance Raman spectroscopy and stopped-flow spectroscopy revealed an allosteric obstruction in the substrate accessing channel as a mechanism of inhibition. Our approach opens fresh avenues in modulating protein functions and broadens our options to overcome AMR.
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Affiliation(s)
- Yuya Nishida
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan
| | | | - Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideki Shigematsu
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, Japan
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8; Sayo, Hyogo, Japan
| | | | - Hitomi Yuki
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takashi Iwamoto
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan
| | - Chisa Nakabayashi
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan
| | - Waka Matsumura
- Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hisakazu Kato
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan
| | | | - Takemasa Nagao
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Tasneem Qaqorh
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan
| | - Yusuke Takahashi
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Satoru Yamazaki
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Katsumasa Kamiya
- Center for Basic Education Integrated Learning, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Nobuhiro Mizuno
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan
| | | | | | | | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Minoru Kubo
- Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Seiji Takashima
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan
| | - Yasunori Shintani
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan.
- Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka, Japan.
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3
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Dolder N, Müller P, von Ballmoos C. Experimental platform for the functional investigation of membrane proteins in giant unilamellar vesicles. SOFT MATTER 2022; 18:5877-5893. [PMID: 35916307 PMCID: PMC9364335 DOI: 10.1039/d2sm00551d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Giant unilamellar vesicles (GUVs) are micrometer-sized model membrane systems that can be viewed directly under the microscope. They serve as scaffolds for the bottom-up creation of synthetic cells, targeted drug delivery and have been widely used to study membrane related phenomena in vitro. GUVs are also of interest for the functional investigation of membrane proteins that carry out many key cellular functions. A major hurdle to a wider application of GUVs in this field is the diversity of existing protocols that are optimized for individual proteins. Here, we compare PVA assisted and electroformation techniques for GUV formation under physiologically relevant conditions, and analyze the effect of immobilization on vesicle structure and membrane tightness towards small substrates and protons. There, differences in terms of yield, size, and leakage of GUVs produced by PVA assisted swelling and electroformation were found, dependent on salt and buffer composition. Using fusion of oppositely charged membranes to reconstitute a model membrane protein, we find that empty vesicles and proteoliposomes show similar fusion behavior, which allows for a rapid estimation of protein incorporation using fluorescent lipids.
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Affiliation(s)
- Nicolas Dolder
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Philipp Müller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Christoph von Ballmoos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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4
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Jose A, Schaefer AW, Roveda AC, Transue WJ, Choi SK, Ding Z, Gennis RB, Solomon EI. The three-spin intermediate at the O-O cleavage and proton-pumping junction in heme-Cu oxidases. Science 2021; 373:1225-1229. [PMID: 34516790 DOI: 10.1126/science.abh3209] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Anex Jose
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Andrew W Schaefer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Antonio C Roveda
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Wesley J Transue
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Sylvia K Choi
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Ziqiao Ding
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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5
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Structure of the cytochrome aa 3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site. Proc Natl Acad Sci U S A 2019; 117:872-876. [PMID: 31888984 DOI: 10.1073/pnas.1915013117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Virtually all proton-pumping terminal respiratory oxygen reductases are members of the heme-copper oxidoreductase superfamily. Most of these enzymes use reduced cytochrome c as a source of electrons, but a group of enzymes have evolved to directly oxidize membrane-bound quinols, usually menaquinol or ubiquinol. All of the quinol oxidases have an additional transmembrane helix (TM0) in subunit I that is not present in the related cytochrome c oxidases. The current work reports the 3.6-Å-resolution X-ray structure of the cytochrome aa 3 -600 menaquinol oxidase from Bacillus subtilis containing 1 equivalent of menaquinone. The structure shows that TM0 forms part of a cleft to accommodate the menaquinol-7 substrate. Crystals which have been soaked with the quinol-analog inhibitor HQNO (N-oxo-2-heptyl-4-hydroxyquinoline) or 3-iodo-HQNO reveal a single binding site where the inhibitor forms hydrogen bonds to amino acid residues shown previously by spectroscopic methods to interact with the semiquinone state of menaquinone, a catalytic intermediate.
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6
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Ding Z, Sun C, Yi SM, Gennis RB, Dikanov SA. The Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Accommodates Menaquinone and Stabilizes a Functional Menasemiquinone. Biochemistry 2019; 58:4559-4569. [PMID: 31644263 DOI: 10.1021/acs.biochem.9b00750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytochrome bo3, one of three terminal oxygen reductases in the aerobic respiratory chain of Escherichia coli, has been well characterized as a ubiquinol oxidase. The ability of cytochrome bo3 to catalyze the two-electron oxidation of ubiquinol-8 requires the enzyme to stabilize the one-electron oxidized ubisemiquinone species that is a transient intermediate in the reaction. Cytochrome bo3 has been shown recently to also utilize demethylmenaquinol-8 as a substrate that, along with menaquinol-8, replaces ubiquinol-8 when E. coli is grown under microaerobic or anaerobic conditions. In this work, we show that its steady-state turnover with 2,3-dimethyl-1,4-naphthoquinol, a water-soluble menaquinol analogue, is just as efficient as with ubiquinol-1. Using pulsed electron paramagnetic resonance spectroscopy, we demonstrate that the same residues in cytochrome bo3 that stabilize the semiquinone state of ubiquinone also stabilize the semiquinone state of menaquinone, with the hydrogen bond strengths and the distribution of unpaired spin density accommodated for the different substrate. Catalytic function with menaquinol is more tolerant of mutations at the active site than with ubiquinol. A mutation of one of the stabilizing residues (R71H in subunit I) that eliminates the ubiquinol oxidase activity of cytochrome bo3 does not abolish activity with soluble menaquinol analogues.
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Affiliation(s)
- Ziqiao Ding
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Chang Sun
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sophia M Yi
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Robert B Gennis
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Center for Biophysics and Computational Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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7
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Choi SK, Schurig-Briccio L, Ding Z, Hong S, Sun C, Gennis RB. Location of the Substrate Binding Site of the Cytochrome bo 3 Ubiquinol Oxidase from Escherichia coli. J Am Chem Soc 2017; 139:8346-8354. [PMID: 28538096 DOI: 10.1021/jacs.7b03883] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome bo3 is a respiratory proton-pumping oxygen reductase that is a member of the heme-copper superfamily that utilizes ubiquinol-8 (Q8H2) as a substrate. The current consensus model has Q8H2 oxidized at a low affinity site (QL), passing electrons to a tightly bound quinone cofactor at a high affinity site (QH site) that stabilizes the one-electron reduced ubisemiquinone, facilitating the transfer of electrons to the redox active metal centers where O2 is reduced to water. The current work shows that the Q8 bound to the QH site is more dynamic than previously thought. In addition, mutations of residues at the QH site that do not abolish activity have been re-examined and shown to have properties expected of mutations at the substrate binding site (QL): an increase in the KM of the substrate ubiquinol-1 (up to 4-fold) and an increase in the apparent Ki of the inhibitor HQNO (up to 8-fold). The data suggest that there is only one binding site for ubiquinol in cyt bo3 and that site corresponds to the QH site.
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Affiliation(s)
- Sylvia K Choi
- Center for Biophysics and Quantitative Biology, University of Illinois , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Lici Schurig-Briccio
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Ziqiao Ding
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Chang Sun
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Robert B Gennis
- Center for Biophysics and Quantitative Biology, University of Illinois , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
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8
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Choi SK, Lin MT, Ouyang H, Gennis RB. Searching for the low affinity ubiquinone binding site in cytochrome bo 3 from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:366-370. [PMID: 28235459 DOI: 10.1016/j.bbabio.2017.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/11/2017] [Accepted: 02/14/2017] [Indexed: 11/25/2022]
Abstract
The cytochrome bo3 ubiquinol oxidase is one of three respiratory oxygen reductases in the aerobic respiratory chain of Escherichia coli. The generally accepted model of catalysis assumes that cyt bo3 contains two distinct ubiquinol binding sites: (i) a low affinity (QL) site which is the traditional substrate binding site; and (ii) a high affinity (QH) site where a "permanently" bound quinone acts as a cofactor, taking two electrons from the substrate quinol and passing them one-by-one to the heme b component of the enzyme which, in turn, transfers them to the heme o3/CuB active site. Whereas the residues at the QH site are well defined, the location of the QL site remains unknown. The published X-ray structure does not contain quinone, and substantial amounts of the protein are missing as well. A recent bioinformatics study by Bossis et al. [Biochem J. (2014) 461, 305-314] identified a sequence motif G163EFX3GWX2Y173 as the likely QL site in the family of related quinol oxidases. In the current work, this was tested by site-directed mutagenesis. The results show that these residues are not important for catalytic function and do not define the QL substrate binding site.
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Affiliation(s)
- Sylvia K Choi
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA
| | - Myat T Lin
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA
| | - Hanlin Ouyang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Robert B Gennis
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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9
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Sun C, Taguchi AT, Vermaas JV, Beal NJ, O'Malley PJ, Tajkhorshid E, Gennis RB, Dikanov SA. Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo 3 from Escherichia coli. Biochemistry 2016; 55:5714-5725. [PMID: 27622672 DOI: 10.1021/acs.biochem.6b00669] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The respiratory cytochrome bo3 ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQH), which is a transient intermediate during the electron-mediated reduction of O2 to water. It is known that SQH is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQH was investigated with orientation-selective Q-band (∼34 GHz) pulsed 1H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo3 in a H2O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor Tz' = 11.8 MHz, whereas for H2, Tz' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo3 QH site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.
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Affiliation(s)
- Chang Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Alexander T Taguchi
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Josh V Vermaas
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Nathan J Beal
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - Patrick J O'Malley
- School of Chemistry, The University of Manchester , Manchester M13 9PL, U.K
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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10
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Abstract
Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate-specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophosphate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and dimethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O₂ is served by two major oxidoreductases (oxidases), cytochrome bo₃ encoded by cyoABCDE and cytochrome bd encoded by cydABX. Terminal oxidases of aerobic respiratory chains of bacteria, which use O₂ as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo₃ and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo₃ and cytochrome bd. The E. coli membrane contains three types of quinones that all have an octaprenyl side chain (C₄₀). It has been proposed that the bo₃ oxidase can have two ubiquinone-binding sites with different affinities. "WHAT'S NEW" IN THE REVISED ARTICLE: The revised article comprises additional information about subunit composition of cytochrome bd and its role in bacterial resistance to nitrosative and oxidative stresses. Also, we present the novel data on the electrogenic function of appBCX-encoded cytochrome bd-II, a second bd-type oxidase that had been thought not to contribute to generation of a proton motive force in E. coli, although its spectral properties closely resemble those of cydABX-encoded cytochrome bd.
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11
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Yi SM, Taguchi AT, Samoilova RI, O'Malley PJ, Gennis RB, Dikanov SA. Plasticity in the High Affinity Menaquinone Binding Site of the Cytochrome aa3-600 Menaquinol Oxidase from Bacillus subtilis. Biochemistry 2015. [PMID: 26196462 DOI: 10.1021/acs.biochem.5b00528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome aa3-600 is a terminal oxidase in the electron transport pathway that contributes to the electrochemical membrane potential by actively pumping protons. A notable feature of this enzyme complex is that it uses menaquinol as its electron donor instead of cytochrome c when it reduces dioxygen to water. The enzyme stabilizes a menasemiquinone radical (SQ) at a high affinity site that is important for catalysis. One of the residues that interacts with the semiquinone is Arg70. We have made the R70H mutant and have characterized the menasemiquinone radical by advanced X- and Q-band EPR. The bound SQ of the R70H mutant exhibits a strong isotropic hyperfine coupling (a(14)N ≈ 2.0 MHz) with a hydrogen bonded nitrogen. This nitrogen originates from a histidine side chain, based on its quadrupole coupling constant, e(2)qQ/h = 1.44 MHz, typical for protonated imidazole nitrogens. In the wild-type cyt aa3-600, the SQ is instead hydrogen bonded with Nε from the Arg70 side chain. Analysis of the (1)H 2D electron spin echo envelope modulation (ESEEM) spectra shows that the mutation also changes the number and strength of the hydrogen bonds between the SQ and the surrounding protein. Despite the alterations in the immediate environment of the SQ, the R70H mutant remains catalytically active. These findings are in contrast to the equivalent mutation in the close homologue, cytochrome bo3 ubiquinol oxidase from Escherichia coli, where the R71H mutation eliminates function.
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Affiliation(s)
- Sophia M Yi
- §Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alexander T Taguchi
- †Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,‡Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rimma I Samoilova
- ⊥V. V. Voevodsky Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Patrick J O'Malley
- ∥School of Chemistry, The University of Manchester, Manchester M13 9PL, U.K
| | - Robert B Gennis
- §Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,†Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sergei A Dikanov
- ‡Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Vennam PR, Fisher N, Krzyaniak MD, Kramer DM, Bowman MK. A caged, destabilized, free radical intermediate in the q-cycle. Chembiochem 2013; 14:1745-53. [PMID: 24009094 PMCID: PMC3951126 DOI: 10.1002/cbic.201300265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 11/12/2022]
Abstract
The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase (Qo ) sites, in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models have been proposed. In previous work, we trapped a Q-cycle semiquinone anion intermediate, termed SQo , in bacterial cytochrome bc1 by rapid freeze-quenching. In this work, we apply pulsed-EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and can even be destabilized with respect to solution. It is trapped in Qo at a site that is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analyses show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves "stripping" of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL while minimizing certain Q-cycle bypass reactions, including oxidation of prereduced cytochrome b and reduction of O2 .
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Affiliation(s)
- Preethi R. Vennam
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - Nicholas Fisher
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Matthew D. Krzyaniak
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - David M. Kramer
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Michael K. Bowman
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
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13
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Dikanov SA. Resolving protein-semiquinone interactions by two-dimensional ESEEM spectroscopy. ELECTRON PARAMAGNETIC RESONANCE 2012. [DOI: 10.1039/9781849734837-00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S. A. Dikanov
- University of Illinois at Urbana-Champaign, Department of Veterinary Clinical Medicine 190 MSB, 506 S. Mathews Ave., Urbana IL 61801 USA
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14
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Flores M, Okamura MY, Niklas J, Pandelia ME, Lubitz W. Pulse Q-band EPR and ENDOR spectroscopies of the photochemically generated monoprotonated benzosemiquinone radical in frozen alcoholic solution. J Phys Chem B 2012; 116:8890-900. [PMID: 22731760 DOI: 10.1021/jp304555u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quinones are essential cofactors in many physiological processes, among them proton-coupled electron transfer (PCET) in photosynthesis and respiration. A key intermediate in PCET is the monoprotonated semiquinone radical. In this work we produced the monoprotonated benzosemiquinone (BQH(•)) by UV illumination of BQ dissolved in 2-propanol at cryogenic temperatures and investigated the electronic and geometric structures of BQH(•) in the solid state (80 K) using EPR and ENDOR techniques at 34 GHz. The g-tensor of BQH(•) was found to be similar to that of the anionic semiquinone species (BQ(•-)) in frozen solution. The peaks present in the ENDOR spectrum of BQH(•) were identified and assigned by (1)H/(2)H substitutions. The experiments reconfirmed that the hydroxyl proton (O-H) on BQH(•), which is abstracted from a solvent molecule, mainly originates from the central CH group of 2-propanol. They also showed that the protonation has a strong impact on the electron spin distribution over the quinone. This is reflected in the hyperfine couplings (hfc's) of the ring protons, which dramatically changed with respect to those typically observed for BQ(•-). The hfc tensor of the O-H proton was determined by a detailed orientation-selection ENDOR study and found to be rhombic, resembling those of protons covalently bound to carbon atoms in a π-system (i.e., α-protons). It was found that the O-H bond lies in the quinone plane and is oriented along the direction of the quinone oxygen lone pair orbital. DFT calculations were performed on different structures of BQH(•) coordinated by four, three, or zero 2-propanol molecules. The O-H bond length was found to be around 1.0 Å, typical for a single covalent O-H bond. Good agreement between experimental and DFT results were found. This study provides a detailed picture of the electronic and geometric structures of BQH(•) and should be applicable to other naturally occurring quinones.
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Affiliation(s)
- Marco Flores
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, D-45470, Germany.
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15
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Lin MT, Baldansuren A, Hart R, Samoilova RI, Narasimhulu KV, Yap LL, Choi SK, O'Malley PJ, Gennis RB, Dikanov SA. Interactions of intermediate semiquinone with surrounding protein residues at the Q(H) site of wild-type and D75H mutant cytochrome bo3 from Escherichia coli. Biochemistry 2012; 51:3827-38. [PMID: 22497216 DOI: 10.1021/bi300151q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Selective (15)N isotope labeling of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli with auxotrophs was used to characterize the hyperfine couplings with the side-chain nitrogens from residues R71, H98, and Q101 and peptide nitrogens from residues R71 and H98 around the semiquinone (SQ) at the high-affinity Q(H) site. The two-dimensional ESEEM (HYSCORE) data have directly identified N(ε) of R71 as an H-bond donor carrying the largest amount of unpaired spin density. In addition, weaker hyperfine couplings with the side-chain nitrogens from all residues around the SQ were determined. These hyperfine couplings reflect a distribution of the unpaired spin density over the protein in the SQ state of the Q(H) site and the strength of interaction with different residues. The approach was extended to the virtually inactive D75H mutant, where the intermediate SQ is also stabilized. We found that N(ε) of a histidine residue, presumably H75, carries most of the unpaired spin density instead of N(ε) of R71, as in wild-type bo(3). However, the detailed characterization of the weakly coupled (15)N atoms from selective labeling of R71 and Q101 in D75H was precluded by overlap of the (15)N lines with the much stronger ~1.6 MHz line from the quadrupole triplet of the strongly coupled (14)N(ε) atom of H75. Therefore, a reverse labeling approach, in which the enzyme was uniformly labeled except for selected amino acid types, was applied to probe the contribution of R71 and Q101 to the (15)N signals. Such labeling has shown only weak coupling with all nitrogens of R71 and Q101. We utilize density functional theory-based calculations to model the available information about (1)H, (15)N, and (13)C hyperfine couplings for the Q(H) site and to describe the protein-substrate interactions in both enzymes. In particular, we identify the factors responsible for the asymmetric distribution of the unpaired spin density and ponder the significance of this asymmetry to the quinone's electron transfer function.
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Affiliation(s)
- Myat T Lin
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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16
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Amorati R, Pedulli GF. Hydrogen bond donating ability of meta and parahydroxy phenoxyl radicals. Org Biomol Chem 2012; 10:814-8. [DOI: 10.1039/c1ob06502e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Grimaldi S, Arias-Cartin R, Lanciano P, Lyubenova S, Szenes R, Endeward B, Prisner TF, Guigliarelli B, Magalon A. Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR. J Biol Chem 2011; 287:4662-70. [PMID: 22190684 DOI: 10.1074/jbc.m111.325100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q(D)) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q(D) site (MSQ(D)) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with (1)H2O/2H2O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ(D) binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in 1H2O and 2H2O samples and by selective detection of the exchanged deuterons using Q-band 2H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b(D). Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q(D) site are discussed, in light of the unusually high thermodynamic stability of MSQ(D).
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Affiliation(s)
- Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, 13009 Marseille, France.
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18
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Abstract
When the superoxide radical O(2)(•-) is generated on reaction of KO(2) with water in dimethyl sulfoxide, the decay of the radical is dramatically accelerated by inclusion of quinones in the reaction mix. For quinones with no or short hydrophobic tails, the radical product is a semiquinone at much lower yield, likely indicating reduction of quinone by superoxide and loss of most of the semiquinone product by disproportionation. In the presence of ubiquinone-10, a different species (I) is generated, which has the EPR spectrum of superoxide radical. However, pulsed EPR shows spin interaction with protons in fully deuterated solvent, indicating close proximity to the ubinquinone-10. We discuss the nature of species I, and possible roles in the physiological reactions through which ubisemiquinone generates superoxide by reduction of O(2) through bypass reactions in electron transfer chains.
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19
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Taylor AM, Stoll S, Britt RD, Jarrett JT. Reduction of the [2Fe-2S] cluster accompanies formation of the intermediate 9-mercaptodethiobiotin in Escherichia coli biotin synthase. Biochemistry 2011; 50:7953-63. [PMID: 21859080 DOI: 10.1021/bi201042r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biotin synthase catalyzes the conversion of dethiobiotin (DTB) to biotin through the oxidative addition of sulfur between two saturated carbon atoms, generating a thiophane ring fused to the existing ureido ring. Biotin synthase is a member of the radical SAM superfamily, composed of enzymes that reductively cleave S-adenosyl-l-methionine (SAM or AdoMet) to generate a 5'-deoxyadenosyl radical that can abstract unactivated hydrogen atoms from a variety of organic substrates. In biotin synthase, abstraction of a hydrogen atom from the C9 methyl group of DTB would result in formation of a dethiobiotinyl methylene carbon radical, which is then quenched by a sulfur atom to form a new carbon-sulfur bond in the intermediate 9-mercaptodethiobiotin (MDTB). We have proposed that this sulfur atom is the μ-sulfide of a [2Fe-2S](2+) cluster found near DTB in the enzyme active site. In the present work, we show that formation of MDTB is accompanied by stoichiometric generation of a paramagnetic FeS cluster. The electron paramagnetic resonance (EPR) spectrum is modeled as a 2:1 mixture of components attributable to different forms of a [2Fe-2S](+) cluster, possibly distinguished by slightly different coordination environments. Mutation of Arg260, one of the ligands to the [2Fe-2S] cluster, causes a distinctive change in the EPR spectrum. Furthermore, magnetic coupling of the unpaired electron with (14)N from Arg260, detectable by electron spin envelope modulation (ESEEM) spectroscopy, is observed in WT enzyme but not in the Arg260Met mutant enzyme. Both results indicate that the paramagnetic FeS cluster formed during catalytic turnover is a [2Fe-2S](+) cluster, consistent with a mechanism in which the [2Fe-2S](2+) cluster simultaneously provides and oxidizes sulfide during carbon-sulfur bond formation.
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Affiliation(s)
- Andrew M Taylor
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
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20
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Lin MT, Shubin AA, Samoilova RI, Narasimhulu KV, Baldansuren A, Gennis RB, Dikanov SA. Exploring by pulsed EPR the electronic structure of ubisemiquinone bound at the QH site of cytochrome bo3 from Escherichia coli with in vivo 13C-labeled methyl and methoxy substituents. J Biol Chem 2011; 286:10105-14. [PMID: 21247900 PMCID: PMC3060462 DOI: 10.1074/jbc.m110.206821] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/13/2011] [Indexed: 11/06/2022] Open
Abstract
The cytochrome bo(3) ubiquinol oxidase from Escherichia coli resides in the bacterial cytoplasmic membrane and catalyzes the two-electron oxidation of ubiquinol-8 and four-electron reduction of O(2) to water. The one-electron reduced semiquinone forms transiently during the reaction, and the enzyme has been demonstrated to stabilize the semiquinone. The semiquinone is also formed in the D75E mutant, where the mutation has little influence on the catalytic activity, and in the D75H mutant, which is virtually inactive. In this work, wild-type cytochrome bo(3) as well as the D75E and D75H mutant proteins were prepared with ubiquinone-8 (13)C-labeled selectively at the methyl and two methoxy groups. This was accomplished by expressing the proteins in a methionine auxotroph in the presence of l-methionine with the side chain methyl group (13)C-labeled. The (13)C-labeled quinone isolated from cytochrome bo(3) was also used for the generation of model anion radicals in alcohol. Two-dimensional pulsed EPR and ENDOR were used for the study of the (13)C methyl and methoxy hyperfine couplings in the semiquinone generated in the three proteins indicated above and in the model system. The data were used to characterize the transferred unpaired spin densities on the methyl and methoxy substituents and the conformations of the methoxy groups. In the wild type and D75E mutant, the constraints on the configurations of the methoxy side chains are similar, but the D75H mutant appears to have altered methoxy configurations, which could be related to the perturbed electron distribution in the semiquinone and the loss of enzymatic activity.
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Affiliation(s)
| | | | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Kuppala V. Narasimhulu
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | | | | | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
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21
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Martin E, Samoilova RI, Narasimhulu KV, Lin TJ, O'Malley PJ, Wraight CA, Dikanov SA. Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site. J Am Chem Soc 2011; 133:5525-37. [PMID: 21417328 DOI: 10.1021/ja2001538] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.
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Affiliation(s)
- Erik Martin
- Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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MacMillan F, Kacprzak S, Hellwig P, Grimaldi S, Michel H, Kaupp M. Elucidating mechanisms in haemcopperoxidases: The high-affinity QHbinding site in quinol oxidase as studied by DONUT-HYSCOREspectroscopy and density functional theory. Faraday Discuss 2011; 148:315-44; discussion 421-41. [DOI: 10.1039/c005149g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Martin E, Samoilova RI, Narasimhulu KV, Wraight CA, Dikanov SA. Hydrogen bonds between nitrogen donors and the semiquinone in the Q(B) site of bacterial reaction centers. J Am Chem Soc 2010; 132:11671-7. [PMID: 20672818 DOI: 10.1021/ja104134e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photosynthetic reaction centers from Rhodobacter sphaeroides have identical ubiquinone-10 molecules functioning as primary (Q(A)) and secondary (Q(B)) electron acceptors. X-band 2D pulsed EPR spectroscopy, called HYSCORE, was applied to study the interaction of the Q(B) site semiquinone with nitrogens from the local protein environment in natural and (15)N uniformly labeled reactions centers. (14)N and (15)N HYSCORE spectra of the Q(B) semiquinone show the interaction with two nitrogens carrying transferred unpaired spin density. Quadrupole coupling constants estimated from (14)N HYSCORE spectra indicate them to be a protonated nitrogen of an imidazole residue and amide nitrogen of a peptide group. (15)N HYSCORE spectra allowed estimation of the isotropic and anisotropic couplings with these nitrogens. From these data, we calculated the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen and analyzed the contribution of different factors to the anisotropic hyperfine tensors. The hyperfine coupling of other protein nitrogens with the semiquinone is weak (<0.1 MHz). These results clearly indicate that the Q(B) semiquinone forms hydrogen bonds with two nitrogens and provide quantitative characteristics of the hyperfine couplings with these nitrogens, which can be used in theoretical modeling of the Q(B) site. On the basis of the quadrupole coupling constant, one nitrogen can only be assigned to N(delta) of His-L190, consistent with all existing structures. However, we cannot specify between two candidates the residue corresponding to the second nitrogen. Further work employing multifrequency spectroscopic approaches or selective isotope labeling would be desirable for unambiguous assignment of this nitrogen.
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Affiliation(s)
- Erik Martin
- Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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24
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Weiss SA, Bushby RJ, Evans SD, Jeuken LJC. A study of cytochrome bo3 in a tethered bilayer lipid membrane. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1797:1917-23. [PMID: 20096262 PMCID: PMC3827738 DOI: 10.1016/j.bbabio.2010.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 12/20/2009] [Accepted: 01/12/2010] [Indexed: 10/19/2022]
Abstract
An assay has been developed in which the activity of an ubiquinol oxidase from Escherichia coli, cytochrome bo(3) (cbo(3)), is determined as a function of the hydrophobic substrate ubiquinol-10 (UQ-10) in tethered bilayer lipid membranes (tBLMs). UQ-10 was added in situ, while the enzyme activity and the UQ-10 concentration in the membrane have been determined by cyclic voltammetry. Cbo(3) is inhibited by UQ-10 at concentrations above 5-10 pmol/cm(2), while product inhibition is absent. Cyclic voltammetry has also been used to characterise the effects of three inhibitors; cyanide, inhibiting oxygen reduction; 2-n-Heptyl-4-hydroxyquinoline N-oxide (HQNO), inhibiting the quinone oxidation and Zn(II), thought to block the proton channels required for oxygen reduction and proton pumping activity. The electrochemical behaviour of cbo(3) inhibited with HQNO and Zn(II) is almost identical, suggesting that Zn(II) ions inhibit the enzyme reduction by quinol, rather than oxygen reduction. This suggests that at Zn(II) concentration below 50µM the proton release of cbo(3) is inhibited, but not the proton uptake required to reduce oxygen to water.
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Affiliation(s)
- Sophie A. Weiss
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Richard J. Bushby
- Centre for Self Organising Molecular Systems, University of Leeds, Leeds, LS2 9JT, UK
| | - Stephen D. Evans
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Lars J. C. Jeuken
- Centre for Self Organising Molecular Systems, University of Leeds, Leeds, LS2 9JT, UK
- Institute of Membrane and Systems Biology, University of Leeds, Leeds, LS2 9JT, UK
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25
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Yap LL, Lin MT, Ouyang H, Samoilova RI, Dikanov SA, Gennis RB. The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1924-32. [PMID: 20416270 DOI: 10.1016/j.bbabio.2010.04.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/04/2010] [Accepted: 04/13/2010] [Indexed: 11/18/2022]
Abstract
Cytochrome bo(3) is the major respiratory oxidase located in the cytoplasmic membrane of Escherichia coli when grown under high oxygen tension. The enzyme catalyzes the 2-electron oxidation of ubiquinol-8 and the 4-electron reduction of dioxygen to water. When solubilized and isolated using dodecylmaltoside, the enzyme contains one equivalent of ubiquinone-8, bound at a high affinity site (Q(H)). The quinone bound at the Q(H) site can form a stable semiquinone, and the amino acid residues which hydrogen bond to the semiquinone have been identified. In the current work, it is shown that the tightly bound ubiquinone-8 at the Q(H) site is not displaced by ubiquinol-1 even during enzyme turnover. Furthermore, the presence of high affinity inhibitors, HQNO and aurachin C1-10, does not displace ubiquinone-8 from the Q(H) site. The data clearly support the existence of a second binding site for ubiquinone, the Q(L) site, which can rapidly exchange with the substrate pool. HQNO is shown to bind to a single site on the enzyme and to prevent formation of the stable ubisemiquinone, though without displacing the bound quinone. Inhibition of the steady state kinetics of the enzyme indicates that aurachin C1-10 may compete for binding with quinol at the Q(L) site while, at the same time, preventing formation of the ubisemiquinone at the Q(H) site. It is suggested that the two quinone binding sites may be adjacent to each other or partially overlap.
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Affiliation(s)
- Lai Lai Yap
- Department of Biochemistry, University of Illinois, 600 S. Goodwin Avenue, Urbana, IL 61801, USA
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Yi SM, Narasimhulu KV, Samoilova RI, Gennis RB, Dikanov SA. Characterization of the semiquinone radical stabilized by the cytochrome aa3-600 menaquinol oxidase of Bacillus subtilis. J Biol Chem 2010; 285:18241-51. [PMID: 20351111 DOI: 10.1074/jbc.m110.116186] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome aa(3)-600 is one of the principle respiratory oxidases from Bacillus subtilis and is a member of the heme-copper superfamily of oxygen reductases. This enzyme catalyzes the two-electron oxidation of menaquinol and the four-electron reduction of O(2) to 2H(2)O. Cytochrome aa(3)-600 is of interest because it is a very close homologue of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli, except that it uses menaquinol instead of ubiquinol as a substrate. One question of interest is how the proteins differ in response to the differences in structure and electrochemical properties between ubiquinol and menaquinol. Cytochrome bo(3) has a high affinity binding site for ubiquinol that stabilizes a ubi-semiquinone. This has permitted the use of pulsed EPR techniques to investigate the protein interaction with the ubiquinone. The current work initiates studies to characterize the equivalent site in cytochrome aa(3)-600. Cytochrome aa(3)-600 has been cloned and expressed in a His-tagged form in B. subtilis. After isolation of the enzyme in dodecylmaltoside, it is shown that the pure enzyme contains 1 eq of menaquinone-7 and that the enzyme stabilizes a mena-semiquinone. Pulsed EPR studies have shown that there are both similarities as well as significant differences in the interactions of the mena-semiquinone with cytochrome aa(3)-600 in comparison with the ubi-semiquinone in cytochrome bo(3). Our data indicate weaker hydrogen bonds of the menaquinone in cytochrome aa(3)-600 in comparison with ubiquinone in cytochrome bo(3). In addition, the electronic structure of the semiquinone cyt aa(3)-600 is more shifted toward the anionic form from the neutral state in cyt bo(3).
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Affiliation(s)
- Sophia M Yi
- Departments of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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Truflandier LA, Boucher F, Payen C, Hajjar R, Millot Y, Bonhomme C, Steunou N. DFT-NMR Investigation and 51V 3QMAS Experiments for Probing Surface OH Ligands and the Hydrogen-Bond Network in a Polyoxovanadate Cluster: The Case of Cs4[H2V10O28]·4H2O. J Am Chem Soc 2010; 132:4653-68. [DOI: 10.1021/ja908973y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lionel A. Truflandier
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Florent Boucher
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Christophe Payen
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Redouane Hajjar
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Yannick Millot
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Christian Bonhomme
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Nathalie Steunou
- Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44340 Nantes Cedex 3, France, Laboratoire des Systèmes Interfaciaux à l’Echelle Nanométrique (SIEN), UMR CNRS 7142, UPMC Univ Paris 06, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR CNRS 7574, UPMC Univ Paris 06, Collège de France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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Boesch SE, Wheeler RA. Isotropic 13C hyperfine coupling constants distinguish neutral from anionic ubiquinone-derived radicals. Chemphyschem 2010; 10:3187-9. [PMID: 19904797 DOI: 10.1002/cphc.200900503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Scott E Boesch
- Department of Chemistry & Biochemistry, University of Oklahoma, 620 Parrington Oval, Room 208, Norman, OK 73019, USA
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Grimaldi S, Arias-Cartin R, Lanciano P, Lyubenova S, Endeward B, Prisner TF, Magalon A, Guigliarelli B. Direct evidence for nitrogen ligation to the high stability semiquinone intermediate in Escherichia coli nitrate reductase A. J Biol Chem 2009; 285:179-87. [PMID: 19892705 DOI: 10.1074/jbc.m109.060251] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound heterotrimeric nitrate reductase A (NarGHI) catalyzes the oxidation of quinols in the cytoplasmic membrane of Escherichia coli and reduces nitrate to nitrite in the cytoplasm. The enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (Q(D)) located in the vicinity of the distal heme b(D). Here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed EPR methods. (14)N and (15)N ESEEM and HYSCORE measurements carried out at X-band ( approximately 9.7 GHz) on the wild-type enzyme or the enzyme uniformly labeled with (15)N nuclei reveal an interaction between the semiquinone and a single nitrogen nucleus. The isotropic hyperfine coupling constant A(iso)((14)N) approximately 0.8 MHz shows that it occurs via an H-bond to one of the quinone carbonyl group. Using (14)N ESEEM and HYSCORE spectroscopies at a lower frequency (S-band, approximately 3.4 GHz), the (14)N nuclear quadrupolar parameters of the interacting nitrogen nucleus (kappa = 0.49, eta = 0.50) were determined and correspond to those of a histidine N(delta), assigned to the heme b(D) ligand His-66 residue. Moreover S-band (15)N ESEEM spectra enabled us to directly measure the anisotropic part of the nitrogen hyperfine interaction (T((15)N) = 0.16 MHz). A distance of approximately 2.2 Abetween the carbonyl oxygen and the nitrogen could then be calculated. Mechanistic implications of these results are discussed in the context of the peculiar properties of the menasemiquinone intermediate stabilized at the Q(D) site of NarGHI.
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Affiliation(s)
- Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036), Institut de Microbiologie de laMéditerranée, CNRS and Aix-Marseille Université, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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Abstract
Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophoshate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and demethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O2 is served by two major oxidoreductases (oxidases), cytochrome bo3 and cytochrome bd. Terminal oxidases of aerobic respiratory chains of bacteria, which use O2 as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo3 and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo3 and cytochrome bd. The E. coli membrane contains three types of quinones which all have an octaprenyl side chain (C40). It has been proposed that the bo3 oxidase can have two ubiquinone-binding sites with different affinities. The spectral properties of cytochrome bd-II closely resemble those of cydAB-encoded cytochrome bd.
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31
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Hayashi T, Lin MT, Ganesan K, Chen Y, Fee JA, Gennis RB, Moënne-Loccoz P. Accommodation of two diatomic molecules in cytochrome bo: insights into NO reductase activity in terminal oxidases. Biochemistry 2009; 48:883-90. [PMID: 19187032 DOI: 10.1021/bi801915r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial heme-copper terminal oxidases react quickly with NO to form a heme-nitrosyl complex, which, in some of these enzymes, can further react with a second NO molecule to produce N(2)O. Previously, we characterized the heme a(3)-NO complex formed in cytochrome ba(3) from Thermus thermophilus and the product of its low-temperature illumination. We showed that the photolyzed NO group binds to Cu(B)(I) to form an end-on NO-Cu(B) or a side-on copper-nitrosyl complex, which is likely to represent the binding characteristics of the second NO molecule at the heme-copper active site. Here we present a comparative study with cytochrome bo(3) from Escherichia coli. Both terminal oxidases are shown to catalyze the same two-electron reduction of NO to N(2)O. The EPR and resonance Raman signatures of the heme o(3)-NO complex are comparable to those of the a(3)-NO complex. However, low-temperature FTIR experiments reveal that photolysis of the heme o(3)-NO complex does not produce a Cu(B)-nitrosyl complex, but that instead, the NO remains unbound in the active-site cavity. Additional FTIR photolysis experiments on the heme-nitrosyl complexes of these terminal oxidases, in the presence of CO, demonstrate that an [o(3)-NO.OC-Cu(B)] tertiary complex can form in bo(3) but not in ba(3). We assign these differences to a greater iron-copper distance in the reduced form of bo(3) compared to that of ba(3). Because this difference in metal-metal distance does not appear to affect the NO reductase activity, our results suggest that the coordination of the second NO to Cu(B) is not an essential step of the reaction mechanism.
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Affiliation(s)
- Takahiro Hayashi
- Department of Science and Engineering, School of Medicine, Oregon Health & Science University, 20,000 NW Walker Road, Beaverton, Oregon 97006-8921, USA
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Kolling DRJ, Samoilova RI, Shubin AA, Crofts AR, Dikanov SA. Proton environment of reduced Rieske iron-sulfur cluster probed by two-dimensional ESEEM spectroscopy. J Phys Chem A 2009; 113:653-67. [PMID: 19099453 PMCID: PMC2680161 DOI: 10.1021/jp806789x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proton environment of the reduced [2Fe-2S] cluster in the water-soluble head domain of the Rieske iron-sulfur protein (ISF) from the cytochrome bc(1) complex of Rhodobacter sphaeroides has been studied by orientation-selected X-band 2D ESEEM. The 2D spectra show multiple cross-peaks from protons, with considerable overlap. Samples in which (1)H(2)O water was replaced by (2)H(2)O were used to determine which of the observed peaks belong to exchangeable protons, likely involved in hydrogen bonds in the neighborhood of the cluster. By correlating the cross-peaks from 2D spectra recorded at different parts of the EPR spectrum, lines from nine distinct proton signals were identified. Assignment of the proton signals was based on a point-dipole model for interaction with electrons of Fe(III) and Fe(II) ions, using the high-resolution structure of ISF from Rb. sphaeroides. Analysis of experimental and calculated tensors has led us to conclude that even 2D spectra do not completely resolve all contributions from nearby protons. Particularly, the seven resolved signals from nonexchangeable protons could be produced by at least 13 protons. The contributions from exchangeable protons were resolved by difference spectra ((1)H(2)O minus (2)H(2)O), and assigned to two groups of protons with distinct anisotropic hyperfine values. The largest measured coupling exceeded any calculated value. This discrepancy could result from limitations of the point dipole approximation in dealing with the distribution of spin density over the sulfur atoms of the cluster and the cysteine ligands, or from differences between the structure in solution and the crystallographic structure. The approach demonstrated here provides a paradigm for a wide range of studies in which hydrogen-bonding interactions with metallic centers has a crucial role in understanding the function.
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Affiliation(s)
- Derrick R. J. Kolling
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Alexander A. Shubin
- Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk 6300090, Russia
| | - Antony R. Crofts
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois 61801
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The Cytochrome bc 1 and Related bc Complexes: The Rieske/Cytochrome b Complex as the Functional Core of a Central Electron/Proton Transfer Complex. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_23] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Lin MT, Samoilova RI, Gennis RB, Dikanov SA. Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli. J Am Chem Soc 2008; 130:15768-9. [PMID: 18983149 PMCID: PMC2645916 DOI: 10.1021/ja805906a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The selective (15)N isotope labeling was used for the identification of the nitrogen involved in a hydrogen bond formation with the semiquinone in the high-affinity Q(H) site in the cytochrome bo(3) ubiquinol oxidase. This nitrogen produces dominating contribution to X-Band (14)N ESEEM spectra. The 2D ESEEM (HYSCORE) experiments with the Q(H) site SQ in the series of selectively (15)N labeled bo(3) oxidase proteins have directly identified the N(epsilon) of R71 as an H-bond donor. In addition, selective (15)N labeling has allowed us for the first time to determine weak hyperfine couplings with the side-chain nitrogens from all residues around the SQ. Those are reflecting a distribution of the unpaired spin density over the protein in the SQ state of the quinone processing site.
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Affiliation(s)
- Myat T. Lin
- Department of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Robert B. Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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Dikanov SA, Holland JT, Endeward B, Kolling DRJ, Samoilova RI, Prisner TF, Antony R. C. Hydrogen bonds between nitrogen donors and the semiquinone in the Qi-site of the bc1 complex. J Biol Chem 2007; 282:25831-41. [PMID: 17616531 PMCID: PMC3060708 DOI: 10.1074/jbc.m702333200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubisemiquinone stabilized at the Qi-site of the bc1 complex of Rhodobacter sphaeroides forms a hydrogen bond with a nitrogen from the local protein environment, tentatively identified as ring N from His-217. The interactions of 14N and 15N have been studied by X-band (approximately 9.7 GHz) and S-band (3.4 GHz) pulsed EPR spectroscopy. The application of S-band spectroscopy has allowed us to determine the complete nuclear quadrupole tensor of the 14N involved in H-bond formation and to assign it unambiguously to the Nepsilon of His-217. This tensor has distinct characteristics in comparison with H-bonds between semiquinones and Ndelta in other quinone-processing sites. The experiments with 15N showed that the Nepsilon of His-217 was the only nitrogen carrying any considerable unpaired spin density in the ubiquinone environment, and allowed calculation of the isotropic and anisotropic couplings with the Nepsilon of His-217. From these data, we could estimate the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen and the distance from the nitrogen to the carbonyl oxygen of 2.38+/-0.13A. The hyperfine coupling of other protein nitrogens with semiquinone is <0.1 MHz. This did not exclude the nitrogen of the Asn-221 as a possible hydrogen bond donor to the methoxy oxygen of the semiquinone. A mechanistic role for this residue is supported by kinetic experiments with mutant strains N221T, N221H, N221I, N221S, N221P, and N221D, all of which showed some inhibition but retained partial turnover.
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Affiliation(s)
- Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois 61801
| | - J. Todd Holland
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Burkhard Endeward
- J. W. Goethe Universitaät, Institut für Physikalische und Theoretische Chemie, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Derrick R. J. Kolling
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Thomas F. Prisner
- J. W. Goethe Universitaät, Institut für Physikalische und Theoretische Chemie, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Crofts Antony R.
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
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Amorati R, Franchi P, Pedulli G. Intermolecular Hydrogen Bonding Modulates the Hydrogen-Atom-Donating Ability of Hydroquinones. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Amorati R, Franchi P, Pedulli GF. Intermolecular Hydrogen Bonding Modulates the Hydrogen-Atom-Donating Ability of Hydroquinones. Angew Chem Int Ed Engl 2007; 46:6336-8. [PMID: 17640006 DOI: 10.1002/anie.200701957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Riccardo Amorati
- Dipartimento di Chimica Organica A. Mangini, Università di Bologna, Via S. Giacomo 11, 40126 Bologna, Italy.
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Yap LL, Samoilova RI, Gennis RB, Dikanov SA. Characterization of Mutants That Change the Hydrogen Bonding of the Semiquinone Radical at the QH Site of the Cytochrome bo3 from Escherichia coli. J Biol Chem 2007; 282:8777-85. [PMID: 17267395 DOI: 10.1074/jbc.m611595200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cytochrome bo3 ubiquinol oxidase catalyzes the two-electron oxidation of ubiquinol in the cytoplasmic membrane of Escherichia coli, and reduces O2 to water. This enzyme has a high affinity quinone binding site (QH), and the quinone bound to this site acts as a cofactor, necessary for rapid electron transfer from substrate ubiquinol, which binds at a separate site (QL), to heme b. Previous pulsed EPR studies have shown that a semiquinone at the QH site formed during the catalytic cycle is a neutral species, with two strong hydrogen bonds to Asp-75 and either Arg-71 or Gln-101. In the current work, pulsed EPR studies have been extended to two mutants at the QH site. The D75E mutation has little influence on the catalytic activity, and the pattern of hydrogen bonding is similar to the wild type. In contrast, the D75H mutant is virtually inactive. Pulsed EPR revealed significant structural changes in this mutant. The hydrogen bond to Arg-71 or Gln-101 that is present in both the wild type and D75E mutant oxidases is missing in the D75H mutant. Instead, the D75H has a single, strong hydrogen bond to a histidine, likely His-75. The D75H mutant stabilizes an anionic form of the semiquinone as a result of the altered hydrogen bond network. Either the redistribution of charge density in the semiquinone species, or the altered hydrogen bonding network is responsible for the loss of catalytic function.
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Affiliation(s)
- Lai Lai Yap
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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