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Starbird C, Tomasiak TM, Singh PK, Yankovskaya V, Maklashina E, Eisenbach M, Cecchini G, Iverson T. New crystal forms of the integral membrane Escherichia coli quinol:fumarate reductase suggest that ligands control domain movement. J Struct Biol 2018; 202:100-104. [PMID: 29158068 PMCID: PMC5835405 DOI: 10.1016/j.jsb.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 01/28/2023]
Abstract
Quinol:fumarate reductase (QFR) is an integral membrane protein and a member of the respiratory Complex II superfamily. Although the structure of Escherichia coli QFR was first reported almost twenty years ago, many open questions of catalysis remain. Here we report two new crystal forms of QFR, one grown from the lipidic cubic phase and one grown from dodecyl maltoside micelles. QFR crystals grown from the lipid cubic phase processed as P1, merged to 7.5 Å resolution, and exhibited crystal packing similar to previous crystal forms. Crystals grown from dodecyl maltoside micelles processed as P21, merged to 3.35 Å resolution, and displayed a unique crystal packing. This latter crystal form provides the first view of the E. coli QFR active site without a dicarboxylate ligand. Instead, an unidentified anion binds at a shifted position. In one of the molecules in the asymmetric unit, this is accompanied by rotation of the capping domain of the catalytic subunit. In the other molecule, this is associated with loss of interpretable electron density for this same capping domain. Analysis of the structure suggests that the ligand adjusts the position of the capping domain.
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Affiliation(s)
- C.A. Starbird
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Thomas M. Tomasiak
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Prashant K. Singh
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Victoria Yankovskaya
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, California 94121, Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, California 94121, Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - Michael Eisenbach
- Department of Biomolecular Sciences, Weizmann Institute of Science, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, California 94121, Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - T.M. Iverson
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee 37232,Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
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Heering HA, Weiner JH, Armstrong FA. Direct Detection and Measurement of Electron Relays in a Multicentered Enzyme: Voltammetry of Electrode-Surface Films of E. coli Fumarate Reductase, an Iron−Sulfur Flavoprotein. J Am Chem Soc 1997. [DOI: 10.1021/ja9723242] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hendrik A. Heering
- Contribution from the Inorganic Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QR, England, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Joel H. Weiner
- Contribution from the Inorganic Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QR, England, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Fraser A. Armstrong
- Contribution from the Inorganic Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QR, England, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Khandekar SS, Eirich LD. Purification and characterization of an anabolic fumarate reductase from Methanobacterium thermoautotrophicum. Appl Environ Microbiol 1989; 55:856-61. [PMID: 2499256 PMCID: PMC184214 DOI: 10.1128/aem.55.4.856-861.1989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An oxygen-sensitive fumarate reductase has been purified from the cytosol fraction of the cells of the archaebacterium Methanobacterium thermoautotrophicum. A major portion of the purification was performed inside an anaerobic chamber, employing reducing agents to maintain low redox potentials. The apparent molecular weight of the native enzyme is 78,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated a minimal subunit molecular weight of about 20,000. Iodoacetamide (1 mM) and copper chloride (5 mM) caused significant loss in the enzyme activity. The optimum temperature for the enzymatic activity was 75 degrees C. The pH optimum was found to be 7.0. The fumarate reductase had an apparent Km of 0.20 mM for fumarate. Purified enzyme was colorless; spectroscopic studies indicated the absence of flavins as a cofactor. The spectral data, however, suggested the presence of an unknown cofactor tightly bound to the enzyme. Fumarate reductase is involved in the anabolic rather than the catabolic metabolism of M. thermoautotrophicum.
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Affiliation(s)
- S S Khandekar
- Environmental Sciences and Resources Program in Chemistry and Biology, Portland State University, Oregon 97207
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Fronticelli C, Bucci E, Zachary A, Rosen BP. Conformational properties of membrane-bound fumarate reductase of Escherichia coli. Arch Biochem Biophys 1986; 249:579-87. [PMID: 3530136 DOI: 10.1016/0003-9861(86)90036-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Anaerobically grown cells of Escherichia coli harboring the plasmid pFRD63 over-produce fumarate reductase, a membrane-bound complex localized in the inner membrane of the cell, where this enzyme represents at least 90% of the total membrane proteins (B. D. Lemire, J. J. Robinson, and J. H. Weiner (1982) J. Bacteriol. 152, 1126-1131). Preparations of inner membrane fractions suspended in 40% sucrose are optically clear, allowing optical spectroscopic measurements. Circular dichroism spectra showed that between pH 6 and 11 the secondary structure of the enzyme is at least 55% in alpha helix and that above pH 11 the structure abruptly changes to a beta-like conformation. The same phenomenon is observed in samples solubilized in the nonionic detergent C12E9. Absorption spectra of the enzyme either membrane bound or solubilized in detergents or exposed to alkaline pH showed that the accessibility of the active site to solvent components is modulated by the interaction of the protein with the membrane. Solubilization of the membrane-bound enzyme with 1% Triton X-100 or C12E9 produced a decrease in ellipticity and in enzymatic activity.
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Cole ST, Condon C, Lemire BD, Weiner JH. Molecular biology, biochemistry and bioenergetics of fumarate reductase, a complex membrane-bound iron-sulfur flavoenzyme of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 811:381-403. [PMID: 3910107 DOI: 10.1016/0304-4173(85)90008-4] [Citation(s) in RCA: 139] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Wetzstein HG, Gottschalk G. A sodium-stimulated membrane-bound fumarate reductase system in Bacteroides amylophilus. Arch Microbiol 1985; 143:157-62. [PMID: 4074073 DOI: 10.1007/bf00411041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane vesicles derived from whole cells of the strictly anaerobic rumen bacterium Bacteroides amylophilus exhibited fumarate reductase activity with NADH, FADH2, FMNH2, or reduced viologens as electron donors. The fumarate reductase system is most likely localized on the cytoplasmic side of the plasma membrane. Cytochromes and menaquinone were not detectable. The NADH-dependent activity was inactivated by oxygen, an endogenous protease, and by irradiation at 254 nm. The electron transport inhibitor HpHOQnO and Zn2+ were identified as strong inhibitors of the fumarate reductase reaction. Two types of functional SH-groups might be operative in this system as probed by ClHgSO3H. The oxidation of NADH by fumarate was stimulated by low concentrations of Na+. Concentrations of Na+ in the range of 4 to 30 mM had a pronounced influence on growth rate and cell yield of B. amylophilus. In the presence of 1 mM NaCl growth was observed only after a lag-period of 15 h.
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Weiner JH, Lemire BD, Jones RW, Anderson WF, Scraba DG. A model for the structure of fumarate reductase in the cytoplasmic membrane of Escherichia coli. J Cell Biochem 1984; 24:205-14. [PMID: 6376524 DOI: 10.1002/jcb.240240303] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
By a recombinant DNA approach we have prepared Escherichia coli cytoplasmic membranes that are highly enriched in the terminal electron transfer enzyme fumarate reductase. This enzyme is composed of four nonidentical subunits in equal molar ratio. A 69,000-dalton covalent flavin-containing subunit and a 27,000-dalton nonheme iron-containing subunit make up a membrane extrinsic catalytic domain. Two very hydrophobic subunits of 15,000 and 13,000 daltons make up the hydrophobic membrane anchor domain. Electron microscopy of negatively stained membranes shows a characteristic knob-and-stalk-type structure composed of the catalytic domain. The anchor polypeptides have been analyzed for hydrophobic segments and alpha-helical content and a model for their organization within the lipid bilayer is presented. The results reviewed in this paper suggest a model for the fumarate reductase complex in the cytoplasmic membrane.
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Kotlyar AB, Vinogradov AD. Sulphate ion-induced slow transformation of succinate dehydrogenase. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 747:182-5. [PMID: 6882777 DOI: 10.1016/0167-4838(83)90138-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A new type of slow change of succinate dehydrogenase (EC 1.3.99), activity which is induced by sulphate ion is described. After preincubation of submitochondrial particles or soluble succinate dehydrogenase with sulphate both preparations catalyze succinate:phenazine methosulphate reductase reaction with a significant lag. When added to the assay medium sulphate ion induces biphasic time-dependent competitive inhibition of the enzyme. The sulphate-induced inhibition is apparently due to a rapid interaction of the anion with an active site of the enzyme which is followed by a slow pH-dependent (pKa = 7.2) transformation of the enzyme-inhibitor complex. pH profiles of the overall succinate dehydrogenase reaction and of equilibrium between fast and slow enzyme-sulphate complexes suggest that the same protolytic equilibrium step is involved in the formation of an active intermediate and an inactive enzyme-sulphate complex.
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Lemire BD, Robinson JJ, Weiner JH. Identification of membrane anchor polypeptides of Escherichia coli fumarate reductase. J Bacteriol 1982; 152:1126-31. [PMID: 6754697 PMCID: PMC221618 DOI: 10.1128/jb.152.3.1126-1131.1982] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Fumarate reductase of Escherichia coli has been shown to be a membrane-bound enzyme composed of a 69,000-dalton catalytic-flavin-containing subunit and a 27,000-dalton nonheme-iron-containing subunit. Using gene cloning and amplification techniques, we have observed two additional polypeptides encoded by the frd operon, with apparent molecular weights of 15,000 and 14,000, which are expressed when E. coli is grown anaerobically on glycerol plus fumarate. Expression of these two small polypeptides is necessary for the two large subunits to associate with the membrane. The four subunits remain associated in Triton X-100 extracts of the membrane, and a holoenzyme form of fumarate reductase containing one copy of each of the four polypeptides has been isolated. Unlike the well-characterized two-subunit form, the holoenzyme is not dependent on anions for activity and is not labile at alkaline pH. In these respects, it more closely resembles the membrane-bound activity.
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