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Curtolo F, Arantes GM. Dissecting Reaction Mechanisms and Catalytic Contributions in Flavoprotein Fumarate Reductases. J Chem Inf Model 2023. [PMID: 37196341 DOI: 10.1021/acs.jcim.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The interconversion between fumarate and succinate is fundamental to the energy metabolism of nearly all organisms. This redox reaction is catalyzed by a large family of enzymes, fumarate reductases and succinate dehydrogenases, using hydride and proton transfers from a flavin cofactor and a conserved Arg side-chain. These flavoenzymes also have substantial biomedical and biotechnological importance. Therefore, a detailed understanding of their catalytic mechanisms is valuable. Here, calibrated electronic structure calculations in a cluster model of the active site of the Fcc3 fumarate reductase were employed to investigate various reaction pathways and possible intermediates in the enzymatic environment and to dissect interactions that contribute to catalysis of fumarate reduction. Carbanion, covalent adduct, carbocation, and radical intermediates were examined. Significantly lower barriers were obtained for mechanisms via carbanion intermediates, with similar activation energies for hydride and proton transfers. Interestingly, the carbanion bound to the active site is best described as an enolate. Hydride transfer is stabilized by a preorganized charge dipole in the active site and by the restriction of the C1-C2 bond in a twisted conformation of the otherwise planar fumarate dianion. But, protonation of a fumarate carboxylate and quantum tunneling effects are not critical for catalysis of the hydride transfer. Calculations also suggest that the driving force for enzyme turnover is provided by regeneration of the catalytic Arg, either coupled with flavin reduction and decomposition of a proposed transient state or directly from the solvent. The detailed mechanistic description of enzymatic reduction of fumarate provided here clarifies previous contradictory views and provides new insights into catalysis by essential flavoenzyme reductases and dehydrogenases.
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Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
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2
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Iverson TM, Singh PK, Cecchini G. An evolving view of Complex II - non-canonical complexes, megacomplexes, respiration, signaling, and beyond. J Biol Chem 2023; 299:104761. [PMID: 37119852 DOI: 10.1016/j.jbc.2023.104761] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023] Open
Abstract
Mitochondrial Complex II is traditionally studied for its participation in two key respiratory processes: the electron transport chain and the Krebs cycle. There is now a rich body of literature explaining how Complex II contributes to respiration. However, more recent research shows that not all of the pathologies associated with altered Complex II activity clearly correlate with this respiratory role. Complex II activity has now been shown to be necessary for a range of biological processes peripherally-related to respiration, including metabolic control, inflammation, and cell fate. Integration of findings from multiple types of studies suggests that Complex II both participates in respiration and controls multiple succinate-dependent signal transduction pathways. Thus, the emerging view is that the true biological function of Complex II is well beyond respiration. This review uses a semi-chronological approach to highlight major paradigm shifts that occurred over time. Special emphasis is given to the more recently identified functions of Complex II and its subunits because these findings have infused new directions into an established field.
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Affiliation(s)
- T M Iverson
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Biochemistry, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232.
| | - Prashant K Singh
- Departments of Pharmacology, Vanderbilt University, Nashville, TN 37232; Departments of Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA 94121; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158.
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3
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Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster. Proc Natl Acad Sci U S A 2021; 118:2022308118. [PMID: 33876763 PMCID: PMC8054011 DOI: 10.1073/pnas.2022308118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Targeting energy metabolism in Mycobacterium tuberculosis has emerged as a new paradigm in antituberculosis drug discovery. Succinate dehydrogenase is considered the regulator of respiration in M. tuberculosis. Mycobacteria contains two different succinate dehydrogenase enzymes designated Sdh1 and Sdh2. Sdh1 has recently been identified as a new class of succinate dehydrogenase. In this study, we have determined M. smegmatis Sdh1 structures alone and in the presence of ubiquinone-1, revealing that Sdh1 has a novel electron transfer pathway and a unique substrate-binding site. These data show that the structure of M. tuberculosis Sdh1 is significantly different by comparison with the human counterpart making a good antituberculosis drug target. Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been identified as a new class of respiratory complex II (type F) but with an unknown electron transfer mechanism. Here, using cryoelectron microscopy, we have determined the structure of Mycobacterium smegmatis Sdh1 in the presence and absence of the substrate, ubiquinone-1, at 2.53-Å and 2.88-Å resolution, respectively. Sdh1 comprises three subunits, two that are water soluble, SdhA and SdhB, and one that is membrane spanning, SdhC. Within these subunits we identified a quinone-binding site and a rarely observed Rieske-type [2Fe-2S] cluster, the latter being embedded in the transmembrane region. A mutant, where two His ligands of the Rieske-type [2Fe-2S] were changed to alanine, abolished the quinone reduction activity of the Sdh1. Our structures allow the proposal of an electron transfer pathway that connects the substrate-binding and quinone-binding sites. Given the unique features of Sdh1 and its essential role in Mycobacteria, these structures will facilitate antituberculosis drug discovery efforts that specifically target this complex.
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The roles of SDHAF2 and dicarboxylate in covalent flavinylation of SDHA, the human complex II flavoprotein. Proc Natl Acad Sci U S A 2020; 117:23548-23556. [PMID: 32887801 DOI: 10.1073/pnas.2007391117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial complex II, also known as succinate dehydrogenase (SDH), is an integral-membrane heterotetramer (SDHABCD) that links two essential energy-producing processes, the tricarboxylic acid (TCA) cycle and oxidative phosphorylation. A significant amount of information is available on the structure and function of mature complex II from a range of organisms. However, there is a gap in our understanding of how the enzyme assembles into a functional complex, and disease-associated complex II insufficiency may result from incorrect function of the mature enzyme or from assembly defects. Here, we investigate the assembly of human complex II by combining a biochemical reconstructionist approach with structural studies. We report an X-ray structure of human SDHA and its dedicated assembly factor SDHAF2. Importantly, we also identify a small molecule dicarboxylate that acts as an essential cofactor in this process and works in synergy with SDHAF2 to properly orient the flavin and capping domains of SDHA. This reorganizes the active site, which is located at the interface of these domains, and adjusts the pKa of SDHAR451 so that covalent attachment of the flavin adenine dinucleotide (FAD) cofactor is supported. We analyze the impact of disease-associated SDHA mutations on assembly and identify four distinct conformational forms of the complex II flavoprotein that we assign to roles in assembly and catalysis.
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5
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Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF. Nat Commun 2020; 11:4245. [PMID: 32843629 PMCID: PMC7447783 DOI: 10.1038/s41467-020-18011-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/24/2020] [Indexed: 11/21/2022] Open
Abstract
Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs. Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Sdh2, which reveals membrane-anchored SdhF as a component of the complex and they discuss the electron/proton transfer pathway in the Sdh2 trimer.
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part III. [4Fe-4S], [3Fe-4S] and [2Fe-2S] iron-sulfur proteins. J Struct Biol 2018; 202:264-274. [DOI: 10.1016/j.jsb.2018.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/16/2018] [Indexed: 11/18/2022]
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Maklashina E, Rajagukguk S, Iverson TM, Cecchini G. The unassembled flavoprotein subunits of human and bacterial complex II have impaired catalytic activity and generate only minor amounts of ROS. J Biol Chem 2018; 293:7754-7765. [PMID: 29610278 PMCID: PMC5961047 DOI: 10.1074/jbc.ra118.001977] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
Complex II (SdhABCD) is a membrane-bound component of mitochondrial and bacterial electron transport chains, as well as of the TCA cycle. In this capacity, it catalyzes the reversible oxidation of succinate. SdhABCD contains the SDHA protein harboring a covalently bound FAD redox center and the iron-sulfur protein SDHB, containing three distinct iron-sulfur centers. When assembly of this complex is compromised, the flavoprotein SDHA may accumulate in the mitochondrial matrix or bacterial cytoplasm. Whether the unassembled SDHA has any catalytic activity, for example in succinate oxidation, fumarate reduction, reactive oxygen species (ROS) generation, or other off-pathway reactions, is not known. Therefore, here we investigated whether unassembled Escherichia coli SdhA flavoprotein, its homolog fumarate reductase (FrdA), and the human SDHA protein have succinate oxidase or fumarate reductase activity and can produce ROS. Using recombinant expression in E. coli, we found that the free flavoproteins from these divergent biological sources have inherently low catalytic activity and generate little ROS. These results suggest that the iron-sulfur protein SDHB in complex II is necessary for robust catalytic activity. Our findings are consistent with those reported for single-subunit flavoprotein homologs that are not associated with iron-sulfur or heme partner proteins.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and
| | - Sany Rajagukguk
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121
| | - T. M. Iverson
- the Departments of Pharmacology and ,Biochemistry, ,the Center for Structural Biology, and ,the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and , Recipient of Senior Research Career Scientist Award IK6BX004215 from the Department of Veterans Affairs. To whom correspondence should be addressed:
Molecular Biology Division (151-S), San Francisco Veterans Affairs Healthcare System, 4150 Clement St., San Francisco, CA 94121. Tel.:
415-221-4810, Ext. 24416; E-mail:
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8
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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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9
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Sharma P, Maklashina E, Cecchini G, Iverson TM. Crystal structure of an assembly intermediate of respiratory Complex II. Nat Commun 2018; 9:274. [PMID: 29348404 PMCID: PMC5773532 DOI: 10.1038/s41467-017-02713-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023] Open
Abstract
Flavin is covalently attached to the protein scaffold in ~10% of flavoenzymes. However, the mechanism of covalent modification is unclear, due in part to challenges in stabilizing assembly intermediates. Here, we capture the structure of an assembly intermediate of the Escherichiacoli Complex II (quinol:fumarate reductase (FrdABCD)). The structure contains the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor, SdhE. The structure contains two global conformational changes as compared to prior structures of the mature protein: the rotation of a domain within the FrdA subunit, and the destabilization of two large loops of the FrdA subunit, which may create a tunnel to the active site. We infer a mechanism for covalent flavinylation. As supported by spectroscopic and kinetic analyses, we suggest that SdhE shifts the conformational equilibrium of the FrdA active site to disfavor succinate/fumarate interconversion and enhance covalent flavinylation. The mechanism for covalent flavinylation of flavoenzymes is still unclear. Here, the authors propose a mechanism based on the crystal structure of a flavinylation assembly intermediate of the E. coli respiratory Complex II comprising the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor SdhE.
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Affiliation(s)
- Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA.,Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA. .,Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA. .,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA. .,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA. .,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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10
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Starbird CA, Maklashina E, Sharma P, Qualls-Histed S, Cecchini G, Iverson TM. Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase. J Biol Chem 2017; 292:12921-12933. [PMID: 28615448 DOI: 10.1074/jbc.m117.795120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/07/2017] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.
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Affiliation(s)
- C A Starbird
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Susan Qualls-Histed
- Departments of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232.
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11
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Maklashina E, Rajagukguk S, Starbird CA, McDonald WH, Koganitsky A, Eisenbach M, Iverson TM, Cecchini G. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II. J Biol Chem 2015; 291:2904-16. [PMID: 26644464 DOI: 10.1074/jbc.m115.690396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 01/23/2023] Open
Abstract
Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158
| | - Sany Rajagukguk
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121
| | | | - W Hayes McDonald
- the Department of Biochemistry and Mass Spectrometry Research Center
| | - Anna Koganitsky
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michael Eisenbach
- the Department of Biological Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tina M Iverson
- the Department of Biochemistry and Mass Spectrometry Research Center, the Department of Pharmacology, the Center for Structural Biology, and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, and
| | - Gary Cecchini
- From the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158,
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12
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Cheng VWT, Piragasam RS, Rothery RA, Maklashina E, Cecchini G, Weiner JH. Redox state of flavin adenine dinucleotide drives substrate binding and product release in Escherichia coli succinate dehydrogenase. Biochemistry 2015; 54:1043-52. [PMID: 25569225 DOI: 10.1021/bi501350j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Complex II family of enzymes, comprising respiratory succinate dehydrogenases and fumarate reductases, catalyzes reversible interconversion of succinate and fumarate. In contrast to the covalent flavin adenine dinucleotide (FAD) cofactor assembled in these enzymes, soluble fumarate reductases (e.g., those from Shewanella frigidimarina) that assemble a noncovalent FAD cannot catalyze succinate oxidation but retain the ability to reduce fumarate. In this study, an SdhA-H45A variant that eliminates the site of the 8α-N3-histidyl covalent linkage between the protein and FAD was examined. Variants SdhA-R286A/K/Y and -H242A/Y that target residues thought to be important for substrate binding and catalysis were also studied. The variants SdhA-H45A and -R286A/K/Y resulted in the assembly of a noncovalent FAD cofactor, which led to a significant decrease (-87 mV or more) in its reduction potential. The variant enzymes were studied by electron paramagnetic resonance spectroscopy following stand-alone reduction and potentiometric titrations. The "free" and "occupied" states of the active site were linked to the reduced and oxidized states of FAD, respectively. Our data allow for a proposed model of succinate oxidation that is consistent with tunnel diode effects observed in the succinate dehydrogenase enzyme and a preference for fumarate reduction catalysis in fumarate reductase homologues that assemble a noncovalent FAD.
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Affiliation(s)
- Victor W T Cheng
- Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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13
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Huang S, Millar AH. Sequence diversity and conservation in factors influencing succinate dehydrogenase flavinylation. PLANT SIGNALING & BEHAVIOR 2013; 8:e22815. [PMID: 23154507 PMCID: PMC3656984 DOI: 10.4161/psb.22815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The mitochondrial enzyme succinate dehydrogenase (SDH) consists of four subunits, a flavoprotein (SDH1), an iron-sulfur (Fe-S) protein (SDH2) and two integral membrane subunits (SDH3/SDH4). In mammals and yeast, an assembly factor termed SDHAF2/SDH5 is required for accumulation of flavinylated SDH1. In Arabidopsis, we have recently reported the characterization of an unknown function protein with low sequence similarity to SDHAF2 that is needed for assembly and activity of SDH and also for normal root elongation. (1) In this short communication, we have reviewed the sequence diversity and conservation of SDHAF2 across kingdoms based on phylogenetic analysis. Given that flavinylation of SDH is dependent on the SDH1:SDHAF2 interaction, we have also discussed the conservation of the C-terminal tail of SDH1, which is required for this interaction process. In combination, we provide comparative evidence for a conserved role of SDHAF2 as an assembly factor from animals to plants.
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14
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Han B, Chen X, Zhao J, Bu Y. A peptide loop and an α-helix N-terminal serving as alternative electron hopping relays in proteins. Phys Chem Chem Phys 2012; 14:15849-59. [PMID: 23093308 DOI: 10.1039/c2cp41566f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This work presents a density functional theory calculational study for clarifying that peptide loops (-[peptide](n)-) including the N-terminal and the C-terminal oligopeptides and the α-helix N-terminal can serve as an intriguing kind of relay elements, as an addition to the known relay stations served by aromatic amino acids for electron hopping migration. For these protein motifs, an excess electron generally prefers to reside at the -NH(3)(+) group in a Rydberg state for the N-terminal peptides, or at the -COOH group in a dipole-bound state for the C-terminal peptides, and at the N-terminal in a dipole-bound π*-orbital state for the peptide loops and α-helices. The electron binding ability can be effectively enhanced by elongation for the α-helix N-terminal, and by bending, twisting, and even β-turning for the peptide chains. The relay property is determined by the local dipole instead of the total dipole of the peptide chains. Although no direct experiment supports this hypothesis, a series of recent studies regarding charge hopping migration associated with the peptide chains and helices could be viewed as strong evidence. But, further studies are still needed by considering the effects from relative redox potential between the donor and acceptor sites, protein environment, and structure water molecules.
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Affiliation(s)
- Boran Han
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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Kim HJ, Jeong MY, Na U, Winge DR. Flavinylation and assembly of succinate dehydrogenase are dependent on the C-terminal tail of the flavoprotein subunit. J Biol Chem 2012; 287:40670-9. [PMID: 23043141 DOI: 10.1074/jbc.m112.405704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Succinate dehydrogenase (SDH) requires a covalent addition of FAD for catalytic function. RESULTS Mutational analyses of Sdh1 implicate C-terminal region Arg residues involvement in covalent flavinylation and SDH assembly. CONCLUSION SDH assembly is dependent on FAD binding to Sdh1 but not covalent binding. SIGNIFICANCE These results document the basis for the SDH deficiency and pathology seen with mutations in human Sdh1. The enzymatic function of succinate dehydrogenase (SDH) is dependent on covalent attachment of FAD on the ~70-kDa flavoprotein subunit Sdh1. We show presently that flavinylation of the Sdh1 subunit of succinate dehydrogenase is dependent on a set of two spatially close C-terminal arginine residues that are distant from the FAD binding site. Mutation of Arg(582) in yeast Sdh1 precludes flavinylation as well as assembly of the tetrameric enzyme complex. Mutation of Arg(638) compromises SDH function only when present in combination with a Cys(630) substitution. Mutations of either Arg(582) or Arg(638)/Cys(630) do not markedly destabilize the Sdh1 polypeptide; however, the steady-state level of Sdh5 is markedly attenuated in the Sdh1 mutant cells. With each mutant Sdh1, second-site Sdh1 suppressor mutations were recovered in Sdh1 permitting flavinylation, stabilization of Sdh5 and SDH tetramer assembly. SDH assembly appears to require FAD binding but not necessarily covalent FAD attachment. The Arg residues may be important not only for Sdh5 association but also in the recruitment and/or guidance of FAD and or succinate to the substrate site for the flavinylation reaction. The impaired assembly of SDH with the C-terminal Sdh1 mutants suggests that FAD binding is important to stabilize the Sdh1 conformation enabling association with Sdh2 and the membrane anchor subunits.
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Affiliation(s)
- Hyung J Kim
- Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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Iverson TM. Catalytic mechanisms of complex II enzymes: a structural perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:648-57. [PMID: 22995215 DOI: 10.1016/j.bbabio.2012.09.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 11/25/2022]
Abstract
Over a decade has passed since the elucidation of the first X-ray crystal structure of any complex II homolog. In the intervening time, the structures of five additional integral-membrane complex II enzymes and three homologs of the soluble domain have been determined. These structures have provided a framework for the analysis of enzymological studies of complex II superfamily enzymes, and have contributed to detailed proposals for reaction mechanisms at each of the two enzyme active sites, which catalyze dicarboxylate and quinone oxidoreduction, respectively. This review focuses on how structural data have augmented our understanding of catalysis by the superfamily. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- T M Iverson
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232-6600, USA.
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Iverson TM, Maklashina E, Cecchini G. Structural basis for malfunction in complex II. J Biol Chem 2012; 287:35430-35438. [PMID: 22904323 DOI: 10.1074/jbc.r112.408419] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Complex II couples oxidoreduction of succinate and fumarate at one active site with that of quinol/quinone at a second distinct active site over 40 Å away. This process links the Krebs cycle to oxidative phosphorylation and ATP synthesis. The pathogenic mutation or inhibition of human complex II or its assembly factors is often associated with neurodegeneration or tumor formation in tissues derived from the neural crest. This brief overview of complex II correlates the clinical presentations of a large number of symptom-associated alterations in human complex II activity and assembly with the biochemical manifestations of similar alterations in the complex II homologs from Escherichia coli. These analyses provide clues to the molecular basis for diseases associated with aberrant complex II function.
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Affiliation(s)
- Tina M Iverson
- Department of Pharmacology and Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
| | - Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Gary Cecchini
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158.
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Iverson TM, Panosian TD, Birmingham WR, Nannemann DP, Bachmann BO. Molecular differences between a mutase and a phosphatase: investigations of the activation step in Bacillus cereus phosphopentomutase. Biochemistry 2012; 51:1964-75. [PMID: 22329805 DOI: 10.1021/bi201761h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prokaryotic phosphopentomutases (PPMs) are di-Mn(2+) enzymes that catalyze the interconversion of α-D-ribose 5-phosphate and α-D-ribose 1-phosphate at an active site located between two independently folded domains. These prokaryotic PPMs belong to the alkaline phosphatase superfamily, but previous studies of Bacillus cereus PPM suggested adaptations of the conserved alkaline phosphatase catalytic cycle. Notably, B. cereus PPM engages substrates when the active site nucleophile, Thr-85, is phosphorylated. Further, the phosphoenzyme is stable throughout purification and crystallization. In contrast, alkaline phosphatase engages substrates when the active site nucleophile is dephosphorylated, and the phosphoenzyme reaction intermediate is only stably trapped in a catalytically compromised enzyme. Studies were undertaken to understand the divergence of these mechanisms. Crystallographic and biochemical investigations of the PPM(T85E) phosphomimetic variant and the neutral corollary PPM(T85Q) determined that the side chain of Lys-240 underwent a change in conformation in response to active site charge, which modestly influenced the affinity for the small molecule activator α-D-glucose 1,6-bisphosphate. More strikingly, the structure of unphosphorylated B. cereus PPM revealed a dramatic change in the interdomain angle and a new hydrogen bonding interaction between the side chain of Asp-156 and the active site nucleophile, Thr-85. This hydrogen bonding interaction is predicted to align and activate Thr-85 for nucleophilic addition to α-D-glucose 1,6-bisphosphate, favoring the observed equilibrium phosphorylated state. Indeed, phosphorylation of Thr-85 is severely impaired in the PPM(D156A) variant even under stringent activation conditions. These results permit a proposal for activation of PPM and explain some of the essential features that distinguish between the catalytic cycles of PPM and alkaline phosphatase.
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Affiliation(s)
- T M Iverson
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.
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Li B, Qin Y, Duan H, Yin W, Xia X. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3765-79. [PMID: 21511902 PMCID: PMC3134338 DOI: 10.1093/jxb/err051] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 01/26/2011] [Accepted: 01/31/2011] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. Populus euphratica is a typical abiotic stress-resistant woody species. This study presents an efficient method for genome-wide discovery of new drought stress responsive miRNAs in P. euphratica. High-throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 58 new miRNAs belonging to 38 families were identified, an increase in the number of P. euphratica miRNAs. Twenty-six new and 21 conserved miRNA targets were verified by degradome sequencing, and target annotation showed that these targets were involved in multiple biological processes, including transcriptional regulation and response to stimulus. Furthermore, comparison of high-throughput sequencing with miRNA microarray profiling data indicated that 104 miRNA sequences were up-regulated, whereas 27 were down-regulated under drought stress. This preliminary characterization provides a framework for future analysis of miRNA genes and their roles in key poplar traits such as stress resistance, and could be useful for plant breeding and environmental protection.
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Affiliation(s)
| | | | | | - Weilun Yin
- To whom correspondence should be addressed. E-mail: ;
| | - Xinli Xia
- To whom correspondence should be addressed. E-mail: ;
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Tomasiak TM, Archuleta TL, Andréll J, Luna-Chávez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, Maklashina E, Cecchini G, Iverson TM. Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. J Biol Chem 2010; 286:3047-56. [PMID: 21098488 DOI: 10.1074/jbc.m110.192849] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complex II superfamily members catalyze the kinetically difficult interconversion of succinate and fumarate. Due to the relative simplicity of complex II substrates and their similarity to other biologically abundant small molecules, substrate specificity presents a challenge in this system. In order to identify determinants for on-pathway catalysis, off-pathway catalysis, and enzyme inhibition, crystal structures of Escherichia coli menaquinol:fumarate reductase (QFR), a complex II superfamily member, were determined bound to the substrate, fumarate, and the inhibitors oxaloacetate, glutarate, and 3-nitropropionate. Optical difference spectroscopy and computational modeling support a model where QFR twists the dicarboxylate, activating it for catalysis. Orientation of the C2-C3 double bond of activated fumarate parallel to the C(4a)-N5 bond of FAD allows orbital overlap between the substrate and the cofactor, priming the substrate for nucleophilic attack. Off-pathway catalysis, such as the conversion of malate to oxaloacetate or the activation of the toxin 3-nitropropionate may occur when inhibitors bind with a similarly activated bond in the same position. Conversely, inhibitors that do not orient an activatable bond in this manner, such as glutarate and citrate, are excluded from catalysis and act as inhibitors of substrate binding. These results support a model where electronic interactions via geometric constraint and orbital steering underlie catalysis by QFR.
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Affiliation(s)
- Thomas M Tomasiak
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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On the catalytic role of the active site residue E121 of E. coli l-aspartate oxidase. Biochimie 2010; 92:1335-42. [DOI: 10.1016/j.biochi.2010.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 06/16/2010] [Indexed: 11/18/2022]
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Rutter J, Winge DR, Schiffman JD. Succinate dehydrogenase - Assembly, regulation and role in human disease. Mitochondrion 2010; 10:393-401. [PMID: 20226277 PMCID: PMC2874626 DOI: 10.1016/j.mito.2010.03.001] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2010] [Indexed: 12/18/2022]
Abstract
Succinate dehydrogenase (or Electron Transport Chain Complex II) has been the subject of a focused but significant renaissance. This complex, which has been the least studied of the mitochondrial respiratory complexes has seen renewed interest due to the discovery of its role in human disease. Under this heightened scrutiny, the succinate dehydrogenase complex has proven to be a fascinating machine, whose regulation and assembly requires additional factors that are beginning to be discovered. Mutations in these factors and in the structural subunits of the complex itself cause a variety of human diseases. The mechanisms underlying the pathogenesis of SDH mutations is beginning to be understood.
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Affiliation(s)
- Jared Rutter
- Departments of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States.
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