1
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX,USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX,USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX,USA
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2
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Neti SS, Sil D, Warui DM, Esakova OA, Solinski AE, Serrano DA, Krebs C, Booker SJ. Characterization of LipS1 and LipS2 from Thermococcus kodakarensis: Proteins Annotated as Biotin Synthases, which Together Catalyze Formation of the Lipoyl Cofactor. ACS BIO & MED CHEM AU 2022; 2:509-520. [PMID: 36281299 PMCID: PMC9585515 DOI: 10.1021/acsbiomedchemau.2c00018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022]
Abstract
Lipoic acid is an eight-carbon sulfur-containing biomolecule that functions primarily as a cofactor in several multienzyme complexes. It is biosynthesized as an attachment to a specific lysyl residue on one of the subunits of these multienzyme complexes. In Escherichia coli and many other organisms, this biosynthetic pathway involves two dedicated proteins: octanoyltransferase (LipB) and lipoyl synthase (LipA). LipB transfers an n-octanoyl chain from the octanoyl-acyl carrier protein to the target lysyl residue, and then, LipA attaches two sulfur atoms (one at C6 and one at C8) to give the final lipoyl cofactor. All classical lipoyl synthases (LSs) are radical S-adenosylmethionine (SAM) enzymes, which use an [Fe4S4] cluster to reductively cleave SAM to generate a 5'-deoxyadenosyl 5'-radical. Classical LSs also contain a second [Fe4S4] cluster that serves as the source of both appended sulfur atoms. Recently, a novel pathway for generating the lipoyl cofactor was reported. This pathway replaces the canonical LS with two proteins, LipS1 and LipS2, which act together to catalyze formation of the lipoyl cofactor. In this work, we further characterize LipS1 and LipS2 biochemically and spectroscopically. Although LipS1 and LipS2 were previously annotated as biotin synthases, we show that both proteins, unlike E. coli biotin synthase, contain two [Fe4S4] clusters. We identify the cluster ligands to both iron-sulfur clusters in both proteins and show that LipS2 acts only on an octanoyl-containing substrate, while LipS1 acts only on an 8-mercaptooctanoyl-containing substrate. Therefore, similarly to E. coli biotin synthase and in contrast to E. coli LipA, sulfur attachment takes place initially at the terminal carbon (C8) and then at the C6 methylene carbon.
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Affiliation(s)
- Syam Sundar Neti
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Douglas M. Warui
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Olga A. Esakova
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amy E. Solinski
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dante A. Serrano
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Squire J. Booker
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Howard
Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
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3
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Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Postbiosynthetic modification of a precursor to the nitrogenase iron-molybdenum cofactor. Proc Natl Acad Sci U S A 2021; 118:2015361118. [PMID: 33836573 DOI: 10.1073/pnas.2015361118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenases utilize Fe-S clusters to reduce N2 to NH3 The large number of Fe sites in their catalytic cofactors has hampered spectroscopic investigations into their electronic structures, mechanisms, and biosyntheses. To facilitate their spectroscopic analysis, we are developing methods for incorporating 57Fe into specific sites of nitrogenase cofactors, and we report herein site-selective 57Fe labeling of the L-cluster-a carbide-containing, [Fe8S9C] precursor to the Mo nitrogenase catalytic cofactor. Treatment of the isolated L-cluster with the chelator ethylenediaminetetraacetate followed by reconstitution with 57Fe2+ results in 57Fe labeling of the terminal Fe sites in high yield and with high selectivity. This protocol enables the generation of L-cluster samples in which either the two terminal or the six belt Fe sites are selectively labeled with 57Fe. Mössbauer spectroscopic analysis of these samples bound to the nitrogenase maturase Azotobacter vinelandii NifX reveals differences in the primary coordination sphere of the terminal Fe sites and that one of the terminal sites of the L-cluster binds to H35 of Av NifX. This work provides molecular-level insights into the electronic structure and biosynthesis of the L-cluster and introduces postbiosynthetic modification as a promising strategy for studies of nitrogenase cofactors.
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Palmieri EM, McGinity C, Wink DA, McVicar DW. Nitric Oxide in Macrophage Immunometabolism: Hiding in Plain Sight. Metabolites 2020; 10:metabo10110429. [PMID: 33114647 PMCID: PMC7693038 DOI: 10.3390/metabo10110429] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Nitric Oxide (NO) is a soluble endogenous gas with various biological functions like signaling, and working as an effector molecule or metabolic regulator. In response to inflammatory signals, immune myeloid cells, like macrophages, increase production of cytokines and NO, which is important for pathogen killing. Under these proinflammatory circumstances, called “M1”, macrophages undergo a series of metabolic changes including rewiring of their tricarboxylic acid (TCA) cycle. Here, we review findings indicating that NO, through its interaction with heme and non-heme metal containing proteins, together with components of the electron transport chain, functions not only as a regulator of cell respiration, but also a modulator of intracellular cell metabolism. Moreover, diverse effects of NO and NO-derived reactive nitrogen species (RNS) involve precise interactions with different targets depending on concentration, temporal, and spatial restrictions. Although the role of NO in macrophage reprogramming has been in evidence for some time, current models have largely minimized its importance. It has, therefore, been hiding in plain sight. A review of the chemical properties of NO, past biochemical studies, and recent publications, necessitates that mechanisms of macrophage TCA reprogramming during stimulation must be re-imagined and re-interpreted as mechanistic results of NO exposure. The revised model of metabolic rewiring we describe here incorporates many early findings regarding NO biochemistry and brings NO out of hiding and to the forefront of macrophages immunometabolism.
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Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe–4S] clusters. J Biol Inorg Chem 2019; 24:793-807. [DOI: 10.1007/s00775-019-01708-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
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7
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Wang B, Blaszczyk A, Knox HL, Zhou S, Blaesi EJ, Krebs C, Wang RX, Booker SJ. Stereochemical and Mechanistic Investigation of the Reaction Catalyzed by Fom3 from Streptomyces fradiae, a Cobalamin-Dependent Radical S-Adenosylmethionine Methylase. Biochemistry 2018; 57:4972-4984. [PMID: 30036047 PMCID: PMC6554712 DOI: 10.1021/acs.biochem.8b00693] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fom3, a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase, has recently been shown to catalyze the methylation of carbon 2″ of cytidylyl-2-hydroxyethylphosphonate (HEP-CMP) to form cytidylyl-2-hydroxypropylphosphonate (HPP-CMP) during the biosynthesis of fosfomycin, a broad-spectrum antibiotic. It has been hypothesized that a 5'-deoxyadenosyl 5'-radical (5'-dA•) generated from the reductive cleavage of SAM abstracts a hydrogen atom from HEP-CMP to prime the substrate for addition of a methyl group from methylcobalamin (MeCbl); however, the mechanistic details of this reaction remain elusive. Moreover, it has been reported that Fom3 catalyzes the methylation of HEP-CMP to give a mixture of the ( S)-HPP and ( R)-HPP stereoisomers, which is rare for an enzyme-catalyzed reaction. Herein, we describe a detailed biochemical investigation of a Fom3 that is purified with 1 equiv of its cobalamin cofactor bound, which is almost exclusively in the form of MeCbl. Electron paramagnetic resonance and Mössbauer spectroscopies confirm that Fom3 contains one [4Fe-4S] cluster. Using deuterated enantiomers of HEP-CMP, we demonstrate that the 5'-dA• generated by Fom3 abstracts the C2″- pro-R hydrogen of HEP-CMP and that methyl addition takes place with inversion of configuration to yield solely ( S)-HPP-CMP. Fom3 also sluggishly converts cytidylyl-ethylphosphonate to the corresponding methylated product but more readily acts on cytidylyl-2-fluoroethylphosphonate, which exhibits a lower C2″ homolytic bond-dissociation energy. Our studies suggest a mechanism in which the substrate C2″ radical, generated upon hydrogen atom abstraction by the 5'-dA•, directly attacks MeCbl to transfer a methyl radical (CH3•) rather than a methyl cation (CH3+), directly forming cob(II)alamin in the process.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Anthony Blaszczyk
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hayley L. Knox
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shengbin Zhou
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth J. Blaesi
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Roy X. Wang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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8
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Tabrizi SG, Pelmenschikov V, Noodleman L, Kaupp M. The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study. J Chem Theory Comput 2015; 12:174-87. [PMID: 26598030 PMCID: PMC4819768 DOI: 10.1021/acs.jctc.5b00854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An unprecedented [4Fe-3S] cluster
proximal to the regular [NiFe]
active site has recently been found to be responsible for the ability
of membrane-bound hydrogenases (MBHs) to oxidize dihydrogen in the
presence of ambient levels of oxygen. Starting from proximal cluster
models of a recent DFT study on the redox-dependent structural transformation
of the [4Fe-3S] cluster, 57Fe Mössbauer parameters
(electric field gradients, isomer shifts, and nuclear hyperfine couplings)
were calculated using DFT. Our results revise the previously reported
correspondence of Mössbauer signals and iron centers in the
[4Fe-3S]3+ reduced-state proximal cluster. Similar conflicting
assignments are also resolved for the [4Fe-3S]5+ superoxidized
state with particular regard to spin-coupling in the broken-symmetry
DFT calculations. Calculated 57Fe hyperfine coupling (HFC)
tensors expose discrepancies in the experimental set of HFC tensors
and substantiate the need for additional experimental work on the
magnetic properties of the MBH proximal cluster in its reduced and
superoxidized redox states.
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Affiliation(s)
- Shadan Ghassemi Tabrizi
- Technical University of Berlin , Institute for Chemistry and Theoretical Chemistry, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Vladimir Pelmenschikov
- Technical University of Berlin , Institute for Chemistry and Theoretical Chemistry, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, CB213, La Jolla, California 92037, United States
| | - Martin Kaupp
- Technical University of Berlin , Institute for Chemistry and Theoretical Chemistry, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
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9
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Cook SA, Hill EA, Borovik AS. Lessons from Nature: A Bio-Inspired Approach to Molecular Design. Biochemistry 2015; 54:4167-80. [PMID: 26079379 DOI: 10.1021/acs.biochem.5b00249] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins contain actives sites with intricate structures that perform specific functions with high selectivity and efficiency. The complexity of these systems complicates the study of their function and the understanding of the properties that give rise to their reactivity. One approach that has contributed to the current level of understanding of their biological function is the study of synthetic constructs that mimic one or more aspects of the native metalloproteins. These systems allow individual contributions to the structure and function to be analyzed and also permit spectroscopic characterization of the metal cofactors without complications from the protein environment. This Current Topic is a review of synthetic constructs as probes for understanding the biological activation of small molecules. These topics are developed from the perspective of seminal molecular design breakthroughs from the past that provide the foundation for the systems used today.
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Affiliation(s)
- Sarah A Cook
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Ethan A Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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10
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Oyala PH, Stich TA, Britt RD. Metal ion oxidation state assignment based on coordinating ligand hyperfine interaction. PHOTOSYNTHESIS RESEARCH 2015; 124:7-18. [PMID: 25663565 DOI: 10.1007/s11120-015-0086-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
In exchange-coupled mixed-valence spin systems, the magnitude and sign of the effective ligand hyperfine interaction (HFI) can be useful in determining the formal oxidation state of the coordinating metal ion, as well as provide information about the coordination geometry. This is due to the fact that the observed ligand HFI is a function of the projection factor (Clebsch-Gordon coefficient) that maps the site spin value S i of the local paramagnetic center onto the total spin of the exchange-coupled system, S T. Recently, this relationship has been successfully exploited in identifying the oxidation state of the Mn ion coordinated by the sole nitrogenous ligand to the oxygen-evolving complex in certain states of photosystem II. The origin and evolution of these efforts is described.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
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11
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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12
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Advanced electron paramagnetic resonance on the catalytic iron–sulfur cluster bound to the CCG domain of heterodisulfide reductase and succinate: quinone reductase. J Biol Inorg Chem 2013; 18:905-15. [DOI: 10.1007/s00775-013-1037-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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14
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Esrafili MD, Rezaei S, Eftekhari E. A theoretical investigation on geometry and electronic structure of small FemSn nanoclusters (1⩽m,n⩽4). COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.09.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Chan A, Clémancey M, Mouesca JM, Amara P, Hamelin O, Latour JM, Ollagnier de Choudens S. Studies of Inhibitor Binding to the [4Fe-4S] Cluster of Quinolinate Synthase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Chan A, Clémancey M, Mouesca JM, Amara P, Hamelin O, Latour JM, Ollagnier de Choudens S. Studies of Inhibitor Binding to the [4Fe-4S] Cluster of Quinolinate Synthase. Angew Chem Int Ed Engl 2012; 51:7711-4. [DOI: 10.1002/anie.201202261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Indexed: 11/08/2022]
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17
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Hoppe A, Pandelia ME, Gärtner W, Lubitz W. [Fe4S4]- and [Fe3S4]-cluster formation in synthetic peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1414-22. [DOI: 10.1016/j.bbabio.2011.06.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/24/2011] [Accepted: 06/27/2011] [Indexed: 12/31/2022]
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18
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Vidal DTR, Augelli MA, Hotta GM, Lopes FS, do Lago CL. Determination of fluoroacetate and fluoride in blood serum by capillary zone electrophoresis using capacitively coupled contactless conductivity detection. Electrophoresis 2011; 32:896-9. [DOI: 10.1002/elps.201000475] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 11/11/2022]
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19
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Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MCY. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry 2010; 49:9269-79. [PMID: 20836570 PMCID: PMC3461317 DOI: 10.1021/bi101102u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-CoA (k(cat)/K(M) = 5 × 10⁷ M⁻¹ s⁻¹) and acetyl-CoA (k(cat)/K(M) = 30 M⁻¹ s⁻¹) based on a single fluorine substitution that originates from differences in both substrate reactivity and binding. We show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that influence substrate selectivity. We propose that FlK minimizes interaction with the thioester carbonyl, leading to selection against acetyl-CoA binding that can be recovered in part by new C═O interactions in the T42S and T42C mutants. We hypothesize that the loss of these interactions is compensated by the entropic driving force for fluorinated substrate binding in a hydrophobic binding pocket created by a lid structure, containing Val 23, Leu 26, Phe 33, and Phe 36, that is not found in other structurally characterized members of this superfamily. We further suggest that water plays a critical role in fluorine specificity based on biochemical and structural studies focused on the unique Phe 36 "gate" residue, which functions to exclude water from the active site. Taken together, the findings from these studies offer molecular insights into organofluorine recognition and design of fluorine-specific enzymes.
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Affiliation(s)
- Amy M. Weeks
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
| | - Scott M. Coyle
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Martin Jinek
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
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Hsieh YC, Liu MY, Wang VCC, Chiang YL, Liu EH, Wu WG, Chan SI, Chen CJ. Structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulphite reductase from Desulfovibrio gigas. Mol Microbiol 2010; 78:1101-16. [DOI: 10.1111/j.1365-2958.2010.07390.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Krebs C, Bollinger JM. Freeze-quench (57)Fe-Mössbauer spectroscopy: trapping reactive intermediates. PHOTOSYNTHESIS RESEARCH 2009; 102:295-304. [PMID: 19238577 DOI: 10.1007/s11120-009-9406-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 01/15/2009] [Indexed: 05/24/2023]
Abstract
(57)Fe-Mössbauer spectroscopy is a method that probes transitions between the nuclear ground state (I=1/2) and the first nuclear excited state (I=3/2). This technique provides detailed information about the chemical environment and electronic structure of iron. Therefore, it has played an important role in studies of the numerous iron-containing proteins and enzymes. In conjunction with the freeze-quench method, (57)Fe-Mössbauer spectroscopy allows for monitoring changes of the iron site(s) during a biochemical reaction. This approach is particularly powerful for detection and characterization of reactive intermediates. Comparison of experimentally determined Mössbauer parameters to those predicted by density functional theory for hypothetical model structures can then provide detailed insight into the structures of reactive intermediates. We have recently used this methodology to study the reactions of various mononuclear non-heme-iron enzymes by trapping and characterizing several Fe(IV)-oxo reaction intermediates. In this article, we summarize these findings and demonstrate the potential of the method.
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Affiliation(s)
- Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, 332 Chemistry Building, Pennsylvania, PA 16802, USA.
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22
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Seemann M, Janthawornpong K, Schweizer J, Böttger LH, Janoschka A, Ahrens-Botzong A, Tambou EN, Rotthaus O, Trautwein AX, Rohmer M. Isoprenoid Biosynthesis via the MEP Pathway: In Vivo Mössbauer Spectroscopy Identifies a [4Fe-4S]2+ Center with Unusual Coordination Sphere in the LytB Protein. J Am Chem Soc 2009; 131:13184-5. [DOI: 10.1021/ja9012408] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Myriam Seemann
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Karnjapan Janthawornpong
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Julia Schweizer
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Lars H. Böttger
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Adam Janoschka
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Anne Ahrens-Botzong
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Erasmienne Ngouamegne Tambou
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Olaf Rotthaus
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Alfred X. Trautwein
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Michel Rohmer
- Université de Strasbourg, Institut de Chimie, UMR CNRS UDS 7177, 4 rue Blaise Pascal, 67070 Strasbourg, France, Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, D-67653 Kaiserslautern, Germany, and Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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Saunders AH, Griffiths AE, Lee KH, Cicchillo RM, Tu L, Stromberg JA, Krebs C, Booker SJ. Characterization of quinolinate synthases from Escherichia coli, Mycobacterium tuberculosis, and Pyrococcus horikoshii indicates that [4Fe-4S] clusters are common cofactors throughout this class of enzymes. Biochemistry 2008; 47:10999-1012. [PMID: 18803397 DOI: 10.1021/bi801268f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quinolinate synthase (NadA) catalyzes a unique condensation reaction between iminoaspartate and dihydroxyacetone phosphate, affording quinolinic acid, a central intermediate in the biosynthesis of nicotinamide adenine dinucleotide (NAD). Iminoaspartate is generated via the action of l-aspartate oxidase (NadB), which catalyzes the first step in the biosynthesis of NAD in most prokaryotes. NadA from Escherichia coli was hypothesized to contain an iron-sulfur cluster as early as 1991, because of its observed labile activity, especially in the presence of hyperbaric oxygen, and because its primary structure contained a CXXCXXC motif, which is commonly found in the [4Fe-4S] ferredoxin class of iron-sulfur (Fe/S) proteins. Indeed, using analytical methods in concert with Mossbauer and electron paramagnetic resonance spectroscopies, the protein was later shown to harbor a [4Fe-4S] cluster. Recently, the X-ray structure of NadA from Pyrococcus horikoshii was solved to 2.0 A resolution [Sakuraba, H., Tsuge, H.,Yoneda, K., Katunuma, N., and Ohshima, T. (2005) J. Biol. Chem. 280, 26645-26648]. This protein does not contain a CXXCXXC motif, and no Fe/S cluster was observed in the structure or even mentioned in the report. Moreover, rates of quinolinic acid production were reported to be 2.2 micromol min (-1) mg (-1), significantly greater than that of E. coli NadA containing an Fe/S cluster (0.10 micromol min (-1) mg (-1)), suggesting that the [4Fe-4S] cluster of E. coli NadA may not be necessary for catalysis. In the study described herein, nadA genes from both Mycobacterium tuberculosis and Pyrococcus horikoshii were cloned, and their protein products shown to contain [4Fe-4S] clusters that are absolutely required for activity despite the absence of a CXXCXXC motif in their primary structures. Moreover, E. coli NadA, which contains nine cysteine residues, is shown to require only three for turnover (C113, C200, and C297), of which only C297 resides in the CXXCXXC motif. These results are consistent with a bioinformatics analysis of NadA sequences, which indicates that three cysteines are strictly conserved across all species. This study concludes that all currently annotated quinolinate synthases harbor a [4Fe-4S] cluster, that the crystal structure reported by Sakuraba et al. does not accurately represent the active site of the protein, and that the "activity" reported does not correspond to quinolinate formation.
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Affiliation(s)
- Allison H Saunders
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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24
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Crooks DR, Ghosh MC, Braun-Sommargren M, Rouault TA, Smith DR. Manganese targets m-aconitase and activates iron regulatory protein 2 in AF5 GABAergic cells. J Neurosci Res 2007; 85:1797-809. [PMID: 17469137 DOI: 10.1002/jnr.21321] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Studies suggest that disturbances of amino acid metabolism and cellular iron regulation are important mechanisms underlying manganese (Mn) neurotoxicity, although the targets underlying these disturbances are poorly defined. Using the AF5 neural-derived cell line, which displays GABAergic properties, we showed that Mn significantly increased glutamate release to 174%-214% of that of the control and that the effects of Mn exposure on the metabolism of glutamate, glutamine, alanine, and GABA resembled the effects of fluorocitrate, an inhibitor of aconitase, but not the effects of other toxicants including paraquat, rotenone, or 3-nitropropionic acid. Consistent with this, Mn inhibited aconitase activity in AF5 cells, resulting in a 90% increase in intracellular citrate; an in vitro assay revealed that m-aconitase was significantly more sensitive to inhibition by Mn than was c-aconitase. RNA mobility shift assay and Western blot showed that Mn treatment caused c-aconitase to be converted to iron regulatory protein 1 (IRP1) and increased the abundance of IRP2, leading to reduced H-ferritin expression, increased transferrin receptor expression, and increased uptake of transferrin. To determine the relative contributions of IRP1 and IRP2 in mediating the effects of Mn on iron homeostasis, we exposed transgenic fibroblasts lacking either c-aconitase/IRP1 or IRP2 to Mn. Manganese exposure minimally altered ferritin levels in cells possessing only c-aconitase/IRP1, whereas cells possessing only IRP2 showed a robust decrease in ferritin, indicating a dominant role of IRP2 in Mn-induced alteration of iron homeostasis. Together, these results demonstrate that m-aconitase is an important target of Mn and thatMn-induced alteration of iron homeostasis is mediated predominantly through IRP2.
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Affiliation(s)
- Daniel R Crooks
- Department of Environmental Toxicology, University of California, Santa Cruz, California 95064, USA
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25
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26
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Goncharov NV, Jenkins RO, Radilov AS. Toxicology of fluoroacetate: a review, with possible directions for therapy research. J Appl Toxicol 2006; 26:148-61. [PMID: 16252258 DOI: 10.1002/jat.1118] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fluoroacetate (FA; CH2FCOOR) is highly toxic towards humans and other mammals through inhibition of the enzyme aconitase in the tricarboxylic acid cycle, caused by 'lethal synthesis' of an isomer of fluorocitrate (FC). FA is found in a range of plant species and their ingestion can cause the death of ruminant animals. Some fluorinated compounds -- used as anticancer agents, narcotic analgesics, pesticides or industrial chemicals -- metabolize to FA as intermediate products. The chemical characteristics of FA and the clinical signs of intoxication warrant the re-evaluation of the toxic danger of FA and renewed efforts in the search for effective therapeutic means. Antidotal therapy for FA intoxication has been aimed at preventing fluorocitrate synthesis and aconitase blockade in mitochondria, and at providing citrate outflow from this organelle. Despite a greatly improved understanding of the biochemical mechanism of FA toxicity, ethanol, if taken immediately after the poisoning, has been the most acceptable antidote for the past six decades. This review deals with the clinical signs and physiological and biochemical mechanisms of FA intoxication to provide an explanation of why, even after decades of investigation, has no effective therapy to FA intoxication been elaborated. An apparent lack of integrated toxicological studies is viewed as a limiter of progress in this regard. Two principal ways of developing effective therapies for FA intoxication are considered. Firstly, competitive inhibition of FA interaction with CoA and of FC interaction with aconitase. Secondly, channeling the alternative metabolic pathways by orienting the fate of citrate via cytosolic aconitase, and by maintaining the flux of reducing equivalents into the TCA cycle via glutamate dehydrogenase.
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Affiliation(s)
- Nikolay V Goncharov
- Research Institute of Hygiene, Occupational Pathology and Human Ecology, Saint-Petersburg, Russia
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27
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Cicchillo RM, Baker MA, Schnitzer EJ, Newman EB, Krebs C, Booker SJ. Escherichia coli L-Serine Deaminase Requires a [4Fe-4S] Cluster in Catalysis. J Biol Chem 2004; 279:32418-25. [PMID: 15155761 DOI: 10.1074/jbc.m404381200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
L-Serine deaminases catalyze the deamination of L-serine, producing pyruvate and ammonia. Two families of these proteins have been described and are delineated by the cofactor that each employs in catalysis. These are the pyridoxal 5'-phosphate-dependent deaminases and the deaminases that are activated in vitro by iron and dithiothreitol. In contrast to the enzymes that employ pyridoxal 5'-phosphate, detailed physical and mechanistic characterization of the iron-dependent deaminases is limited, primarily because of their extreme instability. We report here the characterization of L-serine deaminase from Escherichia coli, which is the product of the sdaA gene. When purified anaerobically, the isolated protein contains 1.86 +/- 0.46 eq of iron and 0.670 +/- 0.019 eq of sulfide per polypeptide and displays a UV-visible spectrum that is consistent with a [4Fe-4S] cluster. Reconstitution of the protein with iron and sulfide generates considerably more of the cluster, and treatment of the reconstituted protein with dithionite gives rise to an axial EPR spectrum, displaying g axially = 2.03 and g radially = 1.93. Mössbauer spectra of the (57)Fe-reconstituted protein reveal that the majority of the iron is in the form of [4Fe-4S](2+) clusters, as evidenced by the typical Mössbauer parameters-isomer shift, delta = 0.47 mm/s, quadrupole splitting of Delta E(Q) = 1.14 mm/s, and a diamagnetic (S = 0) ground state. Treatment of the dithionite-reduced protein with L-serine results in a slight broadening of the feature at g = 2.03 in the EPR spectrum of the protein, and a dramatic loss in signal intensity, suggesting that the amino acid interacts directly with the cluster.
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Affiliation(s)
- Robert M Cicchillo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, 16802, USA
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28
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Venkateswara Rao P, Holm RH. Synthetic Analogues of the Active Sites of Iron−Sulfur Proteins. Chem Rev 2004; 104:527-59. [PMID: 14871134 DOI: 10.1021/cr020615+] [Citation(s) in RCA: 412] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P Venkateswara Rao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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29
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Frey PA, Magnusson OT. S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin? Chem Rev 2003; 103:2129-48. [PMID: 12797826 DOI: 10.1021/cr020422m] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin--Madison, Madison, Wisconsin 53726, USA.
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30
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Chaudhuri TK, Farr GW, Fenton WA, Rospert S, Horwich AL. GroEL/GroES-mediated folding of a protein too large to be encapsulated. Cell 2001; 107:235-46. [PMID: 11672530 DOI: 10.1016/s0092-8674(01)00523-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The chaperonin GroEL binds nonnative proteins too large to fit inside the productive GroEL-GroES cis cavity, but whether and how it assists their folding has remained unanswered. We have examined yeast mitochondrial aconitase, an 82 kDa monomeric Fe(4)S(4) cluster-containing enzyme, observed to aggregate in chaperonin-deficient mitochondria. We observed that aconitase folding both in vivo and in vitro requires both GroEL and GroES, and proceeds via multiple rounds of binding and release. Unlike the folding of smaller substrates, however, this mechanism does not involve cis encapsulation but, rather, requires GroES binding to the trans ring to release nonnative substrate, which likely folds in solution. Following the phase of ATP/GroES-dependent refolding, GroEL stably bound apoaconitase, releasing active holoenzyme upon Fe(4)S(4) cofactor formation, independent of ATP and GroES.
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Affiliation(s)
- T K Chaudhuri
- Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, Boyer Center, New Haven, CT 06510, USA
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31
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Metzler DE, Metzler CM, Sauke DJ. Transition Metals in Catalysis and Electron Transport. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Metzler DE, Metzler CM, Sauke DJ. Enzymatic Addition, Elimination, Condensation, and Isomerization. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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Jung YS, Bonagura CA, Tilley GJ, Gao-Sheridan HS, Armstrong FA, Stout CD, Burgess BK. Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster. J Biol Chem 2000; 275:36974-83. [PMID: 10961993 DOI: 10.1074/jbc.m004947200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All naturally occurring ferredoxins that have Cys-X-X-Asp-X-X-Cys motifs contain [4Fe-4S](2+/+) clusters that can be easily and reversibly converted to [3Fe-4S](+/0) clusters. In contrast, ferredoxins with unmodified Cys-X-X-Cys-X-X-Cys motifs assemble [4Fe-4S](2+/+) clusters that cannot be easily interconverted with [3Fe-4S](+/0) clusters. In this study we changed the central cysteine of the Cys(39)-X-X-Cys(42)-X-X-Cys(45) of Azotobacter vinelandii FdI, which coordinates its [4Fe-4S](2+/+) cluster, into an aspartate. UV-visible, EPR, and CD spectroscopies, metal analysis, and x-ray crystallography show that, like native FdI, aerobically purified C42D FdI is a seven-iron protein retaining its [4Fe-4S](2+/+) cluster with monodentate aspartate ligation to one iron. Unlike known clusters of this type the reduced [4Fe-4S](+) cluster of C42D FdI exhibits only an S = 1/2 EPR with no higher spin signals detected. The cluster shows only a minor change in reduction potential relative to the native protein. All attempts to convert the cluster to a 3Fe cluster using conventional methods of oxygen or ferricyanide oxidation or thiol exchange were not successful. The cluster conversion was ultimately accomplished using a new electrochemical method. Hydrophobic and electrostatic interaction and the lack of Gly residues adjacent to the Asp ligand explain the remarkable stability of this cluster.
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Affiliation(s)
- Y S Jung
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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34
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Lloyd SJ, Lauble H, Prasad GS, Stout CD. The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex. Protein Sci 1999; 8:2655-62. [PMID: 10631981 PMCID: PMC2144235 DOI: 10.1110/ps.8.12.2655] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal structure of the S642A mutant with isocitrate binding provides a control, showing that the Ser --> Ala replacement does not alter the binding of substrates in the active site. The aconitase mechanism requires that the intermediate product, cis-aconitate, flip over by 180 degrees about the C alpha-C beta double bond. Only one of these two alternative modes of binding, that of the isocitrate mode, has been previously visualized. Now, however, the structure revealing the citrate mode of binding provides direct support for the proposed enzyme mechanism.
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Affiliation(s)
- S J Lloyd
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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35
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Hans M, Sievers J, Müller U, Bill E, Vorholt JA, Linder D, Buckel W. 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:404-14. [PMID: 10491198 DOI: 10.1046/j.1432-1327.1999.00748.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Component D (HgdAB) of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum was purified to homogeneity. It is able to use component A from Acidaminococcus fermentans (HgdC) to initiate catalysis together with ATP, Mg2+ and a strong reducing agent such as Ti(III)citrate. Component D from C. symbiosum has a 6 x higher specific activity compared with that from A. fermentans and contains a second [4Fe-4S] cluster but the same amount of riboflavin 5'-phosphate (1.0 per heterodimeric enzyme, m = 100 kDa). Mössbauer spectroscopy revealed symmetric cube-type structures of the two [4Fe-4S]2+ clusters. EPR spectroscopy showed the resistance of the clusters to reducing agents, but detected a sharp signal at g = 2. 004 probably due to a stabilized flavin semiquinone. Three genes from C. symbiosum coding for components D (hgdA and hgdB) and A (hgdC) were cloned and sequenced. Primer extension experiments indicated that the genes are transcribed in the order hgdCAB from an operon only half the size of that from A. fermentans. Sequence comparisons detected a close relationship to the dehydratase system from A. fermentans and HgdA from Fusobacterium nucleatum, as well as to putative proteins of unknown function from Archaeoglobus fulgidus. Lower, but significant, identities were found with putative enzymes from several methanogenic Archaea and Escherichia coli, as well as with the mechanistically related benzoyl-CoA reductases from the Proteobacteria Rhodopseudomonas palustris and Thauera aromatica.
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Affiliation(s)
- M Hans
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
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36
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37
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Gao-Sheridan HS, Kemper MA, Khayat R, Tilley GJ, Armstrong FA, Sridhar V, Prasad GS, Stout CD, Burgess BK. A T14C variant of Azotobacter vinelandii ferredoxin I undergoes facile [3Fe-4S]0 to [4Fe-4S]2+ conversion in vitro but not in vivo. J Biol Chem 1998; 273:33692-701. [PMID: 9837955 DOI: 10.1074/jbc.273.50.33692] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
[4Fe-4S]2+/+ clusters that are ligated by Cys-X-X-Cys-X-X-Cys sequence motifs share the general feature of being hard to convert to [3Fe-4S]+/0 clusters, whereas those that contain a Cys-X-X-Asp-X-X-Cys motif undergo facile and reversible cluster interconversion. Little is known about the factors that control the in vivo assembly and conversion of these clusters. In this study we have designed and constructed a 3Fe to 4Fe cluster conversion variant of Azotobacter vinelandii ferredoxin I (FdI) in which the sequence that ligates the [3Fe-4S] cluster in native FdI was altered by converting a nearby residue, Thr-14, to Cys. Spectroscopic and electrochemical characterization shows that when purified in the presence of dithionite, T14C FdI is an O2-sensitive 8Fe protein. Both the new and the indigenous clusters have reduction potentials that are significantly shifted compared with those in native FdI, strongly suggesting a significantly altered environment around the clusters. Interestingly, whole cell EPR have revealed that T14C FdI exists as a 7Fe protein in vivo. This 7Fe form of T14C FdI is extremely similar to native FdI in its spectroscopic, electrochemical, and structural features. However, unlike native FdI which does not undergo facile cluster conversion, the 7Fe form T14C FdI quickly converts to the 8Fe form with a high efficiency under reducing conditions.
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Affiliation(s)
- H S Gao-Sheridan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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38
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Abstract
Iron-sulfur proteins are found in all life forms. Most frequently, they contain Fe2S2, Fe3S4, and Fe4S4 clusters. These modular clusters undergo oxidation-reduction reactions, may be inserted or removed from proteins, can influence protein structure by preferential side chain ligation, and can be interconverted. In addition to their electron transfer function, iron-sulfur clusters act as catalytic centers and sensors of iron and oxygen. Their most common oxidation states are paramagnetic and present significant challenges for understanding the magnetic properties of mixed valence systems. Iron-sulfur clusters now rank with such biological prosthetic groups as hemes and flavins in pervasive occurrence and multiplicity of function.
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Affiliation(s)
- H Beinert
- Institute for Enzyme Research and the Department of Biochemistry, University of Wisconsin, Madison, WI 53705, USA
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Lauble H, Kennedy MC, Emptage MH, Beinert H, Stout CD. The reaction of fluorocitrate with aconitase and the crystal structure of the enzyme-inhibitor complex. Proc Natl Acad Sci U S A 1996; 93:13699-703. [PMID: 8942997 PMCID: PMC19395 DOI: 10.1073/pnas.93.24.13699] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/1996] [Indexed: 02/03/2023] Open
Abstract
It has been known for many years that fluoroacetate and fluorocitrate when metabolized are highly toxic, and that at least one effect of fluorocitrate is to inactivate aconitase. In this paper we present evidence supporting the hypothesis that the (-)-erythro diastereomer of 2-fluorocitrate acts as a mechanism based inhibitor of aconitase by first being converted to fluoro-cis-aconitate, followed by addition of hydroxide and with loss of fluoride to form 4-hydroxy-trans-aconitate (HTn), which binds very tightly, but not covalently, to the enzyme. Formation of HTn by these reactions is in accord with the working model for the enzyme mechanism. That HTn is the product of fluorocitrate inhibition is supported by the crystal structure of the enzyme-inhibitor complex at 2.05-A resolution, release of fluoride stoichiometric with total enzyme when (-)-erythro-2-fluorocitrate is added, HPLC analysis of the product, slow displacement of HTn by 10(6)-fold excess of isocitrate, and previously published Mössbauer experiments. When (+)-erythro-2-fluorocitrate is added to aconitase, the release of fluoride is stoichiometric with total substrate added, and HPLC analysis of the products indicates the formation of oxalosuccinate, and its derivative alpha-ketoglutarate. This is consistent with the proposed mechanism, as is the formation of HTn from (-)-erythro-2-fluorocitrate. The structure of the inhibited complex reveals that HTn binds like the inhibitor trans-aconitate while providing all the interactions of the natural substrate, isocitrate. The structure exhibits four hydrogen bonds < 2.7 A in length involving HTn, H2O bound to the [4Fe-4S] cluster, Asp-165 and His-167, as well as low temperature factors for these moieties, consistent with the observed very tight binding of the inhibitor.
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Affiliation(s)
- H Lauble
- Universität Stuttgart, Institut für Organische Chemie, Germany
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Beinert H, Kennedy MC, Stout CD. Aconitase as Ironminus signSulfur Protein, Enzyme, and Iron-Regulatory Protein. Chem Rev 1996; 96:2335-2374. [PMID: 11848830 DOI: 10.1021/cr950040z] [Citation(s) in RCA: 422] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Helmut Beinert
- Institute for Enzyme Research, Graduate School, and Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53705, Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
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Caldeira J, Feicht R, White H, Teixeira M, Moura JJ, Simon H, Moura I. EPR and Mössbauer spectroscopic studies on enoate reductase. J Biol Chem 1996; 271:18743-8. [PMID: 8702530 DOI: 10.1074/jbc.271.31.18743] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enoate reductase (EC 1.3.1.31) is a protein isolated from Clostridium tyrobutyricum that contains iron, labile sulfide, FAD, and FMN. The enzyme reduces the alpha,beta carbon-carbon double bond of nonactivated 2-enoates and in a reversible way that of 2-enals at the expense of NADH or reduced methyl viologen. UV-visible and EPR potentiometric titrations detect a semiquinone species in redox intermediate states characterized by an isotropic EPR signal at g = 2.0 without contribution at 580 nm. EPR redox titration shows two widely spread mid-point redox potentials (-190 and -350 mV at pH 7. 0), and a nearly stoichiometric amount of this species is detected. The data suggest the semiquinone radical has an anionic nature. In the reduced form, the [Fe-S] moiety is characterized by a single rhombic EPR spectrum, observed in a wide range of temperatures (4. 2-60 K) with g values at 2.013, 1.943, and 1.860 (-180 mV at pH 7.0). The gmax value is low when compared with what has been reported for other iron-sulfur clusters. Mössbauer studies reveal the presence of a [4Fe-4S]+2/+1 center. One of the subcomponents of the spectrum shows an unusually large value of quadrupole splitting (ferrous character) in both the oxidized and reduced states. Substrate binding to the reduced enzyme induces subtle changes in the spectroscopic Mössbauer parameters. The Mössbauer data together with known kinetic information suggest the involvement of this iron-sulfur center in the enzyme mechanism.
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Affiliation(s)
- J Caldeira
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
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Zhou J, Hu Z, Münck E, Holm RH. The Cuboidal Fe3S4 Cluster: Synthesis, Stability, and Geometric and Electronic Structures in a Non-Protein Environment. J Am Chem Soc 1996. [DOI: 10.1021/ja9537843] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jian Zhou
- Contribution from the Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Zhengguo Hu
- Contribution from the Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - Eckard Münck
- Contribution from the Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
| | - R. H. Holm
- Contribution from the Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213
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These are the Moments when we Live! From Thunberg Tubes and Manometry to Phone, Fax and Fedex. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/b978-0-444-81942-0.50012-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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44
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The electronic structure of FeS centers in proteins and models a contribution to the understanding of their electron transfer properties. STRUCTURE AND BONDING 1995. [DOI: 10.1007/3-540-59105-2_1] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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45
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Castro L, Rodriguez M, Radi R. Aconitase is readily inactivated by peroxynitrite, but not by its precursor, nitric oxide. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43894-x] [Citation(s) in RCA: 440] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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46
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Belinskii M. Spin coupling model for tetrameric iron clusters in ferredoxins. I. Theory, exchange levels, g-factors. Chem Phys 1993. [DOI: 10.1016/0301-0104(93)80116-q] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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47
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Belinskii M. Spin coupling model for tetrameric iron clusters in ferredoxins. II. Hyperfine interactions, magnetism, high-spin systems. Chem Phys 1993. [DOI: 10.1016/0301-0104(93)80117-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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Tomohiro T, Kodaka M, Okuno H(Y. Spectral evidence for stepwise ligand substitution on 4Fe4S clusters. Inorganica Chim Acta 1993. [DOI: 10.1016/s0020-1693(00)88105-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Flint DH. Escherichia coli fumarase A catalyzes the isomerization of enol and keto oxalacetic acid. Biochemistry 1993; 32:799-805. [PMID: 8422384 DOI: 10.1021/bi00054a009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fumarase A, a product of the fumA gene of Escherichia coli, has been found to catalyze the isomerization of enol to keto oxalacetic acid (OAA) in addition to catalyzing the fumarase reaction. The kcat/Km for the isomerization is almost identical to that for the fumarase reaction. The isomerization reaction apparently takes place at the same active site as the fumarase reaction since both reactions show a similar sensitivity to inactivation by O2, both reactions are strongly inhibited by 2-hydroxy-3-nitropropionate, and the isomerization reaction is inhibited by fumarate and malate. The isomerization requires the presence of a [4Fe-4S] or [3Fe-4S] cluster, perhaps for structural rather than catalytic reasons. Hydration of enol OAA to the gem diol has been ruled out as a possible mechanism of isomerization on the basis of the preservation of the oxygen on carbon 2 and the position of protonation on carbon 3. The isomerization is not stereospecific in the position of protonation at carbon 3 but appears to be stereoselective, with protonation preferentially occurring in the 3-pro-S position. Porcine fumarase, isopropyl malate isomerase, and dihydroxyacid dehydratase do not catalyze this isomerization. Fumarase A and aconitase, two enzymes with 4Fe-4S clusters that bind a linear 4-carbon dicarboxylic acid moiety in the trans conformation during their normal hydro-lyase reaction, do catalyze this isomerization.
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Affiliation(s)
- D H Flint
- Central Research and Development Department, E. I. du Pont de Nemours and Company, Wilmington, Delaware 19880
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50
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Metalloenzyme Active-Site Structure and Function through Multifrequency CW and Pulsed ENDOR. EMR OF PARAMAGNETIC MOLECULES 1993. [DOI: 10.1007/978-1-4615-2892-0_4] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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