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Prakash D, Xiong J, Chauhan SS, Walters KA, Kruse H, Yennawar N, Golbeck JH, Guo Y, Ferry JG. Catalytic Activity of the Archetype from Group 4 of the FTR-like Ferredoxin:Thioredoxin Reductase Family Is Regulated by Unique S = 7/2 and S = 1/2 [4Fe-4S] Clusters. Biochemistry 2024; 63:1588-1598. [PMID: 38817151 PMCID: PMC11234629 DOI: 10.1021/acs.biochem.3c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Thioredoxin reductases (TrxR) activate thioredoxins (Trx) that regulate the activity of diverse target proteins essential to prokaryotic and eukaryotic life. However, very little is understood of TrxR/Trx systems and redox control in methanogenic microbes from the domain Archaea (methanogens), for which genomes are abundant with annotations for ferredoxin:thioredoxin reductases [Fdx/thioredoxin reductase (FTR)] from group 4 of the widespread FTR-like family. Only two from the FTR-like family are characterized: the plant-type FTR from group 1 and FDR from group 6. Herein, the group 4 archetype (AFTR) from Methanosarcina acetivorans was characterized to advance understanding of the family and TrxR/Trx systems in methanogens. The modeled structure of AFTR, together with EPR and Mössbauer spectroscopies, supports a catalytic mechanism similar to plant-type FTR and FDR, albeit with important exceptions. EPR spectroscopy of reduced AFTR identified a transient [4Fe-4S]1+ cluster exhibiting a mixture of S = 7/2 and typical S = 1/2 signals, although rare for proteins containing [4Fe-4S] clusters, it is most likely the on-pathway intermediate in the disulfide reduction. Furthermore, an active site histidine equivalent to residues essential for the activity of plant-type FTR and FDR was found dispensable for AFTR. Finally, a unique thioredoxin system was reconstituted from AFTR, ferredoxin, and Trx2 from M. acetivorans, for which specialized target proteins were identified that are essential for growth and other diverse metabolisms.
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Affiliation(s)
- Divya Prakash
- School of Chemical and Biomolecular Sciences, Southern Illinois University-Carbondale, Carbondale, Illinois 62901, United States
| | - Jin Xiong
- Department of Chemistry, The Carnegie Mellon University, Pittsburgh,, Pennsylvania 15213, United States
| | - Shikha S Chauhan
- School of Chemical and Biomolecular Sciences, Southern Illinois University-Carbondale, Carbondale, Illinois 62901, United States
| | - Karim A Walters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hannah Kruse
- School of Chemical and Biomolecular Sciences, Southern Illinois University-Carbondale, Carbondale, Illinois 62901, United States
| | - Neela Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - John H Golbeck
- 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
| | - Yisong Guo
- Department of Chemistry, The Carnegie Mellon University, Pittsburgh,, Pennsylvania 15213, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Taghvimi P, Mohsenzadeh Golfazani M, Taghvaei MM, Samizadeh Lahiji H. Investigating the effect of drought stress and methanol spraying on the influential genes in the Calvin cycle and photorespiration of rapeseed ( Brassica napus). FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23280. [PMID: 38467163 DOI: 10.1071/fp23280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
Due to global warming and changes in precipitation patterns, many regions are prone to permanent drought. Rapeseed (Brassica napus ) is one of the main sources of edible oils worldwide, and its production and yield are affected by drought. In this study, gene expression alterations under drought stress are investigated with bioinformatics studies to examine evolutionary relations of conserved motifs structure and interactions among Calvin cycle and photorespiration pathways key genes in drought-tolerant (SLM046) and drought-sensitive (Hayola308) genotypes of rapeseed. Investigating the conservation and evolutionary relationships revealed high conservation in motifs of FBPase, PRK, GlyK and NADP-ME enzymes. The analysis of protein interactions showed the correlation between FTRC, FBPase1, PRKX1, GlyKX2 and NADP-ME4 genes. Furthermore, in rapeseed, for the GlyKX2 and NADP-ME4 genes, four microRNAs of the miR172 family and four members of the miR167 family were identified as post-transcriptional regulators, respectively. The expression of ferredoxin thioredoxin reductase, fructose-1,6-bisphosphatase genes, phosphoribulokinase, glycerate kinase and malic enzyme 4 genes in the two rapeseed genotypes were evaluated by real-time qPCR method under 72h of drought stress and methanol foliar application. As a result, the highest expression levels of FTRC, PRKX1, GlyKX2, NADP-ME4 and FBPase1 were observed in methanol foliar application on the SLM046 genotype at 24h. In contrast, in methanol foliar application on the Hayola308 genotype, the highest expression levels of FTRC, PRKX1, GlyKX2, NADP-ME4 and FBPase1 were observed 8h after the treatment. Our study illustrated that methanol foliar application enhanced plant tolerance under drought stress.
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Affiliation(s)
- Parisa Taghvimi
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | - Mohammad Mahdi Taghvaei
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Habibollah Samizadeh Lahiji
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
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Ghebreamlak S, Stoian SA, Lees NS, Cronin B, Smith F, Ross MO, Telser J, Hoffman BM, Duin EC. The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis. J Am Chem Soc 2024; 146:3926-3942. [PMID: 38291562 DOI: 10.1021/jacs.3c11674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase, or IspH (formerly known as LytB), catalyzes the terminal step of the bacterial methylerythritol phosphate (MEP) pathway for isoprene synthesis. This step converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into one of two possible isomeric products, either isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). This reaction involves the removal of the C4 hydroxyl group of HMBPP and addition of two electrons. IspH contains a [4Fe-4S] cluster in its active site, and multiple cluster-based paramagnetic species of uncertain redox and ligation states can be detected after incubation with reductant, addition of a ligand, or during catalysis. To characterize the clusters in these species, 57Fe-labeled samples of IspH were prepared and studied by electron paramagnetic resonance (EPR), 57Fe electron-nuclear double resonance (ENDOR), and Mössbauer spectroscopies. Notably, this ENDOR study provides a rarely reported, complete determination of the 57Fe hyperfine tensors for all four Fe ions in a [4Fe-4S] cluster. The resting state of the enzyme (Ox) has a diamagnetic [4Fe-4S]2+ cluster. Reduction generates [4Fe-4S]+ (Red) with both S = 1/2 and S = 3/2 spin ground states. When the reduced enzyme is incubated with substrate, a transient paramagnetic reaction intermediate is detected (Int) which is thought to contain a cluster-bound substrate-derived species. The EPR properties of Int are indicative of a 3+ iron-sulfur cluster oxidation state, and the Mössbauer spectra presented here confirm this. Incubation of reduced enzyme with the product IPP induced yet another paramagnetic [4Fe-4S]+ species (Red+P) with S = 1/2. However, the g-tensor of this state is commonly associated with a 3+ oxidation state, while Mössbauer parameters show features typical for 2+ clusters. Implications of these complicated results are discussed.
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Affiliation(s)
- Selamawit Ghebreamlak
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Sebastian A Stoian
- Department of Chemistry, University of Idaho, 875 Perimeter Drive, MS 2343 Moscow, Idaho 83844, United States
| | - Nicholas S Lees
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Bryan Cronin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Forrest Smith
- Department of Drug Discovery & Development, Auburn University, 4306 Walker Building, Auburn, Alabama 36849, United States
| | - Matthew O Ross
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, 430 S. Michigan Avenue, Chicago, Illinois 60605, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
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Schut GJ, Haja DK, Feng X, Poole FL, Li H, Adams MWW. An Abundant and Diverse New Family of Electron Bifurcating Enzymes With a Non-canonical Catalytic Mechanism. Front Microbiol 2022; 13:946711. [PMID: 35875533 PMCID: PMC9304861 DOI: 10.3389/fmicb.2022.946711] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms utilize electron bifurcating enzymes in metabolic pathways to carry out thermodynamically unfavorable reactions. Bifurcating FeFe-hydrogenases (HydABC) reversibly oxidize NADH (E′∼−280 mV, under physiological conditions) and reduce protons to H2 gas (E°′−414 mV) by coupling this endergonic reaction to the exergonic reduction of protons by reduced ferredoxin (Fd) (E′∼−500 mV). We show here that HydABC homologs are surprisingly ubiquitous in the microbial world and are represented by 57 phylogenetically distinct clades but only about half are FeFe-hydrogenases. The others have replaced the hydrogenase domain with another oxidoreductase domain or they contain additional subunits, both of which enable various third reactions to be reversibly coupled to NAD+ and Fd reduction. We hypothesize that all of these enzymes carry out electron bifurcation and that their third substrates can include hydrogen peroxide, pyruvate, carbon monoxide, aldehydes, aryl-CoA thioesters, NADP+, cofactor F420, formate, and quinones, as well as many yet to be discovered. Some of the enzymes are proposed to be integral membrane-bound proton-translocating complexes. These different functionalities are associated with phylogenetically distinct clades and in many cases with specific microbial phyla. We propose that this new and abundant class of electron bifurcating enzyme be referred to as the Bfu family whose defining feature is a conserved bifurcating BfuBC core. This core contains FMN and six iron sulfur clusters and it interacts directly with ferredoxin (Fd) and NAD(H). Electrons to or from the third substrate are fed into the BfuBC core via BfuA. The other three known families of electron bifurcating enzyme (abbreviated as Nfn, EtfAB, and HdrA) contain a special FAD that bifurcates electrons to high and low potential pathways. The Bfu family are proposed to use a different electron bifurcation mechanism that involves a combination of FMN and three adjacent iron sulfur clusters, including a novel [2Fe-2S] cluster with pentacoordinate and partial non-Cys coordination. The absolute conservation of the redox cofactors of BfuBC in all members of the Bfu enzyme family indicate they have the same non-canonical mechanism to bifurcate electrons. A hypothetical catalytic mechanism is proposed as a basis for future spectroscopic analyses of Bfu family members.
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Affiliation(s)
- Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Dominik K. Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Farris L. Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Michael W. W. Adams, ; orcid.org/0000-0002-9796-5014
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Structural Insights into a Fusion Protein between a Glutaredoxin-like and a Ferredoxin-Disulfide Reductase Domain from an Extremophile Bacterium. INORGANICS 2022. [DOI: 10.3390/inorganics10020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In eukaryotic photosynthetic organisms, ferredoxin–thioredoxin reductases (FTRs) are key proteins reducing several types of chloroplastic thioredoxins (TRXs) in light conditions. The electron cascade necessary to reduce oxidized TRXs involves a pair of catalytic cysteines and a [4Fe–4S] cluster present at the level of the FTR catalytic subunit, the iron–sulfur cluster receiving electrons from ferredoxins. Genomic analyses revealed the existence of FTR orthologs in non-photosynthetic organisms, including bacteria and archaea, referred to as ferredoxin-disulfide reductase (FDR) as they reduce various types of redoxins. In this study, we describe the tridimensional structure of a natural hybrid protein formed by an N-terminal glutaredoxin-like domain fused to a FDR domain present in the marine bacterium Desulfotalea psychrophila Lsv54. This structure provides information on how and why the absence of the variable subunit present in FTR heterodimer which normally protects the Fe–S cluster is dispensable in FDR proteins. In addition, modelling of a tripartite complex based on the existing structure of a rubredoxin (RBX)–FDR fusion present in anaerobic methanogen archaea allows recapitulating the electron flow involving these RBX, FDR and GRX protein domains.
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6
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Jobelius H, Bianchino GI, Borel F, Chaignon P, Seemann M. The Reductive Dehydroxylation Catalyzed by IspH, a Source of Inspiration for the Development of Novel Anti-Infectives. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030708. [PMID: 35163971 PMCID: PMC8837944 DOI: 10.3390/molecules27030708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
The non-mevalonate or also called MEP pathway is an essential route for the biosynthesis of isoprenoid precursors in most bacteria and in microorganisms belonging to the Apicomplexa phylum, such as the parasite responsible for malaria. The absence of this pathway in mammalians makes it an interesting target for the discovery of novel anti-infectives. As last enzyme of this pathway, IspH is an oxygen sensitive [4Fe-4S] metalloenzyme that catalyzes 2H+/2e− reductions and a water elimination by involving non-conventional bioinorganic and bioorganometallic intermediates. After a detailed description of the discovery of the [4Fe-4S] cluster of IspH, this review focuses on the IspH mechanism discussing the results that have been obtained in the last decades using an approach combining chemistry, enzymology, crystallography, spectroscopies, and docking calculations. Considering the interesting druggability of this enzyme, a section about the inhibitors of IspH discovered up to now is reported as well. The presented results constitute a useful and rational help to inaugurate the design and development of new potential chemotherapeutics against pathogenic organisms.
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Affiliation(s)
- Hannah Jobelius
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Gabriella Ines Bianchino
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Franck Borel
- Institut de Biologie Structurale, Université Grenoble Alpes/CEA/CNRS, 38000 Grenoble, France;
| | - Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
- Correspondence:
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7
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White RH. Identification of an Enzyme Catalyzing the Conversion of Sulfoacetaldehyde to 2-Mercaptoethanesulfonic Acid in Methanogens. Biochemistry 2019; 58:1958-1962. [PMID: 30932481 DOI: 10.1021/acs.biochem.9b00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coenzyme M is an essential coenzyme for the biochemical production of methane. This Communication reports on the identification of an enzyme catalyzing the last step in the biosynthesis of coenzyme M in methanogens. Data presented here show that the enzyme, derived from mj1681, catalyzes the conversion of the aldehyde functional group of sulfoacetaldehyde into the thiol group of 2-mercaptoethanesulfonic acid. Thus, a putative coenzyme M synthase (comF) has similarities in sequence with both MJ0100 and MJ0099 proteins previously shown to be involved in the biosynthesis of homocysteine [Allen, K. D., et al. (2015) Biochemistry 54, 3129-3132], and both reactions likely proceed by the same mechanism. In the MJ0100-catalyzed reaction, Rauch has proposed [Rauch, B. L. (2017) Biochemistry 56, 1051-1061] that MJ1526 and its homologues in other methanogens likely supply the sulfane sulfur required for the reaction.
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Affiliation(s)
- Robert H White
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
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8
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Prakash D, Walters KA, Martinie RJ, McCarver AC, Kumar AK, Lessner DJ, Krebs C, Golbeck JH, Ferry JG. Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria. J Biol Chem 2018; 293:9198-9209. [PMID: 29720404 DOI: 10.1074/jbc.ra118.002473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Indexed: 11/06/2022] Open
Abstract
Disulfide reductases reduce other proteins and are critically important for cellular redox signaling and homeostasis. Methanosarcina acetivorans is a methane-producing microbe from the domain Archaea that produces a ferredoxin:disulfide reductase (FDR) for which the crystal structure has been reported, yet its biochemical mechanism and physiological substrates are unknown. FDR and the extensively characterized plant-type ferredoxin:thioredoxin reductase (FTR) belong to a distinct class of disulfide reductases that contain a unique active-site [4Fe-4S] cluster. The results reported here support a mechanism for FDR similar to that reported for FTR with notable exceptions. Unlike FTR, FDR contains a rubredoxin [1Fe-0S] center postulated to mediate electron transfer from ferredoxin to the active-site [4Fe-4S] cluster. UV-visible, EPR, and Mössbauer spectroscopic data indicated that two-electron reduction of the active-site disulfide in FDR involves a one-electron-reduced [4Fe-4S]1+ intermediate previously hypothesized for FTR. Our results support a role for an active-site tyrosine in FDR that occupies the equivalent position of an essential histidine in the active site of FTR. Of note, one of seven Trxs encoded in the genome (Trx5) and methanoredoxin, a glutaredoxin-like enzyme from M. acetivorans, were reduced by FDR, advancing the physiological understanding of FDR's role in the redox metabolism of methanoarchaea. Finally, bioinformatics analyses show that FDR homologs are widespread in diverse microbes from the domain Bacteria.
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Affiliation(s)
- Divya Prakash
- From the Departments of Biochemistry and Molecular Biology and
| | - Karim A Walters
- From the Departments of Biochemistry and Molecular Biology and
| | - Ryan J Martinie
- Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Addison C McCarver
- the Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Adepu K Kumar
- From the Departments of Biochemistry and Molecular Biology and
| | - Daniel J Lessner
- the Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Carsten Krebs
- From the Departments of Biochemistry and Molecular Biology and.,Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - John H Golbeck
- From the Departments of Biochemistry and Molecular Biology and.,Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - James G Ferry
- From the Departments of Biochemistry and Molecular Biology and
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9
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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10
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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11
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Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis. Nat Chem 2017. [PMID: 28644475 DOI: 10.1038/nchem.2714] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor. Unexpectedly, these D-amino acid residues proved to be essential for the activity of a peptide that induces the expression of LiaRS, a major component of the bacterial cell envelope stress-response system. Present in B. subtilis and in several members of the human microbiome, these epipeptides and radical SAM epimerases broaden the landscape of peptidyl structures accessible to living organisms.
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12
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Unanticipated coordination of tris buffer to the Radical SAM cluster of the RimO methylthiotransferase. J Biol Inorg Chem 2016; 21:549-57. [PMID: 27259294 DOI: 10.1007/s00775-016-1365-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/27/2016] [Indexed: 10/21/2022]
Abstract
Radical SAM enzymes generally contain a [4Fe-4S](2+/1+) (RS cluster) cluster bound to the protein via the three cysteines of a canonical motif CxxxCxxC. The non-cysteinyl iron is used to coordinate SAM via its amino-carboxylate moiety. The coordination-induced proximity between the cluster acting as an electron donor and the adenosyl-sulfonium bond of SAM allows for the homolytic cleavage of the latter leading to the formation of the reactive 5'-deoxyadenosyl radical used for substrate activation. Most of the structures of Radical SAM enzymes have been obtained in the presence of SAM, and therefore, little is known about the situation when SAM is not present. In this report, we show that RimO, a methylthiotransferase belonging to the radical SAM superfamily, binds a Tris molecule in the absence of SAM leading to specific spectroscopic signatures both in Mössbauer and pulsed EPR spectroscopies. These data provide a cautionary note for researchers who work with coordinative unsaturated iron sulfur clusters.
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13
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Expression of spinach ferredoxin-thioredoxin reductase using tandem T7 promoters and application of the purified protein for in vitro light-dependent thioredoxin-reduction system. Protein Expr Purif 2016; 121:46-51. [PMID: 26773743 DOI: 10.1016/j.pep.2016.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 11/22/2022]
Abstract
Thioredoxins (Trxs) regulate the activity of target proteins in the chloroplast redox regulatory system. In vivo, a disulfide bond within Trxs is reduced by photochemically generated electrons via ferredoxin (Fd) and ferredoxin-thioredoxin reductase (FTR: EC 1.8.7.2). FTR is an αβ-heterodimer, and the β-subunit has a 4Fe-4S cluster that is indispensable for the electron transfer from Fd to Trxs. Reconstitution of the light-dependent Fd/Trx system, including FTR, is required for the biochemical characterization of the Trx-dependent reduction pathway in the chloroplasts. In this study, we generated functional FTR by simultaneously expressing FTR-α and -β subunits under the control of tandem T7 promoters in Escherichia coli, and purifying the resulting FTR complex protein. The purified FTR complex exhibited spectroscopic absorption at 410 nm, indicating that it contained the Fe-S cluster. Modification of the expression system and simplification of the purification steps resulted in improved FTR complex yields compared to those obtained in previous studies. Furthermore, the light-dependent Trx-reduction system was reconstituted by using Fd, the purified FTR, and intact thylakoids.
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14
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Kumar AK, Kumar RSS, Yennawar NH, Yennawar HP, Ferry JG. Structural and Biochemical Characterization of a Ferredoxin:Thioredoxin Reductase-like Enzyme from Methanosarcina acetivorans. Biochemistry 2015; 54:3122-8. [PMID: 25915695 DOI: 10.1021/acs.biochem.5b00137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bioinformatics analyses predict the distribution in nature of several classes of diverse disulfide reductases that evolved from an ancestral plant-type ferredoxin:thioredoxin reductase (FTR) catalytic subunit to meet a variety of ecological needs. Methanosarcina acetivorans is a methane-producing species from the domain Archaea predicted to encode an FTR-like enzyme with two domains, one resembling the FTR catalytic subunit and the other containing a rubredoxin-like domain replacing the variable subunit of present-day FTR enzymes. M. acetivorans is of special interest as it was recently proposed to have evolved at the time of the end-Permian extinction and to be largely responsible for the most severe biotic crisis in the fossil record by converting acetate to methane. The crystal structure and biochemical characteristics were determined for the FTR-like enzyme from M. acetivorans, here named FDR (ferredoxin disulfide reductase). The results support a role for the rubredoxin-like center of FDR in transfer of electrons from ferredoxin to the active-site [Fe₄S₄] cluster adjacent to a pair of redox-active cysteines participating in reduction of disulfide substrates. A mechanism is proposed for disulfide reduction similar to one of two mechanisms previously proposed for the plant-type FTR. Overall, the results advance the biochemical and evolutionary understanding of the FTR-like family of enzymes and the conversion of acetate to methane that is an essential link in the global carbon cycle and presently accounts for most of this greenhouse gas that is biologically generated.
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Wen HR, Qi TT, Liu SJ, Liu CM, Tang YZ, Chen JL. Syntheses and structures of chiral tri- and tetranuclear Cd(II) clusters with luminescent and ferroelectric properties. Polyhedron 2015. [DOI: 10.1016/j.poly.2014.10.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Mössbauer spectroscopy of Fe/S proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1395-405. [PMID: 25498248 DOI: 10.1016/j.bbamcr.2014.12.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/17/2014] [Accepted: 12/03/2014] [Indexed: 01/02/2023]
Abstract
Iron-sulfur (Fe/S) clusters are structurally and functionally diverse cofactors that are found in all domains of life. (57)Fe Mössbauer spectroscopy is a technique that provides information about the chemical nature of all chemically distinct Fe species contained in a sample, such as Fe oxidation and spin state, nuclearity of a cluster with more than one metal ion, electron spin ground state of the cluster, and delocalization properties in mixed-valent clusters. Moreover, the technique allows for quantitation of all Fe species, when it is used in conjunction with electron paramagnetic resonance (EPR) spectroscopy and analytical methods. (57)Fe-Mössbauer spectroscopy played a pivotal role in unraveling the electronic structures of the "well-established" [2Fe-2S](2+/+), [3Fe-4S](1+/0), and [4Fe-4S](3+/2+/1+/0) clusters and -more-recently- was used to characterize novel Fe/S clustsers, including the [4Fe-3S] cluster of the O2-tolerant hydrogenase from Aquifex aeolicus and the 3Fe-cluster intermediate observed during the reaction of lipoyl synthase, a member of the radical SAM enzyme superfamily.
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17
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 589] [Impact Index Per Article: 58.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Wang W, Oldfield E. Biometallorganische Chemie mit IspG und IspH: Struktur, Funktion und Hemmung der an der Isoprenoid-Biosynthese beteiligten [Fe 4S 4]-Proteine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Shisler KA, Broderick JB. Glycyl radical activating enzymes: structure, mechanism, and substrate interactions. Arch Biochem Biophys 2014; 546:64-71. [PMID: 24486374 PMCID: PMC4083501 DOI: 10.1016/j.abb.2014.01.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/20/2022]
Abstract
The glycyl radical enzyme activating enzymes (GRE-AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe-4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE-AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE-AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE-AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes.
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Affiliation(s)
- Krista A Shisler
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States.
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20
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Wang W, Oldfield E. Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis. Angew Chem Int Ed Engl 2014; 53:4294-310. [PMID: 24481599 DOI: 10.1002/anie.201306712] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 11/12/2022]
Abstract
Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4 S4 ] proteins that are not produced by humans and catalyze 2 H(+) / 2 e(-) reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4 S4 ] clusters in proteins.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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21
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013; 52:2002-6. [DOI: 10.1002/anie.201209063] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Indexed: 11/08/2022]
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22
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2
Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Couturier J, Touraine B, Briat JF, Gaymard F, Rouhier N. The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions. FRONTIERS IN PLANT SCIENCE 2013; 4:259. [PMID: 23898337 PMCID: PMC3721309 DOI: 10.3389/fpls.2013.00259] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/25/2013] [Indexed: 05/18/2023]
Abstract
Many metabolic pathways and cellular processes occurring in most sub-cellular compartments depend on the functioning of iron-sulfur (Fe-S) proteins, whose cofactors are assembled through dedicated protein machineries. Recent advances have been made in the knowledge of the functions of individual components through a combination of genetic, biochemical and structural approaches, primarily in prokaryotes and non-plant eukaryotes. Whereas most of the components of these machineries are conserved between kingdoms, their complexity is likely increased in plants owing to the presence of additional assembly proteins and to the existence of expanded families for several assembly proteins. This review focuses on the new actors discovered in the past few years, such as glutaredoxin, BOLA and NEET proteins as well as MIP18, MMS19, TAH18, DRE2 for the cytosolic machinery, which are integrated into a model for the plant Fe-S cluster biogenesis systems. It also discusses a few issues currently subjected to an intense debate such as the role of the mitochondrial frataxin and of glutaredoxins, the functional separation between scaffold, carrier and iron-delivery proteins and the crosstalk existing between different organelles.
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Affiliation(s)
- Jérémy Couturier
- Interactions Arbres/Micro-organismes, Faculté des Sciences, UMR1136 Université de Lorraine-INRAVandoeuvre, France
| | - Brigitte Touraine
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Jean-François Briat
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Frédéric Gaymard
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Nicolas Rouhier
- Interactions Arbres/Micro-organismes, Faculté des Sciences, UMR1136 Université de Lorraine-INRAVandoeuvre, France
- *Correspondence: Nicolas Rouhier, Université de Lorraine, UMR1136 Université de Lorraine-INRA, Interactions Arbres/Micro-organismes, Faculté des Sciences, Bd des aiguillettes, BP 239,54506 Vandoeuvre, France e-mail:
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24
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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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Wang W, Wang K, Span I, Jauch J, Bacher A, Groll M, Oldfield E. Are free radicals involved in IspH catalysis? An EPR and crystallographic investigation. J Am Chem Soc 2012; 134:11225-34. [PMID: 22687151 DOI: 10.1021/ja303445z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The [4Fe-4S] protein IspH in the methylerythritol phosphate isoprenoid biosynthesis pathway is an important anti-infective drug target, but its mechanism of action is still the subject of debate. Here, by using electron paramagnetic resonance (EPR) spectroscopy and (2)H, (17)O, and (57)Fe isotopic labeling, we have characterized and assigned two key reaction intermediates in IspH catalysis. The results are consistent with the bioorganometallic mechanism proposed earlier, and the mechanism is proposed to have similarities to that of ferredoxin, thioredoxin reductase, in that one electron is transferred to the [4Fe-4S](2+) cluster, which then performs a formal two-electron reduction of its substrate, generating an oxidized high potential iron-sulfur protein (HiPIP)-like intermediate. The two paramagnetic reaction intermediates observed correspond to the two intermediates proposed in the bioorganometallic mechanism: the early π-complex in which the substrate's 3-CH(2)OH group has rotated away from the reduced iron-sulfur cluster, and the next, η(3)-allyl complex formed after dehydroxylation. No free radical intermediates are observed, and the two paramagnetic intermediates observed do not fit in a Birch reduction-like or ferraoxetane mechanism. Additionally, we show by using EPR spectroscopy and X-ray crystallography that two substrate analogues (4 and 5) follow the same reaction mechanism.
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Affiliation(s)
- Weixue Wang
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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26
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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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27
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Xu W, Lees NS, Hall D, Welideniya D, Hoffman BM, Duin EC. A closer look at the spectroscopic properties of possible reaction intermediates in wild-type and mutant (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase. Biochemistry 2012; 51:4835-49. [PMID: 22646150 DOI: 10.1021/bi3001215] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) into the two products, isopentenyl diphosphate and dimethylallyl diphosphate. The reaction involves the reductive elimination of the C4 hydroxyl group, using a total of two electrons. Here we show that the active form of IspH contains a [4Fe-4S] cluster and not the [3Fe-4S] form. Our studies show that the cluster is the direct electron source for the reaction and that a reaction intermediate is bound directly to the cluster. This active form has been trapped in a state, dubbed FeS(A), that was detected by electron paramagnetic resonance (EPR) spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH have been prepared and studied, His42, His124, and Glu126 (Aquifex aeolicus numbering), with particular attention paid to the effects on the cluster properties and possible reaction intermediates. None of the mutants significantly affected the properties of the [4Fe-4S](+) cluster, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing His42 led to an increased K(M) value and a much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in a lower catalytic efficiency. In this case, however, the enzyme showed the loss of the [4Fe-4S](+) EPR signal upon addition of HMBPP without the subsequent formation of the FeS(A) signal. Instead, a radical-type signal was observed in some of the samples, indicating that this residue plays a role in the correct positioning of the substrate. The incorrect orientation in the mutant leads to the formation of substrate-based radicals instead of the cluster-bound intermediate complex FeS(A). Replacing the Glu126 also resulted in a lower catalytic efficiency, with yet a third type of EPR signal being detected upon incubation with HMBPP. (31)P and (2)H ENDOR measurements of the FeS(A) species incubated with regular and (2)H-C4-labeled HMBPP reveal that the substrate binds to the enzyme in the proximity of the active-site cluster with C4 adjacent to the site of linkage between the FeS cluster and HMBPP. Comparison of the spectroscopic properties of this intermediate to those of intermediates detected in (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin:thioredoxin reductase suggests that HMBPP binds to the FeS cluster via its hydroxyl group instead of a side-on binding as previously proposed for the species detected in the inactive Glu126 variant. Consequences for the IspH reaction mechanism are discussed.
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Affiliation(s)
- Weiya Xu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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28
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El Khoury Y, Hellwig P. A combined far-infrared spectroscopic and electrochemical approach for the study of iron-sulfur proteins. Chemphyschem 2011; 12:2669-74. [PMID: 21887734 DOI: 10.1002/cphc.201100165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/15/2011] [Indexed: 11/11/2022]
Abstract
Herein, we present the development of a far-infrared spectroscopic approach for studying metalloenzyme active sites in a redox-dependent manner. An electrochemical cell with 5 mm path and based on silicon windows was found to be appropriate for the measurement of aqueous solutions down to 200 cm(-1) . The cell was probed with the infrared redox signature of the metal-ligand vibrations of different iron-sulfur proteins. Each Fe-S cluster type was found to show a specific spectral signature. As a common feature, a downshift of the frequency of the Fe-S vibrations was seen upon reduction, in line with the increase of the Fe-S bond. This downshift was found to be fully reversible. Electrochemically induced FTIR difference spectroscopy in the far infrared is now possible, opening new perspectives on the understanding of metalloproteins in function of the redox state.
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Affiliation(s)
- Youssef El Khoury
- Institut de Chimie, UMR, Laboratoire de spectroscopie vibrationnelle et électrochimie des biomolécules Université de Strasbourg, France
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29
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Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus. Proc Natl Acad Sci U S A 2011; 108:6097-102. [PMID: 21444783 DOI: 10.1073/pnas.1100610108] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron "wires" form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O(2) to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of (57)Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S](3+) state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress.
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30
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Xu W, Lees NS, Adedeji D, Wiesner J, Jomaa H, Hoffman BM, Duin EC. Paramagnetic Intermediates of (E)-4-Hydroxy-3-methylbut-2-enyl Diphosphate Synthase (GcpE/IspG) under Steady-State and Pre-Steady-State Conditions. J Am Chem Soc 2010; 132:14509-20. [DOI: 10.1021/ja101764w] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weiya Xu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Nicholas S. Lees
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Dolapo Adedeji
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Jochen Wiesner
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Hassan Jomaa
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Brian M. Hoffman
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
| | - Evert C. Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and Institut für Klinische Chemie und Pathobiochemie, Universitätsklinikum Giessen und Marburg, D-Giessen, 35392 Giessen, Germany
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31
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Arragain S, Garcia-Serres R, Blondin G, Douki T, Clemancey M, Latour JM, Forouhar F, Neely H, Montelione GT, Hunt JF, Mulliez E, Fontecave M, Atta M. Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. J Biol Chem 2009; 285:5792-801. [PMID: 20007320 DOI: 10.1074/jbc.m109.065516] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 A crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.
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Affiliation(s)
- Simon Arragain
- Institut de Recherches en Technologie et Sciences pour le Vivant-Laboratoire de Chimie et Biologie des Métaux (iRTSV-LCBM), UMR 5249, CEA-CNRS-UJF, Commissariat à l'Energie Atomique Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France
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32
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Lee KH, Saleh L, Anton BP, Madinger CL, Benner JS, Iwig DF, Roberts RJ, Krebs C, Booker SJ. Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry 2009; 48:10162-74. [PMID: 19736993 DOI: 10.1021/bi900939w] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RimO, encoded by the yliG gene in Escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of Asp88 of the small ribosomal protein S12 [Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 1826-1831]. To date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modifications have been observed on tRNA. All members of the methylthiotransferase (MTTase) family, to which RimO belongs, have been shown to contain the canonical CxxxCxxC motif in their primary structures that is typical of the radical S-adenosylmethionine (SAM) family of proteins. MiaB, the only characterized MTTase, and the enzyme experimentally shown to be responsible for methylthiolation of N(6)-isopentenyladenosine of tRNA in E. coli and Thermotoga maritima, has been demonstrated to harbor two distinct [4Fe-4S] clusters. Herein, we report in vitro biochemical and spectroscopic characterization of RimO. We show by analytical and spectroscopic methods that RimO, overproduced in E. coli in the presence of iron-sulfur cluster biosynthesis proteins from Azotobacter vinelandii, contains one [4Fe-4S](2+) cluster. Reconstitution of this form of RimO (RimO(rcn)) with (57)Fe and sodium sulfide results in a protein that contains two [4Fe-4S](2+) clusters, similar to MiaB. We also show by mass spectrometry that RimO(rcn) catalyzes the attachment of a methylthio group to a peptide substrate analogue that mimics the loop structure bearing aspartyl 88 of the S12 ribosomal protein from E. coli. Kinetic analysis of this reaction shows that the activity of RimO(rcn) in the presence of the substrate analogue does not support a complete turnover. We discuss the possible requirement for an assembled ribosome for fully active RimO in vitro. Our findings are consistent with those of other enzymes that catalyze sulfur insertion, such as biotin synthase, lipoyl synthase, and MiaB.
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Affiliation(s)
- Kyung-Hoon Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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33
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Yang J, Naik SG, Ortillo DO, García-Serres R, Li M, Broderick WE, Huynh BH, Broderick JB. The iron-sulfur cluster of pyruvate formate-lyase activating enzyme in whole cells: cluster interconversion and a valence-localized [4Fe-4S]2+ state. Biochemistry 2009; 48:9234-41. [PMID: 19711960 DOI: 10.1021/bi9010286] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyruvate formate-lyase activating enzyme (PFL-AE) catalyzes the generation of a catalytically essential glycyl radical on pyruvate formate-lyase (PFL). Purified PFL-AE contains an oxygen-sensitive, labile [4Fe-4S] cluster that undergoes cluster interconversions in vitro, with only the [4Fe-4S](+) cluster state being catalytically active. Such cluster interconversions could play a role in regulating the activity of PFL-AE, and thus of PFL, in response to oxygen levels in vivo. Here we report a Mossbauer investigation on whole cells overexpressing PFL-AE following incubation under aerobic and/or anaerobic conditions and provide evidence that PFL-AE undergoes cluster interconversions in vivo. After 2 h aerobic induction of PFL-AE expression, approximately 44% of the total iron is present in [4Fe-4S](2+) clusters, 6% in [2Fe-2S](2+) clusters, and the remainder as noncluster Fe(III) (29%) and Fe(II) (21%) species. Subsequent anaerobic incubation of the culture results in approximately 75% of the total iron being present as [4Fe-4S](2+) clusters, with no detectable [2Fe-2S](2+). Ensuing aerobic incubation of the culture converts the iron species nearly back to the original composition (42% [4Fe-4S](2+), 10% [2Fe-2S](2+), 19% Fe(III), and 29% Fe(II)). The results provide evidence for changes in cluster composition of PFL-AE in response to the redox state of the cell. Furthermore, the Mossbauer spectra reveal that the [4Fe-4S](2+) cluster of PFL-AE in whole cells contains a valence-localized Fe(III)Fe(II) pair which has not been previously observed in the purified enzyme. Addition of certain small molecules containing adenosyl moieties, including 5'-deoxyadenosine, AMP, ADP, and methylthioadenosine, to purified PFL-AE reproduces the valence-localized state of the [4Fe-4S](2+) cluster. It is speculated that the [4Fe-4S](2+) cluster of PFL-AE in whole cells may be coordinated by a small molecule, probably AMP, and that such coordination may protect this labile cluster from oxidative damage.
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Affiliation(s)
- Jian Yang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Xu X, Schürmann P, Chung JS, Hass MAS, Kim SK, Hirasawa M, Tripathy JN, Knaff DB, Ubbink M. Ternary Protein Complex of Ferredoxin, Ferredoxin:Thioredoxin Reductase, and Thioredoxin Studied by Paramagnetic NMR Spectroscopy. J Am Chem Soc 2009; 131:17576-82. [DOI: 10.1021/ja904205k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xingfu Xu
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Peter Schürmann
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Jung-Sung Chung
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Mathias A. S. Hass
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Sung-Kun Kim
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Masakazu Hirasawa
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Jatindra N. Tripathy
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - David B. Knaff
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel CH-2009, Switzerland, Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, and Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409-3132
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Jacquot JP, Eklund H, Rouhier N, Schürmann P. Structural and evolutionary aspects of thioredoxin reductases in photosynthetic organisms. TRENDS IN PLANT SCIENCE 2009; 14:336-43. [PMID: 19446492 DOI: 10.1016/j.tplants.2009.03.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 03/27/2009] [Accepted: 03/31/2009] [Indexed: 05/24/2023]
Abstract
Thioredoxins (Trxs) are small oxidoreductases that are involved in redox homeostasis and are found in large numbers in the subcellular compartments of eukaryotic plant cells, including the chloroplasts. Also present in chloroplasts are two forms of thioredoxin reductase (TR), which use either NADPH or ferredoxin as an electron donor. In other compartments, two additional TR forms also use NADPH: one is distributed in all photosynthetic organisms and is similar to prokaryotic enzymes, whereas the other is restricted to algae and is similar to mammalian selenoproteins. Here, we review current knowledge of the different forms of TRs across organisms and discuss the possible evolutionary fate of this class of enzymes, which provide an example of convergent functional evolution.
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Affiliation(s)
- Jean-Pierre Jacquot
- Interactions Arbres Microorganismes UMR 1136, IFR 110, Nancy University, BP 239, 54506 Vandoeuvre Cedex, France.
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Walters EM, Garcia-Serres R, Naik SG, Bourquin F, Glauser DA, Schürmann P, Huynh BH, Johnson MK. Role of histidine-86 in the catalytic mechanism of ferredoxin:thioredoxin reductase. Biochemistry 2009; 48:1016-24. [PMID: 19132843 DOI: 10.1021/bi802074p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ferredoxin:thioredoxin reductase catalyzes the reduction of thioredoxins in plant chloroplasts using the [Fe2S2] ferredoxin as a one-electron donor and as such plays a central role in light regulation of oxygenic photosynthesis. The active-site comprises a [Fe4S4] cluster next to a redox-active disulfide that is cleaved in sequential one-electron steps and the combination of spectroscopic and crystallographic studies have revealed a catalytic mechanism involving novel site specific cluster chemistry in the oxidized, one-electron- and two-electron-reduced redox states. Histidine-86 has emerged as a potential proton donor/acceptor in the catalytic mechanism based on redox-related changes in the positioning of the imidazole ring during redox cycling and greatly decreased activity for the H86Y variant. Here we report on spectroscopic and redox characterization of the [Fe4S4] center in Synechocystis sp. PCC 6803 H86Y ferredoxin:thoredoxin reductase in the accessible redox states of both the as purified and N-ethylmaleimide-modified forms, using the combination of UV-visible absorption and variable-temperature magnetic circular dichroism, EPR, resonance Raman and Mössbauer spectroscopies. The results demonstrate that His86 is required for formation of the partially valence-localized [Fe4S4]2+ cluster that is the hallmark of two-electron-reduced intermediate. Taken together with the available structural data, the spectroscopic results indicate a functional role for His86 in protonation/deprotonation of the cluster-interacting thiol and anchoring the cluster interacting thiol in close proximity to the cluster in the two-electron-reduced intermediate.
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Affiliation(s)
- Elizabeth M Walters
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602, USA
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Hamann N, Bill E, Shokes JE, Scott RA, Bennati M, Hedderich R. The CCG-domain-containing subunit SdhE of succinate:quinone oxidoreductase from Sulfolobus solfataricus P2 binds a [4Fe-4S] cluster. J Biol Inorg Chem 2008; 14:457-70. [PMID: 19085017 PMCID: PMC2754724 DOI: 10.1007/s00775-008-0462-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 12/03/2008] [Indexed: 11/03/2022]
Abstract
In type E succinate:quinone reductase (SQR), subunit SdhE (formerly SdhC) is thought to function as monotopic membrane anchor of the enzyme. SdhE contains two copies of a cysteine-rich sequence motif (CX(n)CCGX(m)CXXC), designated as the CCG domain in the Pfam database and conserved in many proteins. On the basis of the spectroscopic characterization of heterologously produced SdhE from Sulfolobus tokodaii, the protein was proposed in a previous study to contain a labile [2Fe-2S] cluster ligated by cysteine residues of the CCG domains. Using UV/vis, electron paramagnetic resonance (EPR), (57)Fe electron-nuclear double resonance (ENDOR) and Mössbauer spectroscopies, we show that after an in vitro cluster reconstitution, SdhE from S. solfataricus P2 contains a [4Fe-4S] cluster in reduced (2+) and oxidized (3+) states. The reduced form of the [4Fe-4S](2+) cluster is diamagnetic. The individual iron sites of the reduced cluster are noticeably heterogeneous and show partial valence localization, which is particularly strong for one unique ferrous site. In contrast, the paramagnetic form of the cluster exhibits a characteristic rhombic EPR signal with g (zyx) = 2.015, 2.008, and 1.947. This EPR signal is reminiscent of a signal observed previously in intact SQR from S. tokodaii with g (zyx) = 2.016, 2.00, and 1.957. In addition, zinc K-edge X-ray absorption spectroscopy indicated the presence of an isolated zinc site with an S(3)(O/N)(1) coordination in reconstituted SdhE. Since cysteine residues in SdhE are restricted to the two CCG domains, we conclude that these domains provide the ligands to both the iron-sulfur cluster and the zinc site.
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Affiliation(s)
- Nils Hamann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043, Marburg, Germany
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Abstract
Forty years ago, ferredoxin (Fdx) was shown to activate fructose 1,6-bisphosphatase in illuminated chloroplast preparations, thereby laying the foundation for the field now known as "redox biology." Enzyme activation was later shown to require the ubiquitous protein thioredoxin (Trx), reduced photosynthetically by Fdx via an enzyme then unknown-ferredoxin:thioredoxin reductase (FTR). These proteins, Fdx, FTR, and Trx, constitute a regulatory ensemble, the "Fdx/Trx system." The redox biology field has since grown beyond all expectations and now embraces a spectrum of processes throughout biology. Progress has been notable with plants that possess not only the plastid Fdx/Trx system, but also the earlier known NADP/Trx system in the cytosol, endoplasmic reticulum, and mitochondria. Plants contain at least 19 types of Trx (nine in chloroplasts). In this review, we focus on the structure and mechanism of action of members of the photosynthetic Fdx/Trx system and on biochemical processes linked to Trx. We also summarize recent evidence that extends the Fdx/Trx system to amyloplasts-heterotrophic plastids functional in the biosynthesis of starch and other cell components. The review highlights the plant as a model system to uncover principles of redox biology that apply to other organisms.
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Affiliation(s)
- Peter Schürmann
- Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, Neuchâtel, Switzerland.
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Vita N, Hatchikian EC, Nouailler M, Dolla A, Pieulle L. Disulfide Bond-Dependent Mechanism of Protection against Oxidative Stress in Pyruvate-Ferredoxin Oxidoreductase of Anaerobic Desulfovibrio Bacteria. Biochemistry 2007; 47:957-64. [DOI: 10.1021/bi7014713] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Vita
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - E. Claude Hatchikian
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - Matthieu Nouailler
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - Alain Dolla
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
| | - Laetitia Pieulle
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Unité Propre de Recherche (UPR) 9036, Centre National de la Recherche Scientifique (CNRS) 31, Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France
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Hamann N, Mander GJ, Shokes JE, Scott RA, Bennati M, Hedderich R. A cysteine-rich CCG domain contains a novel [4Fe-4S] cluster binding motif as deduced from studies with subunit B of heterodisulfide reductase from Methanothermobacter marburgensis. Biochemistry 2007; 46:12875-85. [PMID: 17929940 PMCID: PMC3543786 DOI: 10.1021/bi700679u] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]3+ cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX31-39CCX35-36CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusual [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron-sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (gzyx = 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. 57Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with 57Fe hyperfine couplings very similar to that of CoM-HDR. CoM-33SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S3(O/N)1 geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn site.
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Affiliation(s)
| | | | | | | | | | - Reiner Hedderich
- To whom correspondence should be addressed. Phone: +49-(0)-6421-178-230. Fax: +49-(0)6421-178-299.
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Dai S, Friemann R, Glauser DA, Bourquin F, Manieri W, Schürmann P, Eklund H. Structural snapshots along the reaction pathway of ferredoxin–thioredoxin reductase. Nature 2007; 448:92-6. [PMID: 17611542 DOI: 10.1038/nature05937] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 05/17/2007] [Indexed: 11/08/2022]
Abstract
Oxygen-evolving photosynthetic organisms regulate carbon metabolism through a light-dependent redox signalling pathway. Electrons are shuttled from photosystem I by means of ferredoxin (Fdx) to ferredoxin-thioredoxin reductase (FTR), which catalyses the two-electron-reduction of chloroplast thioredoxins (Trxs). These modify target enzyme activities by reduction, regulating carbon flow. FTR is unique in its use of a [4Fe-4S] cluster and a proximal disulphide bridge in the conversion of a light signal into a thiol signal. We determined the structures of FTR in both its one- and its two-electron-reduced intermediate states and of four complexes in the pathway, including the ternary Fdx-FTR-Trx complex. Here we show that, in the first complex (Fdx-FTR) of the pathway, the Fdx [2Fe-2S] cluster is positioned suitably for electron transfer to the FTR [4Fe-4S] centre. After the transfer of one electron, an intermediate is formed in which one sulphur atom of the FTR active site is free to attack a disulphide bridge in Trx and the other sulphur atom forms a fifth ligand for an iron atom in the FTR [4Fe-4S] centre--a unique structure in biology. Fdx then delivers a second electron that cleaves the FTR-Trx heterodisulphide bond, which occurs in the Fdx-FTR-Trx complex. In this structure, the redox centres of the three proteins are aligned to maximize the efficiency of electron transfer from the Fdx [2Fe-2S] cluster to the active-site disulphide of Trxs. These results provide a structural framework for understanding the mechanism of disulphide reduction by an iron-sulphur enzyme and describe previously unknown interaction networks for both Fdx and Trx (refs 4-6).
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Affiliation(s)
- Shaodong Dai
- Howard Hughes Medical Institute, Integrated Department of Immunology, National Jewish Medical and Research Center & University of Colorado Health Sciences Center, 1400 Jackson Street, Denver, Colorado 80206, USA.
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Gao H, Carroll KS, Chen H, Bertozzi CR, Leary J. Noncovalent complexes of APS reductase from M. tuberculosis: delineating a mechanistic model using ESI-FTICR MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:167-78. [PMID: 17023175 PMCID: PMC2755055 DOI: 10.1016/j.jasms.2006.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 08/16/2006] [Accepted: 08/17/2006] [Indexed: 05/12/2023]
Abstract
ESI-FTICR MS was utilized to characterize a 4Fe-4S containing protein Mycobacterium tuberculosis APS reductase. This enzyme catalyzes the reduction of APS to sulfite and AMP with reducing equivalents from the protein cofactor, thioredoxin. Under nondenaturing conditions, a distribution of the apoprotein, a 2Fe-2S intermediate, and the 4Fe-4S holoprotein were observed. Accurate mass measurements indicated an oxidation state of +2 for the 4Fe-4S cluster, with no disulfide bond in the holoenzyme. Gas-phase stability of the 4Fe-4S cluster was investigated using both in-source and collision induced dissociation, which provided information regarding the relative gas-phase binding strength of iron towards protein ligands and inorganic sulfides. Noncovalent complexes of the holoprotein with several ligands, including APS, thioredoxin, and AMP, were also investigated. Calculated values of dissociation constants for the complexes indicate that AMP binds with a higher affinity to the enzyme intermediate than to the free enzyme. The implications of the binary and ternary complexes observed by gas-phase noncovalent interactions in the mechanism of APS reduction are discussed.
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Affiliation(s)
- Hong Gao
- Section of Molecular Cell Biology and Department of Chemistry, University of California, Davis, CA 95616
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kate S. Carroll
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Huiyi Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute
| | - Julie Leary
- Section of Molecular Cell Biology and Department of Chemistry, University of California, Davis, CA 95616
- Correspondence should be addressed to: Julie A. Leary, Genome Center, One Shields Ave, Davis, CA 95616, USA, , Tel: 530-754-4987, Fax: 530-754-8370
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Adedeji D, Hernandez H, Wiesner J, Köhler U, Jomaa H, Duin EC. Possible direct involvement of the active-site [4Fe-4S] cluster of the GcpE enzyme fromThermus thermophilusin the conversion of MEcPP. FEBS Lett 2006; 581:279-83. [PMID: 17214985 DOI: 10.1016/j.febslet.2006.12.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/05/2006] [Accepted: 12/08/2006] [Indexed: 11/15/2022]
Abstract
The GcpE enzyme converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) in the penultimate step of the DOXP pathway for isoprene biosynthesis. Purification of the enzyme under exclusion of air leads to a preparation that contains solely [4Fe-4S] clusters. Kinetic studies showed that in the presence of the artificial reductant dithionite and MEcPP a new transient iron-sulfur-based signal is detected in electron paramagnetic resonance (EPR) spectroscopy. Similarity of this EPR signal to that detected in ferredoxin:thioredoxin reductase indicates that during the reaction an intermediate is directly bound to the active-site cluster.
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Affiliation(s)
- Dolapo Adedeji
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849, USA
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