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Xin J, Min Z, Yu L, Yuan X, Liu A, Wu W, Zhang X, He H, Wu J, Xin Y, Blankenship RE, Tian C, Xu X. Cryo-EM structure of HQNO-bound alternative complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus. THE PLANT CELL 2024; 36:4212-4233. [PMID: 38299372 DOI: 10.1093/plcell/koae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/14/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the cytochrome bc1/b6f complexes but functionally replaces these enzymes in the photosynthetic and/or respiratory electron transport chains (ETCs) of many bacteria. However, the true compositions and architectures of ACIIIs remain unclear, as do their structural and functional relevance in mediating the ETCs. We here determined cryogenic electron microscopy structures of photosynthetic ACIII isolated from Chloroflexus aurantiacus (CaACIIIp), in apo-form and in complexed form bound to a menadiol analog 2-heptyl-4-hydroxyquinoline-N-oxide. Besides 6 canonical subunits (ActABCDEF), the structures revealed conformations of 2 previously unresolved subunits, ActG and I, which contributed to the complex stability. We also elucidated the structural basis of menaquinol oxidation and subsequent electron transfer along the [3Fe-4S]-6 hemes wire to its periplasmic electron acceptors, using electron paramagnetic resonance, spectroelectrochemistry, enzymatic analyses, and molecular dynamics simulations. A unique insertion loop in ActE was shown to function in determining the binding specificity of CaACIIIp for downstream electron acceptors. This study broadens our understanding of the structural diversity and molecular evolution of ACIIIs, enabling further investigation of the (mena)quinol oxidoreductases-evolved coupling mechanism in bacterial energy conservation.
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Affiliation(s)
- Jiyu Xin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhenzhen Min
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Xinyi Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Aokun Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Bioanalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Wenping Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
| | - Xin Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Huimin He
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jingyi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yueyong Xin
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Robert E Blankenship
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Bioanalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xiaoling Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Zhejiang Key Laboratory of Medical Epigenetics, Hangzhou Normal University, Hangzhou 311121, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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Duarte AG, Barbosa ACC, Ferreira D, Manteigas G, Domingos RM, Pereira IAC. Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148416. [PMID: 33753023 DOI: 10.1016/j.bbabio.2021.148416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
| | - Ana C C Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Gonçalo Manteigas
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Renato M Domingos
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
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3
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Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli. J Mol Biol 2021; 433:166944. [PMID: 33741411 DOI: 10.1016/j.jmb.2021.166944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Genome-wide protein-protein interaction (PPI) determination remains a significant unsolved problem in structural biology. The difficulty is twofold since high-throughput experiments (HTEs) have often a relatively high false-positive rate in assigning PPIs, and PPI quaternary structures are more difficult to solve than tertiary structures using traditional structural biology techniques. We proposed a uniform pipeline, Threpp, to address both problems. Starting from a pair of monomer sequences, Threpp first threads both sequences through a complex structure library, where the alignment score is combined with HTE data using a naïve Bayesian classifier model to predict the likelihood of two chains to interact with each other. Next, quaternary complex structures of the identified PPIs are constructed by reassembling monomeric alignments with dimeric threading frameworks through interface-specific structural alignments. The pipeline was applied to the Escherichia coli genome and created 35,125 confident PPIs which is 4.5-fold higher than HTE alone. Graphic analyses of the PPI networks show a scale-free cluster size distribution, consistent with previous studies, which was found critical to the robustness of genome evolution and the centrality of functionally important proteins that are essential to E. coli survival. Furthermore, complex structure models were constructed for all predicted E. coli PPIs based on the quaternary threading alignments, where 6771 of them were found to have a high confidence score that corresponds to the correct fold of the complexes with a TM-score >0.5, and 39 showed a close consistency with the later released experimental structures with an average TM-score = 0.73. These results demonstrated the significant usefulness of threading-based homologous modeling in both genome-wide PPI network detection and complex structural construction.
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Affiliation(s)
- Weikang Gong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Aysam Guerler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elisa Warner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chunhua Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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The structure of hydrogenase-2 from Escherichia coli: implications for H 2-driven proton pumping. Biochem J 2018; 475:1353-1370. [PMID: 29555844 PMCID: PMC5902676 DOI: 10.1042/bcj20180053] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 01/19/2023]
Abstract
Under anaerobic conditions, Escherichia coli is able to metabolize molecular hydrogen via the action of several [NiFe]-hydrogenase enzymes. Hydrogenase-2, which is typically present in cells at low levels during anaerobic respiration, is a periplasmic-facing membrane-bound complex that functions as a proton pump to convert energy from hydrogen (H2) oxidation into a proton gradient; consequently, its structure is of great interest. Empirically, the complex consists of a tightly bound core catalytic module, comprising large (HybC) and small (HybO) subunits, which is attached to an Fe–S protein (HybA) and an integral membrane protein (HybB). To date, efforts to gain a more detailed picture have been thwarted by low native expression levels of Hydrogenase-2 and the labile interaction between HybOC and HybA/HybB subunits. In the present paper, we describe a new overexpression system that has facilitated the determination of high-resolution crystal structures of HybOC and, hence, a prediction of the quaternary structure of the HybOCAB complex.
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Chan CS, Turner RJ. Biogenesis of Escherichia coli DMSO Reductase: A Network of Participants for Protein Folding and Complex Enzyme Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:215-34. [PMID: 26621470 DOI: 10.1007/978-3-319-23603-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Protein folding and structure have been of interest since the dawn of protein chemistry. Following translation from the ribosome, a protein must go through various steps to become a functional member of the cellular society. Every protein has a unique function in the cell and is classified on this basis. Proteins that are involved in cellular respiration are the bioenergetic workhorses of the cell. Bacteria are resilient organisms that can survive in diverse environments by fine tuning these workhorses. One class of proteins that allow survival under anoxic conditions are anaerobic respiratory oxidoreductases, which utilize many different compounds other than oxygen as its final electron acceptor. Dimethyl sulfoxide (DMSO) is one such compound. Respiration using DMSO as a final electron acceptor is performed by DMSO reductase, converting it to dimethyl sulfide in the process. Microbial respiration using DMSO is reviewed in detail by McCrindle et al. (Adv Microb Physiol 50:147-198, 2005). In this chapter, we discuss the biogenesis of DMSO reductase as an example of the participant network for complex iron-sulfur molybdoenzyme maturation pathways.
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Affiliation(s)
- Catherine S Chan
- Department of Biological Sciences, University of Calgary, BI156 Biological Sciences Bldg, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, BI156 Biological Sciences Bldg, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.
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Leimkühler S, Iobbi-Nivol C. Bacterial molybdoenzymes: old enzymes for new purposes. FEMS Microbiol Rev 2015; 40:1-18. [PMID: 26468212 DOI: 10.1093/femsre/fuv043] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2015] [Indexed: 02/06/2023] Open
Abstract
Molybdoenzymes are widespread in eukaryotic and prokaryotic organisms where they play crucial functions in detoxification reactions in the metabolism of humans and bacteria, in nitrate assimilation in plants and in anaerobic respiration in bacteria. To be fully active, these enzymes require complex molybdenum-containing cofactors, which are inserted into the apoenzymes after folding. For almost all the bacterial molybdoenzymes, molybdenum cofactor insertion requires the involvement of specific chaperones. In this review, an overview on the molybdenum cofactor biosynthetic pathway is given together with the role of specific chaperones dedicated for molybdenum cofactor insertion and maturation. Many bacteria are involved in geochemical cycles on earth and therefore have an environmental impact. The roles of molybdoenzymes in bioremediation and for environmental applications are presented.
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Affiliation(s)
- Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
| | - Chantal Iobbi-Nivol
- The Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS, Aix Marseille Université, 13402 Marseille cedex 20, France
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Abstract
Escherichia coli is a versatile facultative anaerobe that can respire on a number of terminal electron acceptors, including oxygen, fumarate, nitrate, and S- and N-oxides. Anaerobic respiration using S- and N-oxides is accomplished by enzymatic reduction of these substrates by dimethyl sulfoxide reductase (DmsABC) and trimethylamine N-oxide reductase (TorCA). Both DmsABC and TorCA are membrane-associated redox enzymes that couple the oxidation of menaquinol to the reduction of S- and N-oxides in the periplasm. DmsABC is membrane bound and is composed of a membrane-extrinsic dimer with a 90.4-kDa catalytic subunit (DmsA) and a 23.1-kDa electron transfer subunit (DmsB). These subunits face the periplasm and are held to the membrane by a 30.8-kDa membrane anchor subunit (DmsC). The enzyme provides the scaffold for an electron transfer relay composed of a quinol binding site, five [4Fe-4S] clusters, and a molybdo-bis(molybdopterin guanine dinucleotide) (present nomenclature: Mo-bis-pyranopterin) (Mo-bisMGD) cofactor. TorCA is composed of a soluble periplasmic subunit (TorA, 92.5 kDa) containing a Mo-bis-MGD. TorA is coupled to the quinone pool via a pentaheme c subunit (TorC, 40.4 kDa) in the membrane. Both DmsABC and TorCA require system-specific chaperones (DmsD or TorD) for assembly, cofactor insertion, and/or targeting to the Tat translocon. In this chapter, we discuss the complex regulation of the dmsABC and torCAD operons, the poorly understood paralogues, and what is known about the assembly and translocation to the periplasmic space by the Tat translocon.
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Yokoyama K, Leimkühler S. The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1335-49. [PMID: 25268953 DOI: 10.1016/j.bbamcr.2014.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) has been intensively studied, in addition to its insertion into molybdoenzymes. In particular, a link between the assembly of molybdoenzymes and the biosynthesis of FeS clusters has been identified in the recent years: 1) the synthesis of the first intermediate in Moco biosynthesis requires an FeS-cluster containing protein, 2) the sulfurtransferase for the dithiolene group in Moco is also involved in the synthesis of FeS clusters, thiamin and thiolated tRNAs, 3) the addition of a sulfido-ligand to the molybdenum atom in the active site additionally involves a sulfurtransferase, and 4) most molybdoenzymes in bacteria require FeS clusters as redox active cofactors. In this review we will focus on the biosynthesis of the molybdenum cofactor in bacteria, its modification and insertion into molybdoenzymes, with an emphasis to its link to FeS cluster biosynthesis and sulfur transfer.
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Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
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Cheng VWT, Tran QM, Boroumand N, Rothery RA, Maklashina E, Cecchini G, Weiner JH. A conserved lysine residue controls iron-sulfur cluster redox chemistry in Escherichia coli fumarate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1141-7. [PMID: 23711795 DOI: 10.1016/j.bbabio.2013.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 11/16/2022]
Abstract
The Escherichia coli respiratory complex II paralogs succinate dehydrogenase (SdhCDAB) and fumarate reductase (FrdABCD) catalyze interconversion of succinate and fumarate coupled to quinone reduction or oxidation, respectively. Based on structural comparison of the two enzymes, equivalent residues at the interface between the highly homologous soluble domains and the divergent membrane anchor domains were targeted for study. This included the residue pair SdhB-R205 and FrdB-S203, as well as the conserved SdhB-K230 and FrdB-K228 pair. The close proximity of these residues to the [3Fe-4S] cluster and the quinone binding pocket provided an excellent opportunity to investigate factors controlling the reduction potential of the [3Fe-4S] cluster, the directionality of electron transfer and catalysis, and the architecture and chemistry of the quinone binding sites. Our results indicate that both SdhB-R205 and SdhB-K230 play important roles in fine tuning the reduction potential of both the [3Fe-4S] cluster and the heme. In FrdABCD, mutation of FrdB-S203 did not alter the reduction potential of the [3Fe-4S] cluster, but removal of the basic residue at FrdB-K228 caused a significant downward shift (>100mV) in potential. The latter residue is also indispensable for quinone binding and enzyme activity. The differences observed for the FrdB-K228 and Sdh-K230 variants can be attributed to the different locations of the quinone binding site in the two paralogs. Although this residue is absolutely conserved, they have diverged to achieve different functions in Frd and Sdh.
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Affiliation(s)
- Victor W T Cheng
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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EPR characterization of the new Qrc complex from sulfate reducing bacteria and its ability to form a supercomplex with hydrogenase and TpIc
3. FEBS Lett 2011; 585:2177-81. [DOI: 10.1016/j.febslet.2011.05.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 05/24/2011] [Indexed: 11/23/2022]
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Tang H, Rothery RA, Voss JE, Weiner JH. Correct assembly of iron-sulfur cluster FS0 into Escherichia coli dimethyl sulfoxide reductase (DmsABC) is a prerequisite for molybdenum cofactor insertion. J Biol Chem 2011; 286:15147-54. [PMID: 21357619 DOI: 10.1074/jbc.m110.213306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The FS0 [4Fe-4S] cluster of the catalytic subunit (DmsA) of Escherichia coli dimethyl sulfoxide reductase (DmsABC) plays a key role in the electron transfer relay. We have now established an additional role for the cluster in directing molybdenum cofactor assembly during enzyme maturation. EPR spectroscopy indicates that FS0 has a high spin ground state (S = 3/2) in its reduced form, resulting in an EPR spectrum with a peak at g ∼ 5.0. The cluster is predicted to be in close proximity to the molybdo-bis(pyranopterin guanine dinucleotide) (Mo-bisPGD) cofactor, which provides the site of dimethyl sulfoxide reduction. Comparison with nitrate reductase A (NarGHI) indicates that a sequence of residues ((18)CTVNC(22)) plays a role in both FS0 and Mo-bisPGD coordination. A DmsA(ΔN21) mutant prevented Mo-bisPGD binding and resulted in a degenerate [3Fe-4S] cluster form of FS0 being assembled. DmsA belongs to the Type II subclass of Mo-bisPGD-containing catalytic subunits that is distinguished from the Type I subclass by having three rather than two residues between the first two Cys residues coordinating FS0 and a conserved Arg residue rather than a Lys residue following the fourth cluster coordinating Cys. We introduced a Type I Cys group into DmsA in two stages. We changed its sequence from (18)C(A)TVNC(B)GSRC(C)P(27) to (18)C(A)TYC(B)GVGC(C)G(26) (similar to that of formate dehydrogenase (FdnG)) and demonstrated that this eliminated both Mo-bisPGD binding and EPR-detectable FS0. We then combined this change with a DmsA(R61K) mutation and demonstrated that this additional change partially rescued Mo-bisPGD insertion.
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Affiliation(s)
- Huipo Tang
- Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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The alternative complex III of Rhodothermus marinus and its structural and functional association with caa3 oxygen reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1477-82. [DOI: 10.1016/j.bbabio.2010.02.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 11/21/2022]
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Venceslau SS, Lino RR, Pereira IAC. The Qrc membrane complex, related to the alternative complex III, is a menaquinone reductase involved in sulfate respiration. J Biol Chem 2010; 285:22774-83. [PMID: 20498375 PMCID: PMC2906268 DOI: 10.1074/jbc.m110.124305] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 05/07/2010] [Indexed: 11/06/2022] Open
Abstract
Biological sulfate reduction is a process with high environmental significance due to its major contribution to the carbon and sulfur cycles in anaerobic environments. However, the respiratory chain of sulfate-reducing bacteria is still poorly understood. Here we describe a new respiratory complex that was isolated as a major protein present in the membranes of Desulfovibrio vulgaris Hildenborough. The complex, which was named Qrc, is the first representative of a new family of redox complexes. It has three subunits related to the complex iron-sulfur molybdoenzyme family and a multiheme cytochrome c and binds six hemes c, one [3Fe-4S](+1/0) cluster, and several interacting [4Fe-4S](2+/1+) clusters but no molybdenum. Qrc is related to the alternative complex III, and we show that it has the reverse catalytic activity, acting as a Type I cytochrome c(3):menaquinone oxidoreductase. The qrc genes are found in the genomes of deltaproteobacterial sulfate reducers, which have periplasmic hydrogenases and formate dehydrogenases that lack a membrane subunit for reduction of the quinone pool. In these organisms, Qrc acts as a menaquinone reductase with electrons from periplasmic hydrogen or formate oxidation. Binding of a menaquinone analogue affects the EPR spectrum of the [3Fe-4S](+1/0) cluster, indicating the presence of a quinone-binding site close to the periplasmic subunits. Qrc is the first respiratory complex from sulfate reducers to have its physiological function clearly elucidated.
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Affiliation(s)
- Sofia S. Venceslau
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Rita R. Lino
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Ines A. C. Pereira
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
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Tsutsumi M, Tsujimura S, Shirai O, Kano K. Stopped flow kinetic studies on reductive half-reaction of histamine dehydrogenase from Nocardioides simplex with histamine. J Biochem 2010; 148:47-54. [PMID: 20305273 DOI: 10.1093/jb/mvq032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Histamine dehydrogenase from Nocardioides simplex (HmDH) which catalyzes the oxidative deamination of histamine is an iron-sulphur-containing flavoprotein. For our further understanding on the intramolecular electron transfer process, the reductive half reaction of HmDH with histamine has been studied by stopped flow spectrophotometry at pH 7.5 and 10. The reaction at pH 7.5 is found to be analysed on a kinetic model composed of three sequential first-order reactions. The first fast phase, of which the rate constant shows a hyperbolic dependence on the histamine concentration, is assigned to a direct two-electron reduction of the oxidized flavin (CFMN(O)) by histamine with no involvement of the semiquinone form of the flavin (CFMN(S)). The second moderate process is the substrate-independent intramolecular single-electron transfer from the reduced flavin to the oxidized iron-sulphur cluster. The third slow process is considered to reflect the second binding of histamine to CFMN(S), which is responsible for the substrate inhibition. At pH 10, the reaction is analysed with one pseudo-first-order reaction phase which is substrate-dependent two-electron reduction of CFMN(O) coupled with the subsequent fast intersubunit single-electron transfer. The UV-vis spectroscopy of HmDH suggests the deprotonation of Tyr residues, which seems to cause the switching of the electron transfer property.
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Affiliation(s)
- Maiko Tsutsumi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Rothery RA, Workun GJ, Weiner JH. The prokaryotic complex iron–sulfur molybdoenzyme family. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1897-929. [DOI: 10.1016/j.bbamem.2007.09.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2007] [Revised: 08/17/2007] [Accepted: 09/02/2007] [Indexed: 10/22/2022]
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Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, Iwata S. Molecular mechanism of energy conservation in polysulfide respiration. Nat Struct Mol Biol 2008; 15:730-7. [PMID: 18536726 DOI: 10.1038/nsmb.1434] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Accepted: 04/23/2008] [Indexed: 11/09/2022]
Abstract
Bacterial polysulfide reductase (PsrABC) is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. We determined the structure of polysulfide reductase from Thermus thermophilus at 2.4-A resolution, revealing how the PsrA subunit recognizes and reduces its unique polyanionic substrate. The integral membrane subunit PsrC was characterized using the natural substrate menaquinone-7 and inhibitors, providing a comprehensive representation of a quinone binding site and revealing the presence of a water-filled cavity connecting the quinone binding site on the periplasmic side to the cytoplasm. These results suggest that polysulfide reductase could be a key energy-conserving enzyme of the T. thermophilus respiratory chain, using polysulfide as the terminal electron acceptor and pumping protons across the membrane via a previously unknown mechanism.
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Affiliation(s)
- Mika Jormakka
- Department of Biophysics, University of New South Wales, Barker Street, Sydney, New South Wales 2052, Australia.
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Dridge E, Watts C, Jepson B, Line K, Santini J, Richardson D, Butler C. Investigation of the redox centres of periplasmic selenate reductase from Thauera selenatis by EPR spectroscopy. Biochem J 2007; 408:19-28. [PMID: 17688424 PMCID: PMC2049085 DOI: 10.1042/bj20070669] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Periplasmic SER (selenate reductase) from Thauera selenatis is classified as a member of the Tat (twin-arginine translocase)-translocated (Type II) molybdoenzymes and comprises three subunits each containing redox cofactors. Variable-temperature X-band EPR spectra of the purified SER complex showed features attributable to centres [3Fe-4S]1+, [4Fe-4S]1+, Mo(V) and haem-b. EPR-monitored redox-potentiometric titration of the SerABC complex (SerA-SerB-SerC, a hetero-trimetric complex of alphabetagamma subunits) revealed that the [3Fe-4S] cluster (FS4, iron-sulfur cluster 4) titrated as n=1 Nernstian component with a midpoint redox potential (E(m)) of +118+/-10 mV for the [3Fe-4S]1+/0 couple. A [4Fe-4S]1+ cluster EPR signal developed over a range of potentials between 300 and -200 mV and was best fitted to two sequential Nernstian n=1 curves with midpoint redox potentials of +183+/-10 mV (FS1) and -51+/-10 mV (FS3) for the two [4Fe-4S]1+/2+ cluster couples. Upon further reduction, the observed signal intensity of the [4Fe-4S]1+ cluster decreases. This change in intensity can again be fitted to an n=1 Nernstian component with a midpoint potential (E(m)) of about -356 mV (FS2). It is considered likely that, at low redox potential (E(m) less than -300 mV), the remaining oxidized cluster is reduced (spin S=1/2) and strongly spin-couples to a neighbouring [4Fe-4S]1+ cluster rendering both centres EPR-silent. The involvement of both [3Fe-4S] and [4Fe-4S] clusters in electron transfer to the active site of the periplasmic SER was demonstrated by the re-oxidation of the clusters under anaerobic selenate turnover conditions. Attempts to detect a high-spin [4Fe-4S] cluster (FS0) in SerA at low temperature (5 K) and high power (100 mW) were unsuccessful. The Mo(V) EPR recorded at 60 K, in samples poised at pH 6.0, displays principal g values of g3 approximately 1.999, g2 approximately 1.996 and g1 approximately 1.965 (g(av) 1.9867). The dominant features at g2 and g3 are not split, but hyperfine splitting is observed in the g1 region of the spectrum and can be best simulated as arising from a single proton with a coupling constant of A1 (1H)=1.014 mT. The presence of the haem-b moiety in SerC was demonstrated by the detection of a signal at g approximately 3.33 and is consistent with haem co-ordinated by methionine and lysine axial ligands. The combined evidence from EPR analysis and sequence alignments supports the assignment of the periplasmic SER as a member of the Type II molybdoenzymes and provides the first spectro-potentiometric insight into an enzyme that catalyses a key reductive reaction in the biogeochemical selenium cycle.
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Affiliation(s)
- Elizabeth J. Dridge
- *School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
- †Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, U.K
| | - Carys A. Watts
- †Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, U.K
| | - Brian J. N. Jepson
- ‡School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Kirsty Line
- *School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
| | - Joanne M. Santini
- §Department of Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - David J. Richardson
- ‡School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Clive S. Butler
- *School of Biosciences, Centre for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
- To whom correspondence should be addressed (email )
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Oloo EO, Kandt C, O'Mara ML, Tieleman DP. Computer simulations of ABC transporter componentsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease. Biochem Cell Biol 2006; 84:900-11. [PMID: 17215877 DOI: 10.1139/o06-182] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Current computer simulation techniques provide robust tools for studying the detailed structure and functional dynamics of proteins, as well as their interaction with each other and with other biomolecules. In this minireview, we provide an illustration of recent progress and future challenges in computer modeling by discussing computational studies of ATP-binding cassette (ABC) transporters. ABC transporters have multiple components that work in a well coordinated fashion to enable active transport across membranes. The mechanism by which members of this superfamily execute transport remains largely unknown. Molecular dynamics simulations initiated from high-resolution crystal structures of several ABC transporters have proven to be useful in the investigation of the nature of conformational coupling events that may drive transport. In addition, fruitful efforts have been made to predict unknown structures of medically relevant ABC transporters, such as P-glycoprotein, using homology-based computational methods. The various techniques described here are also applicable to gaining an atomically detailed understanding of the functional mechanisms of proteins in general.
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Affiliation(s)
- Eliud O Oloo
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
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Cheng VWT, Ma E, Zhao Z, Rothery RA, Weiner JH. The Iron-Sulfur Clusters in Escherichia coli Succinate Dehydrogenase Direct Electron Flow. J Biol Chem 2006; 281:27662-8. [PMID: 16864590 DOI: 10.1074/jbc.m604900200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Succinate dehydrogenase is an indispensable enzyme involved in the Krebs cycle as well as energy coupling in the mitochondria and certain prokaryotes. During catalysis, succinate oxidation is coupled to ubiquinone reduction by an electron transfer relay comprising a flavin adenine dinucleotide cofactor, three iron-sulfur clusters, and possibly a heme b556. At the heart of the electron transport chain is a [4Fe-4S] cluster with a low midpoint potential that acts as an energy barrier against electron transfer. Hydrophobic residues around the [4Fe-4S] cluster were mutated to determine their effects on the midpoint potential of the cluster as well as electron transfer rates. SdhB-I150E and SdhB-I150H mutants lowered the midpoint potential of this cluster; surprisingly, the His variant had a lower midpoint potential than the Glu mutant. Mutation of SdhB-Leu-220 to Ser did not alter the redox behavior of the cluster but instead lowered the midpoint potential of the [3Fe-4S] cluster. To correlate the midpoint potential changes in these mutants to enzyme function, we monitored aerobic growth in succinate minimal medium, anaerobic growth in glycerol-fumarate minimal medium, non-physiological and physiological enzyme activities, and heme reduction. It was discovered that a decrease in midpoint potential of either the [4Fe-4S] cluster or the [3Fe-4S] cluster is accompanied by a decrease in the rate of enzyme turnover. We hypothesize that this occurs because the midpoint potentials of the [Fe-S] clusters in the native enzyme are poised such that direction of electron transfer from succinate to ubiquinone is favored.
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Affiliation(s)
- Victor W T Cheng
- Membrane Protein Research Group, Department of Biochemistry, University of Alberta, 473 Medical Sciences Building, Edmonton, Alberta T6G 2H7, Canada
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Giastas P, Pinotsis N, Efthymiou G, Wilmanns M, Kyritsis P, Moulis JM, Mavridis IM. The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J Biol Inorg Chem 2006; 11:445-58. [PMID: 16596388 DOI: 10.1007/s00775-006-0094-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
The structure of the 2[4Fe-4S] ferredoxin (PaFd) from Pseudomonas aeruginosa, which belongs to the Allochromatium vinosum (Alvin) subfamily, has been determined by X-ray crystallography at 1.32-A resolution, which is the highest up to now for a member of this subfamily of Fds. The main structural features of PaFd are similar to those of AlvinFd. However, the significantly higher resolution of the PaFd structure makes possible a reliable comparison with available high-resolution structures of [4Fe-4S]-containing Fds, in an effort to rationalize the unusual electrochemical properties of Alvin-like Fds. Three major factors contributing to the reduction potential values of [4Fe-4S]2+/+ clusters of Fds, namely, the surface accessibility of the clusters, the N-H...S hydrogen-bonding network, and the volume of the cavities hosting the clusters, are extensively discussed. The volume of the cavities is introduced in the present work for the first time, and can in part explain the very negative potential of cluster I of Alvin-like Fds.
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Affiliation(s)
- Petros Giastas
- Institute of Physical Chemistry, NCSR Demokritos, Aghia Paraskevi, 15310, PO Box 60228, Athens, Greece
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