1
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Blomberg MRA, Ädelroth P. Reduction of molecular oxygen in flavodiiron proteins - Catalytic mechanism and comparison to heme-copper oxidases. J Inorg Biochem 2024; 255:112534. [PMID: 38552360 DOI: 10.1016/j.jinorgbio.2024.112534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
The family of flavodiiron proteins (FDPs) plays an important role in the scavenging and detoxification of both molecular oxygen and nitric oxide. Using electrons from a flavin mononucleotide cofactor molecular oxygen is reduced to water and nitric oxide is reduced to nitrous oxide and water. While the mechanism for NO reduction in FDPs has been studied extensively, there is very little information available about O2 reduction. Here we use hybrid density functional theory (DFT) to study the mechanism for O2 reduction in FDPs. An important finding is that a proton coupled reduction is needed after the O2 molecule has bound to the diferrous diiron active site and before the OO bond can be cleaved. This is in contrast to the mechanism for NO reduction, where both NN bond formation and NO bond cleavage occurs from the same starting structure without any further reduction, according to both experimental and computational results. This computational result for the O2 reduction mechanism should be possible to evaluate experimentally. Another difference between the two substrates is that the actual OO bond cleavage barrier is low, and not involved in rate-limiting the reduction process, while the barrier connected with bond cleavage/formation in the NO reduction process is of similar height as the rate-limiting steps. We suggest that these results may be part of the explanation for the generally higher activity for O2 reduction as compared to NO reduction in most FDPs. Comparisons are also made to the O2 reduction reaction in the family of heme‑copper oxidases.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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2
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Martins MC, Alves CM, Teixeira M, Folgosa F. The flavodiiron protein from Syntrophomonas wolfei has five domains and acts both as an NADH:O 2 or an NADH:H 2 O 2 oxidoreductase. FEBS J 2024; 291:1275-1294. [PMID: 38129989 DOI: 10.1111/febs.17040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/10/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
Flavodiiron proteins (FDPs) are a family of enzymes with a significant role in O2 /H2 O2 and/or NO detoxification through the reduction of these species to H2 O or N2 O, respectively. All FDPs contain a minimal catalytic unit of two identical subunits, each one having a metallo-β-lactamase-like domain harboring the catalytic diiron site, and a flavodoxin-like domain. However, more complex and diverse arrangements in terms of domains are found in this family, of which the class H enzymes are among the most complex. One of such FDPs is encoded in the genome of the anaerobic bacterium Syntrophomonas wolfei subsp. wolfei str. Goettingen G311. Besides the core domains, this protein is predicted to have three additional ones after the flavodoxin core domain: two short-chain rubredoxins and a NAD(P)H:rubredoxin oxidoreductase-like domain. This enzyme, FDP_H, was produced and characterized and the presence of the predicted cofactors was investigated by a set of biochemical and spectroscopic methodologies. Syntrophomonas wolfei FDP_H exhibited a remarkable O2 reduction activity with a kcat = 52.0 ± 1.2 s-1 and a negligible NO reduction activity (~ 100 times lower than with O2 ), with NADH as an electron donor, that is, it is an oxygen-selective FDP. In addition, this enzyme showed the highest turnover value for H2 O2 reduction (kcat = 19.1 ± 2.2 s-1 ) ever observed among FDPs. Kinetic studies of site-directed mutants of iron-binding cysteines at the two rubredoxin domains demonstrated the essential role of these centers since their absence leads to a significant decrease or even abolishment of O2 and H2 O2 reduction activities.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Catarina M Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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3
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Blomberg MRA, Ädelroth P. Reduction of Nitric Oxide to Nitrous Oxide in Flavodiiron Proteins: Catalytic Mechanism and Plausible Intermediates. ACS Catal 2023. [DOI: 10.1021/acscatal.2c04932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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4
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White CJ, Lengel MO, Bracken AJ, Kampf JW, Speelman AL, Alp EE, Hu MY, Zhao J, Lehnert N. Distortion of the [FeNO] 2 Core in Flavodiiron Nitric Oxide Reductase Models Inhibits N-N Bond Formation and Promotes Formation of Unusual Dinitrosyl Iron Complexes: Implications for Catalysis and Reactivity. J Am Chem Soc 2022; 144:3804-3820. [PMID: 35212523 DOI: 10.1021/jacs.1c10388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flavodiiron nitric oxide reductases (FNORs) carry out the reduction of nitric oxide (NO) to nitrous oxide (N2O), allowing infectious pathogens to mitigate toxic levels of NO generated in the human immune response. We previously reported the model complex [Fe2(BPMP)(OPr)(NO)2](OTf)2 (1, OPr- = propionate) that contains two coplanar NO ligands and that is capable of quantitative NO reduction to N2O [White et al. J. Am. Chem. Soc. 2018, 140, 2562-2574]. Here we investigate, for the first time, how a distortion of the active site affects the ability of the diiron core to mediate N2O formation. For this purpose, we prepared several analogues of 1 that contain two monodentate ligands in place of the bridging carboxylate, [Fe2(BPMP)(X)2(NO)2]3+/1+ (2-X; X = triflate, 1-methylimidazole, or methanol). Structural data of 2-X show that without the bridging carboxylate, the diiron core expands, leading to elongated (O)N-N(O) distances (from 2.80 Å in 1 to 3.00-3.96 Å in 2-X) and distorted (O)N-Fe-Fe-N(O) dihedral angles (from coplanarity (5.9°) in 1 to 52.9-85.1° in 2-X). Whereas 1 produces quantitative amounts of N2O upon one-electron reduction, N2O production is substantially impeded in 2-X, to an initial 5-10% N2O yield. The main products after reduction are unprecedented hs-FeII/{Fe(NO)2}9/10 dinitrosyl iron complexes (DNICs). Even though mononuclear DNICs are stable and do not show N-N coupling (since it is a spin-forbidden process), the hs-FeII/{Fe(NO)2}9/10 DNICs obtained from 2-X show unexpected reactivity and produce up to quantitative N2O yields after 2 h. The implications of these results for the active site structure of FNORs are discussed.
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Affiliation(s)
- Corey J White
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Michael O Lengel
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Abigail J Bracken
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jeff W Kampf
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Amy L Speelman
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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5
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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6
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Pal N, Jana M, Majumdar A. Reduction of NO by diiron complexes in relation to flavodiiron nitric oxide reductases. Chem Commun (Camb) 2021; 57:8682-8698. [PMID: 34373873 DOI: 10.1039/d1cc03149j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reduction of nitric oxide (NO) to nitrous oxide (N2O) is associated with immense biological and health implications. Flavodiiron nitric oxide reductases (FNORs) are diiron containing enzymes that catalyze the two electron reduction of NO to N2O and help certain pathogenic bacteria to survive under "nitrosative stress" in anaerobic growth conditions. Consequently, invading bacteria can proliferate inside the body of mammals by bypassing the immune defense mechanism involving NO and may thus lead to harmful infections. Various mechanisms, namely the direct reduction, semireduction, superreduction and hyponitrite mechanisms, have been proposed over time for catalytic NO reduction by FNORs. Model studies in relation to the diiron active site of FNORs have immensely helped to replicate the minimal structure-reactivity relationship and to understand the mechanism of NO reduction. A brief overview of the FNOR activity and the proposed reaction mechanisms followed by a systematic description and detailed analysis of the model studies is presented, which describes the development in the area of NO reduction by diiron complexes and its implications. A great deal of successful modeling chemistry as well as the shortcomings related to the synthesis and reactivity studies is discussed in detail. Finally, future prospects in this particular area of research are proposed, which in due course may bring more clarity in the understanding of this important redox reaction.
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Affiliation(s)
- Nabhendu Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India.
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7
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Rubredoxin from the green sulfur bacterium Chlorobaculum tepidum donates a redox equivalent to the flavodiiron protein in an NAD(P)H dependent manner via ferredoxin-NAD(P) + oxidoreductase. Arch Microbiol 2020; 203:799-808. [PMID: 33051772 DOI: 10.1007/s00203-020-02079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
Abstract
The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)+ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.
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8
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Abstract
Although the gastrointestinal tract is regarded as mainly anoxic, low O2 tension is present in the gut and tends to increase following antibiotic-induced disruption of the host microbiota. Two decreasing O2 gradients are observed, a longitudinal one from the small to the large intestine and a second one from the intestinal epithelium toward the colon lumen. Thus, O2 concentration fluctuations within the gastrointestinal tract are a challenge for anaerobic bacteria such as C. difficile. This enteropathogen has developed efficient strategies to detoxify O2. In this work, we identified reverse rubrerythrins and flavodiiron proteins as key actors for O2 tolerance in C. difficile. These enzymes are responsible for the reduction of O2 protecting C. difficile vegetative cells from associated damages. Original and complex detoxification pathways involving O2-reductases are crucial in the ability of C. difficile to tolerate O2 and survive to O2 concentrations encountered in the gastrointestinal tract. Clostridioides difficile is a major cause of diarrhea associated with antibiotherapy. After germination of C. difficile spores in the small intestine, vegetative cells are exposed to low oxygen (O2) tensions. While considered strictly anaerobic, C. difficile is able to grow in nonstrict anaerobic conditions (1 to 3% O2) and tolerates brief air exposure indicating that this bacterium harbors an arsenal of proteins involved in O2 detoxification and/or protection. Tolerance of C. difficile to low O2 tensions requires the presence of the alternative sigma factor, σB, involved in the general stress response. Among the genes positively controlled by σB, four encode proteins likely involved in O2 detoxification: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). As previously observed for FdpF, we showed that both purified revRbr1 and revRbr2 harbor NADH-linked O2- and H2O2-reductase activities in vitro, while purified FdpA mainly acts as an O2-reductase. The growth of a fdpA mutant is affected at 0.4% O2, while inactivation of both revRbrs leads to a growth defect above 0.1% O2. O2-reductase activities of these different proteins are additive since the quadruple mutant displays a stronger phenotype when exposed to low O2 tensions compared to the triple mutants. Our results demonstrate a key role for revRbrs, FdpF, and FdpA proteins in the ability of C. difficile to grow in the presence of physiological O2 tensions such as those encountered in the colon.
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9
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Biswas S, Kurtz DM, Montoya SR, Hendrich MP, Bominaar EL. The Catalytic Role of a Conserved Tyrosine in Nitric Oxide-Reducing Non-heme Diiron Enzymes. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Samuel R. Montoya
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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10
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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11
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Jana M, White CJ, Pal N, Demeshko S, Cordes (née Kupper) C, Meyer F, Lehnert N, Majumdar A. Functional Models for the Mono- and Dinitrosyl Intermediates of FNORs: Semireduction versus Superreduction of NO. J Am Chem Soc 2020; 142:6600-6616. [DOI: 10.1021/jacs.9b13795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Manish Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Corey J. White
- Department of Chemistry, The University of Michigan, 930 N. University Avenue, Ann Arbor 48109, Michigan, United States
| | - Nabhendu Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Serhiy Demeshko
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, Göttingen 37077, Germany
| | | | - Franc Meyer
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, Göttingen 37077, Germany
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, 930 N. University Avenue, Ann Arbor 48109, Michigan, United States
| | - Amit Majumdar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
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12
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Engilberge S, Wagner T, Carpentier P, Girard E, Shima S. Krypton-derivatization highlights O 2-channeling in a four-electron reducing oxidase. Chem Commun (Camb) 2020; 56:10863-10866. [DOI: 10.1039/d0cc04557h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kr-derivatization and X-ray structures indicated O2-channel and gating-loop that prevent side-reaction in reduction of O2 to water in F420H2 oxidase.
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Affiliation(s)
| | - Tristan Wagner
- Microbial Metabolism Group
- Max-Planck-Institut für Marine Mikrobiologie
- Celsiusstraße 1
- Bremen
- Germany
| | - Philippe Carpentier
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM)
- Université Grenoble Alpes, CNRS, CEA
- Grenoble
- France
- European Synchrotron Radiation Facility (ESRF)
| | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS
- F-38000 Grenoble
- France
| | - Seigo Shima
- Microbial Protein Structure Group
- Max Planck Institute for Terrestrial Microbiology
- Karl-von-Frisch Straße 10
- 35043 Marburg
- Germany
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13
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Lehnert N, Fujisawa K, Camarena S, Dong HT, White CJ. Activation of Non-Heme Iron-Nitrosyl Complexes: Turning Up the Heat. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kiyoshi Fujisawa
- Department of Chemistry, Ibaraki University, Mito 310-8512, Japan
| | - Stephanie Camarena
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Hai T. Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Corey J. White
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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14
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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15
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A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species. Proc Natl Acad Sci U S A 2019; 116:14955-14960. [PMID: 31270241 DOI: 10.1073/pnas.1904234116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Many bacteria contain cytoplasmic chemoreceptors that lack sensor domains. Here, we demonstrate that such cytoplasmic receptors found in 8 different bacterial and archaeal phyla genetically couple to metalloproteins related to β-lactamases and nitric oxide reductases. We show that this oxygen-binding di-iron protein (ODP) acts as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable μ-peroxo adduct. Crystal structures of ODP from Td and the thermophile Thermotoga maritima (Tm) in the Fe[III]2-O2 2-, Zn[II], and apo states display differences in subunit association, conformation, and metal coordination that indicate potential mechanisms for sensing. In reconstituted systems, iron-peroxo ODP destabilizes the phosphorylated form of the receptor-coupled histidine kinase CheA, thereby providing a biochemical link between oxygen sensing and chemotaxis in diverse prokaryotes, including anaerobes of ancient origin.
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16
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Borges PT, Romão CV, Saraiva LM, Gonçalves VL, Carrondo MA, Teixeira M, Frazão C. Analysis of a new flavodiiron core structural arrangement in Flv1-ΔFlR protein from Synechocystis sp. PCC6803. J Struct Biol 2019; 205:91-102. [DOI: 10.1016/j.jsb.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/24/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
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17
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Weitz AC, Giri N, Frederick RE, Kurtz DM, Bominaar EL, Hendrich MP. Spectroscopy and DFT Calculations of Flavo-Diiron Nitric Oxide Reductase Identify Bridging Structures of NO-Coordinated Diiron Intermediates. ACS Catal 2018; 8:11704-11715. [PMID: 31263628 PMCID: PMC6602092 DOI: 10.1021/acscatal.8b03051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flavo-diiron proteins (FDPs) are widespread in anaerobic bacteria, archaea, and protozoa, where they serve as the terminal components of dioxygen and nitric oxide reductive scavenging pathways. FDPs contain an N,O-ligated diiron site adjacent to a flavin mononucleotide (FMN) cofactor. The diiron site is structurally similar to those in hemerythrin, ribonucleotide reductase, and methane monooxygenase. However, only FDPs turn over NO to N2O at significant rates and yields. Previous studies revealed sequential binding of two NO molecules to the diferrous site, forming mono- and dinitrosyl intermediates leading to N2O formation. In the present work, these mono- and dinitrosyl intermediates have been characterized by EPR and Mössbauer spectroscopies and DFT calculations. Our results show that the iron proximal to the cofactor binds the first NO to form the diiron mononitrosyl complex, implying the iron distal to the FMN binds the second NO to form the diiron dinitrosyl intermediate. The exchange-coupling constants, J (H = JS1·S2), were found to differ substantially, +17 cm-1 for the diiron mononitrosyl and +60 cm-1 for the diiron dinitrosyl. Notwithstanding this large difference, our findings indicate retention of at least one hydroxo bridge throughout the NOR catalytic cycle. The Mossbauer hyperfine parameters and DFT calculations confirmed a semibridging NO- ligand in the mononitrosyl intermediate that lowers the exchange parameter. The DFT calculations on the dinitrosyl intermediate suggest a contribution to J from direct exchange between the S = 1 spins on the NO- ligands, which could initiate N-N bond formation. Our results provide insight into why FDPs are the only known nonheme diiron enzymes that competently turn over NO to N2O.
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Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nitai Giri
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Rosanne E. Frederick
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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18
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The multidomain flavodiiron protein from Clostridium difficile 630 is an NADH:oxygen oxidoreductase. Sci Rep 2018; 8:10164. [PMID: 29977056 PMCID: PMC6033852 DOI: 10.1038/s41598-018-28453-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Flavodiiron proteins (FDPs) are enzymes with a minimal core of two domains: a metallo-β-lactamase-like, harbouring a diiron center, and a flavodoxin, FMN containing, domains. FDPs are O2 or NO reducing enzymes; for many pathogens, they help mitigate the NO produced by the immune system of the host, and aid survival during fluctuating concentrations concentrations of oxygen. FDPs have a mosaic structure, being predicted to contain multiple extra domains. Clostridium difficile, a threatening human pathogen, encodes two FDPs: one with the two canonical domains, and another with a larger polypeptide chain of 843 amino acids, CD1623, with two extra domains, predicted to be a short-rubredoxin-like and an NAD(P)H:rubredoxin oxidoreductase. This multi-domain protein is the most complex FDP characterized thus far. Each of the predicted domains was characterized and the presence of the predicted cofactors confirmed by biochemical and spectroscopic analysis. Results show that this protein operates as a standalone FDP, receiving electrons directly from NADH, and reducing oxygen to water, precluding the need for extra partners. CD1623 displayed negligible NO reductase activity, and is thus considered an oxygen selective FDP, that may contribute to the survival of C. difficile in the human gut and in the environment.
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19
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White CJ, Speelman AL, Kupper C, Demeshko S, Meyer F, Shanahan JP, Alp EE, Hu M, Zhao J, Lehnert N. The Semireduced Mechanism for Nitric Oxide Reduction by Non-Heme Diiron Complexes: Modeling Flavodiiron Nitric Oxide Reductases. J Am Chem Soc 2018; 140:2562-2574. [DOI: 10.1021/jacs.7b11464] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Corey J. White
- Department
of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Amy L. Speelman
- Department
of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Claudia Kupper
- Institut
für Anorganische Chemie, Universität Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Serhiy Demeshko
- Institut
für Anorganische Chemie, Universität Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - Franc Meyer
- Institut
für Anorganische Chemie, Universität Göttingen, Tammannstrasse
4, D-37077 Göttingen, Germany
| | - James P. Shanahan
- Department
of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - E. Ercan Alp
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael Hu
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced
Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Nicolai Lehnert
- Department
of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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20
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Weitz AC, Giri N, Caranto JD, Kurtz DM, Bominaar EL, Hendrich MP. Spectroscopy and DFT Calculations of a Flavo-diiron Enzyme Implicate New Diiron Site Structures. J Am Chem Soc 2017; 139:12009-12019. [PMID: 28756660 PMCID: PMC5898632 DOI: 10.1021/jacs.7b06546] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavo-diiron proteins (FDPs) are non-heme iron containing enzymes that are widespread in anaerobic bacteria, archaea, and protozoa, serving as the terminal components to dioxygen and nitric oxide reductive scavenging pathways in these organisms. FDPs contain a dinuclear iron active site similar to that in hemerythrin, ribonucleotide reductase, and methane monooxygenase, all of which can bind NO and O2. However, only FDP competently turns over NO to N2O. Here, EPR and Mössbauer spectroscopies allow electronic characterization of the diferric and diferrous species of FDP. The exchange-coupling constant J (Hex = JS1·S2) was found to increase from +20 cm-1 to +32 cm-1 upon reduction of the diferric to the diferrous species, indicative of (1) at least one hydroxo bridge between the iron ions for both states and (2) a change to the diiron core structure upon reduction. In comparison to characterized diiron proteins and synthetic complexes, the experimental values were consistent with a dihydroxo bridged diferric core, which loses one hydroxo bridge upon reduction. DFT calculations of these structures gave values of J and Mössbauer parameters in agreement with experiment. Although the crystal structure shows a hydrogen bond between the iron bound aspartate and the bridging solvent molecule, the DFT calculations of structures consistent with the crystal structure gave calculated values of J incompatible with the spectroscopic results. We conclude that the crystal structure of the diferric state does not represent the frozen solution structure and that a mono-μ-hydroxo diferrous species is the catalytically functional state that reacts with NO and O2. The new EPR spectroscopic probe of the diferric state indicated that the diferric structure of FDP prior to and immediately after turnover with NO are flavin mononucleotide (FMN) dependent, implicating an additional proton transfer role for FMN in turnover of NO.
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Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nitai Giri
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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21
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Solomon EI, Park K. Structure/function correlations over binuclear non-heme iron active sites. J Biol Inorg Chem 2016; 21:575-88. [PMID: 27369780 PMCID: PMC5010389 DOI: 10.1007/s00775-016-1372-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/14/2016] [Indexed: 11/30/2022]
Abstract
Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.
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Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea
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22
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Oleskin AV, Shenderov BA. Neuromodulatory effects and targets of the SCFAs and gasotransmitters produced by the human symbiotic microbiota. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2016; 27:30971. [PMID: 27389418 PMCID: PMC4937721 DOI: 10.3402/mehd.v27.30971] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022]
Abstract
The symbiotic gut microbiota plays an important role in the development and homeostasis of the host organism. Its physiological, biochemical, behavioral, and communicative effects are mediated by multiple low molecular weight compounds. Recent data on small molecules produced by gut microbiota in mammalian organisms demonstrate the paramount importance of these biologically active molecules in terms of biology and medicine. Many of these molecules are pleiotropic mediators exerting effects on various tissues and organs. This review is focused on the functional roles of gaseous molecules that perform neuromediator and/or endocrine functions. The molecular mechanisms that underlie the effects of microbial fermentation-derived gaseous metabolites are not well understood. It is possible that these metabolites produce their effects via immunological, biochemical, and neuroendocrine mechanisms that involve endogenous and microbial modulators and transmitters; of considerable importance are also changes in epigenetic transcriptional factors, protein post-translational modification, lipid and mitochondrial metabolism, redox signaling, and ion channel/gap junction/transporter regulation. Recent findings have revealed that interactivity among such modulators/transmitters is a prerequisite for the ongoing dialog between microbial cells and host cells, including neurons. Using simple reliable methods for the detection and measurement of short-chain fatty acids (SCFAs) and small gaseous molecules in eukaryotic tissues and prokaryotic cells, selective inhibitors of enzymes that participate in their synthesis, as well as safe chemical and microbial donors of pleiotropic mediators and modulators of host intestinal microbial ecology, should enable us to apply these chemicals as novel therapeutics and medical research tools.
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Affiliation(s)
- Alexander V Oleskin
- General Ecology Department, Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Boris A Shenderov
- Moscow Research Institute of Epidemiology and Microbiology after G.N. Gabrichevsky, Moscow, Russia; ;
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23
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Romão CV, Vicente JB, Borges PT, Frazão C, Teixeira M. The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases. J Biol Inorg Chem 2016; 21:39-52. [PMID: 26767750 DOI: 10.1007/s00775-015-1329-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/28/2015] [Indexed: 12/27/2022]
Abstract
Flavodiiron proteins have emerged in the last two decades as a newly discovered family of oxygen and/or nitric oxide reductases widespread in the three life domains, and present in both aerobic and anaerobic organisms. Herein we present the main features of these fascinating enzymes, with a particular emphasis on the metal sites, as more appropriate for this special issue in memory of the exceptional bioinorganic scientist R. J. P. Williams who pioneered the notion of (metal) element availability-driven evolution. We also compare the flavodiiron proteins with the other oxygen and nitric oxide reductases known until now, highlighting how throughout evolution Nature arrived at different solutions for similar functions, in some cases adding extra features, such as energy conservation. These enzymes are an example of the (bioinorganic) unpredictable diversity of the living world.
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Affiliation(s)
- Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157, Oeiras, Portugal.
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24
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Snyder RA, Butch SE, Reig AJ, DeGrado WF, Solomon EI. Molecular-Level Insight into the Differential Oxidase and Oxygenase Reactivities of de Novo Due Ferri Proteins. J Am Chem Soc 2015; 137:9302-14. [PMID: 26090726 DOI: 10.1021/jacs.5b03524] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the single-chain due ferri (DFsc) peptide scaffold, the differential oxidase and oxygenase reactivities of two 4A→4G variants, one with two histidines at the diiron center (G4DFsc) and the other with three histidines (3His-G4DFsc(Mut3)), are explored. By controlling the reaction conditions, the active form responsible for 4-aminophenol (4-AP) oxidase activity in both G4DFsc and 3His-G4DFsc(Mut3) is determined to be the substrate-bound biferrous site. Using circular dichroism (CD), magnetic CD (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies, 4-AP is found to bind directly to the biferrous sites of the DF proteins. In G4DFsc, 4-AP increases the coordination of the biferrous site, while in 3His-G4DFsc(Mut3), the coordination number remains the same and the substrate likely replaces the additional bound histidine. This substrate binding enables a two-electron process where 4-AP is oxidized to benzoquinone imine and O2 is reduced to H2O2. In contrast, only the biferrous 3His variant is found to be active in the oxygenation of p-anisidine to 4-nitroso-methoxybenzene. From CD, MCD, and VTVH MCD, p-anisidine addition is found to minimally perturb the biferrous centers of both G4DFsc and 3His-G4DFsc(Mut3), indicating that this substrate binds near the biferrous site. In 3His-G4DFsc(Mut3), the coordinative saturation of one iron leads to the two-electron reduction of O2 at the second iron to generate an end-on hydroperoxo-Fe(III) active oxygenating species.
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Affiliation(s)
- Rae Ana Snyder
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Susan E Butch
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - Amanda J Reig
- ‡Department of Chemistry, Ursinus College, Collegeville, Pennsylvania 19426, United States
| | - William F DeGrado
- ⊥Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Edward I Solomon
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States.,§Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, Menlo Park, California 94025, United States
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25
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Frederick RE, Caranto JD, Masitas CA, Gebhardt LL, MacGowan CE, Limberger RJ, Kurtz DM. Dioxygen and nitric oxide scavenging by Treponema denticola flavodiiron protein: a mechanistic paradigm for catalysis. J Biol Inorg Chem 2015; 20:603-13. [PMID: 25700637 PMCID: PMC4768905 DOI: 10.1007/s00775-015-1248-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/13/2015] [Indexed: 10/24/2022]
Abstract
Flavodiiron proteins (FDPs) contain a unique active site consisting of a non-heme diiron carboxylate site proximal to a flavin mononucleotide (FMN). FDPs serve as the terminal components for reductive scavenging of dioxygen (to water) or nitric oxide (to nitrous oxide), which combats oxidative or nitrosative stress in many bacteria. Characterizations of FDPs from spirochetes or from any oral microbes have not been previously reported. Here, we report characterization of an FDP from the anaerobic spirochete, Treponema (T.) denticola, which is associated with chronic periodontitis. The isolated T. denticola FDP exhibited efficient four-electron dioxygen reductase activity and lower but significant anaerobic nitric oxide reductase activity. A mutant T. denticola strain containing the inactivated FDP-encoding gene was significantly more air-sensitive than the wild-type strain. Single turnover reactions of the four-electron-reduced FDP (FMNH2-Fe(II)Fe(II)) (FDPred) with O2 monitored on the milliseconds to seconds time scale indicated initial rapid formation of a spectral feature consistent with a cis-μ-1,2-peroxo-diferric intermediate, which triggered two-electron oxidation of FMNH2. Reaction of FDPred with NO showed apparent cooperativity between binding of the first and second NO to the diferrous site. The resulting diferrous dinitrosyl complex triggered two-electron oxidation of the FMNH2. Our cumulative results on this and other FDPs indicate that smooth two-electron FMNH2 oxidation triggered by the FDPred/substrate complex and overall four-electron oxidation of FDPred to FDPox constitutes a mechanistic paradigm for both dioxygen and nitric oxide reductase activities of FDPs. Four-electron reductive O2 scavenging by FDPs could contribute to oxidative stress protection in many other oral bacteria.
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Affiliation(s)
- Rosanne E. Frederick
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Cesar A. Masitas
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Linda L. Gebhardt
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Charles E. MacGowan
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Ronald J. Limberger
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
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26
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Khatua S, Majumdar A. Flavodiiron nitric oxide reductases: Recent developments in the mechanistic study and model chemistry for the catalytic reduction of NO. J Inorg Biochem 2015; 142:145-53. [DOI: 10.1016/j.jinorgbio.2014.09.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 11/24/2022]
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27
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Caranto JD, Weitz A, Giri N, Hendrich MP, Kurtz DM. A diferrous-dinitrosyl intermediate in the N2O-generating pathway of a deflavinated flavo-diiron protein. Biochemistry 2014; 53:5631-7. [PMID: 25144650 PMCID: PMC4159209 DOI: 10.1021/bi500836z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Flavo-diiron proteins (FDPs) function
as anaerobic nitric oxide
scavengers in some microorganisms, catalyzing reduction of nitric
to nitrous oxide. The FDP from Thermotoga maritima can be prepared in a deflavinated form with an intact diferric site
(deflavo-FDP). Hayashi et al. [(2010) Biochemistry 49, 7040–7049] reported that reaction of NO with reduced deflavo-FDP
produced substoichiometric N2O. Here we report a multispectroscopic
approach to identify the iron species in the reactions of deflavo-FDP
with NO. Mössbauer spectroscopy identified two distinct ferrous
species after reduction of the antiferromagnetically coupled diferric
site. Approximately 60% of the total ferrous iron was assigned to
a diferrous species associated with the N2O-generating
pathway. This pathway proceeds through successive diferrous-mononitrosyl
(S = 1/2 FeII{FeNO}7) and diferrous-dinitrosyl (S = 0 [{FeNO}7]2) species that form within ∼100 ms of
mixing of the reduced protein with NO. The diferrous-dinitrosyl intermediate
converted to an antiferromagnetically coupled diferric species that
was spectroscopically indistinguishable from that in the starting
deflavinated protein. These diiron species closely resembled those
reported for the flavinated FDP [Caranto et al. (2014) J.
Am. Chem. Soc. 136, 7981–7992], and
the time scales of their formation and decay were consistent with
the steady state turnover of the flavinated protein. The remaining
∼40% of ferrous iron was inactive in N2O generation
but reversibly bound NO to give an S = 3/2 {FeNO}7 species. The results demonstrate
that N2O formation in FDPs can occur via conversion of S = 0 [{FeNO}7]2 to a diferric form
without participation of the flavin cofactor.
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Affiliation(s)
- Jonathan D Caranto
- Department of Chemistry, University of Texas at San Antonio , San Antonio, Texas 78249, United States
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28
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Gonçalves VL, Vicente JB, Pinto L, Romão CV, Frazão C, Sarti P, Giuffrè A, Teixeira M. Flavodiiron oxygen reductase from Entamoeba histolytica: modulation of substrate preference by tyrosine 271 and lysine 53. J Biol Chem 2014; 289:28260-70. [PMID: 25151360 DOI: 10.1074/jbc.m114.579086] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Flavodiiron proteins (FDPs) are a family of enzymes endowed with bona fide oxygen- and/or nitric-oxide reductase activity, although their substrate specificity determinants remain elusive. After a comprehensive comparison of available three-dimensional structures, particularly of FDPs with a clear preference toward either O2 or NO, two main differences were identified near the diiron active site, which led to the construction of site-directed mutants of Tyr(271) and Lys(53) in the oxygen reducing Entamoeba histolytica EhFdp1. The biochemical and biophysical properties of these mutants were studied by UV-visible and electron paramagnetic resonance (EPR) spectroscopies coupled to potentiometry. Their reactivity with O2 and NO was analyzed by stopped-flow absorption spectroscopy and amperometric methods. These mutations, whereas keeping the overall properties of the redox cofactors, resulted in increased NO reductase activity and faster inactivation of the enzyme in the reaction with O2, pointing to a role of the mutated residues in substrate selectivity.
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Affiliation(s)
- Vera L Gonçalves
- From the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2781-901 Oeiras, Portugal, the Metabolism and Genetics Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João B Vicente
- the Metabolism and Genetics Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal, the Department of Biochemistry and Human Biology, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal,
| | - Liliana Pinto
- From the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2781-901 Oeiras, Portugal
| | - Célia V Romão
- From the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2781-901 Oeiras, Portugal
| | - Carlos Frazão
- From the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2781-901 Oeiras, Portugal
| | - Paolo Sarti
- the Department of Biochemical Sciences and Istituto Pasteur, Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and the CNR Institute of Biology, Molecular Medicine and Nanobiotechnology, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Alessandro Giuffrè
- the CNR Institute of Biology, Molecular Medicine and Nanobiotechnology, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Miguel Teixeira
- From the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2781-901 Oeiras, Portugal,
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Caranto J, Weitz A, Hendrich MP, Kurtz DM. The nitric oxide reductase mechanism of a flavo-diiron protein: identification of active-site intermediates and products. J Am Chem Soc 2014; 136:7981-92. [PMID: 24828196 PMCID: PMC4063189 DOI: 10.1021/ja5022443] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Indexed: 11/30/2022]
Abstract
The unique active site of flavo-diiron proteins (FDPs) consists of a nonheme diiron-carboxylate site proximal to a flavin mononucleotide (FMN) cofactor. FDPs serve as the terminal components for reductive scavenging of dioxygen or nitric oxide to combat oxidative or nitrosative stress in bacteria, archaea, and some protozoan parasites. Nitric oxide is reduced to nitrous oxide by the four-electron reduced (FMNH2-Fe(II)Fe(II)) active site. In order to clarify the nitric oxide reductase mechanism, we undertook a multispectroscopic presteady-state investigation, including the first Mössbauer spectroscopic characterization of diiron redox intermediates in FDPs. A new transient intermediate was detected and determined to be an antiferromagnetically coupled diferrous-dinitrosyl (S = 0, [{FeNO}(7)]2) species. This species has an exchange energy, J ≥ 40 cm(-1) (JS1 ° S2), which is consistent with a hydroxo or oxo bridge between the two irons. The results show that the nitric oxide reductase reaction proceeds through successive formation of diferrous-mononitrosyl (S = ½, Fe(II){FeNO}(7)) and the S = 0 diferrous-dinitrosyl species. In the rate-determining process, the diferrous-dinitrosyl converts to diferric (Fe(III)Fe(III)) and by inference N2O. The proximal FMNH2 then rapidly rereduces the diferric site to diferrous (Fe(II)Fe(II)), which can undergo a second 2NO → N2O turnover. This pathway is consistent with previous results on the same deflavinated and flavinated FDP, which detected N2O as a product (Hayashi Biochemistry 2010, 49, 7040). Our results do not support other proposed mechanisms, which proceed either via "super-reduction" of [{FeNO}(7)]2 by FMNH2 or through Fe(II){FeNO}(7) directly to a diferric-hyponitrite intermediate. The results indicate that an S = 0 [{FeNO}(7)}]2 complex is a proximal precursor to N-N bond formation and N-O bond cleavage to give N2O and that this conversion can occur without redox participation of the FMN cofactor.
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Affiliation(s)
- Jonathan
D. Caranto
- Department
of Chemistry, University of Texas at San
Antonio, San Antonio, Texas 78249, United
States
| | - Andrew Weitz
- Department
of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department
of Chemistry, Carnegie-Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Donald M. Kurtz
- Department
of Chemistry, University of Texas at San
Antonio, San Antonio, Texas 78249, United
States
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30
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Tinajero-Trejo M, Jesse HE, Poole RK. Gasotransmitters, poisons, and antimicrobials: it's a gas, gas, gas! F1000PRIME REPORTS 2013; 5:28. [PMID: 23967379 PMCID: PMC3732073 DOI: 10.12703/p5-28] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We review recent examples of the burgeoning literature on three gases that have major impacts in biology and microbiology. NO, CO and H2S are now co-classified as endogenous gasotransmitters with profound effects on mammalian physiology and, potentially, major implications in therapeutic applications. All are well known to be toxic yet, at tiny concentrations in human and cell biology, play key signalling and regulatory functions. All may also be endogenously generated in microbes. NO and H2S share the property of being biochemically detoxified, yet are beneficial in resisting the bactericidal properties of antibiotics. The mechanism underlying this protection is currently under debate. CO, in contrast, is not readily removed; mounting evidence shows that CO, and especially organic donor compounds that release the gas in biological environments, are themselves effective, novel antimicrobial agents.
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