1
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Johansen C, Peters JC. Catalytic Reduction of Cyanide to Ammonia and Methane at a Mononuclear Fe Site. J Am Chem Soc 2024; 146:5343-5354. [PMID: 38361429 PMCID: PMC10910527 DOI: 10.1021/jacs.3c12395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Nitrogenase enzymes catalyze nitrogen reduction (N2R) to ammonia and also the reduction of non-native substrates, including the 7H+/6e- reduction of cyanide to CH4 and NH3. CN- and N2 are isoelectronic, and it is hence fascinating to compare the mechanisms of synthetic Fe catalysts capable of both CN- and N2 reduction. Here, we describe the catalytic reduction of CN- to NH3 and CH4 by a highly selective (P3Si)Fe(CN) catalyst (P3Si represents a tris(phosphine)silyl ligand). Catalysis is driven in the presence of excess acid ([Ph2NH2]OTf) and reductant ((C6H6)2Cr), with turnover as high as 73 demonstrated. This catalyst system is also modestly competent for N2R and structurally related to other tris(phosphine)Fe-based N2R catalysts. The choice of catalyst and reductant is important to observe high yields. Mechanistic studies elucidate several intermediates of CN- reduction, including iron isocyanides (P3SiFeCNH+/0) and terminal iron aminocarbynes (P3SiFeCNH2+/0). Aminocarbynes are isoelectronic to iron hydrazidos (Fe═N-NH2+/0), which have been invoked as selectivity-determining intermediates of N2R (NH3 versus N2H4 products). For the present CN- reduction catalysis, reduction of aminocarbyne P3SiFeCNH2+ is proposed to be rate but not selectivity contributing. Instead, by comparison with the reactivity of a methylated aminocarbyne analogue (P3SiFeCNMe2), and associated computational studies, formation of a Fischer carbene (P3SiFeC(H)(NH2)+) intermediate that is on path for either CH4 and NH3 (6 e-) or CH3NH2 (4 e-) products is proposed. From this carbene intermediate, pathways to the observed CH4 and NH3 products (distinct from CH3NH2 formation) are considered to compare and contrast the (likely) mechanism/s of CN- and N2 reduction.
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Affiliation(s)
- Christian
M. Johansen
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
| | - Jonas C. Peters
- Division of Chemistry and
Chemical Engineering, California Institute
of Technology, Pasadena, California 91125, United States
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2
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An Overview of Emerging Cyanide Bioremediation Methods. Processes (Basel) 2022. [DOI: 10.3390/pr10091724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Cyanide compounds are hazardous compounds which are extremely toxic to living organisms, especially free cyanide in the form of hydrogen cyanide gas (HCN) and cyanide ion (CN−). These cyanide compounds are metabolic inhibitors since they can tightly bind to the metals of metalloenzymes. Anthropogenic sources contribute significantly to CN− contamination in the environment, more specifically to surface and underground waters. The treatment processes, such as chemical and physical treatment processes, have been implemented. However, these processes have drawbacks since they generate additional contaminants which further exacerbates the environmental pollution. The biological treatment techniques are mostly overlooked as an alternative to the conventional physical and chemical methods. However, the recent research has focused substantially on this method, with different reactor configurations that were proposed. However, minimal attention was given to the emerging technologies that sought to accelerate the treatment with a subsequent resource recovery from the process. Hence, this review focuses on the recent emerging tools that can be used to accelerate cyanide biodegradation. These tools include, amongst others, electro-bioremediation, anaerobic biodegradation and the use of microbial fuel cell technology. These processes were demonstrated to have the possibility of producing value-added products, such as biogas, co-factors of neurotransmitters and electricity from the treatment process.
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3
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Gayakwad SV, Shejul DR, Lokhande MN, Bhosale HJ, Wankhede DS. Synthesis, Characterization, Antimicrobial, Antioxidant, Antidiabetic, Anticancer, and Cytotoxic Activities of Mixed Ligand Complexes of Vanadium(IV). RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221040241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Rohde M, Grunau K, Einsle O. CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew Chem Int Ed Engl 2020; 59:23626-23630. [PMID: 32915491 PMCID: PMC7756900 DOI: 10.1002/anie.202010790] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Indexed: 11/24/2022]
Abstract
Nitrogenases reduce N2 , the most abundant element in Earth's atmosphere that is otherwise resistant to chemical conversions due to its stable triple bond. Vanadium nitrogenase stands out in that it additionally processes carbon monoxide, a known inhibitor of the reduction of all substrates other than H+ . The reduction of CO leads to the formation of hydrocarbon products, holding the potential for biotechnological applications in analogy to the industrial Fischer-Tropsch process. Here we report the most highly resolved structure of vanadium nitrogenase to date at 1.0 Å resolution, with CO bound to the active site cofactor after catalytic turnover. CO bridges iron ions Fe2 and Fe6, replacing sulfide S2B, in a binding mode that is in line with previous reports on the CO complex of molybdenum nitrogenase. We discuss the structural consequences of continued turnover when CO is removed, which involve the replacement of CO possibly by OH- , the movement of Q176D and K361D , the return of sulfide and the emergence of two additional water molecules that are absent in the CO-bound state.
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Affiliation(s)
- Michael Rohde
- Institut für BiochemieFakultät für Chemie und PharmazieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104Freiburg im BreisgauGermany
| | - Katharina Grunau
- Institut für BiochemieFakultät für Chemie und PharmazieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104Freiburg im BreisgauGermany
| | - Oliver Einsle
- Institut für BiochemieFakultät für Chemie und PharmazieAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179104Freiburg im BreisgauGermany
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5
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Rohde M, Grunau K, Einsle O. Bindung von CO am FeV‐Cofaktor der CO‐reduzierenden Vanadium‐Nitrogenase bei atomarer Auflösung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael Rohde
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| | - Katharina Grunau
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
| | - Oliver Einsle
- Institut für Biochemie Fakultät für Chemie und Pharmazie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg im Breisgau Deutschland
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6
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 PMCID: PMC7491575 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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7
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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8
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Noar JD, Bruno-Bárcena JM. Azotobacter vinelandii: the source of 100 years of discoveries and many more to come. MICROBIOLOGY-SGM 2018. [PMID: 29533747 DOI: 10.1099/mic.0.000643] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Azotobacter vinelandii has been studied for over 100 years since its discovery as an aerobic nitrogen-fixing organism. This species has proved useful for the study of many different biological systems, including enzyme kinetics and the genetic code. It has been especially useful in working out the structures and mechanisms of different nitrogenase enzymes, how they can function in oxic environments and the interactions of nitrogen fixation with other aspects of metabolism. Interest in studying A. vinelandii has waned in recent decades, but this bacterium still possesses great potential for new discoveries in many fields and commercial applications. The species is of interest for research because of its genetic pliability and natural competence. Its features of particular interest to industry are its ability to produce multiple valuable polymers - bioplastic and alginate in particular; its nitrogen-fixing prowess, which could reduce the need for synthetic fertilizer in agriculture and industrial fermentations, via coculture; its production of potentially useful enzymes and metabolic pathways; and even its biofuel production abilities. This review summarizes the history and potential for future research using this versatile microbe.
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Affiliation(s)
- Jesse D Noar
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Jose M Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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9
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Imhoff JF, Rahn T, Künzel S, Neulinger SC. New insights into the metabolic potential of the phototrophic purple bacterium Rhodopila globiformis DSM 161 T from its draft genome sequence and evidence for a vanadium-dependent nitrogenase. Arch Microbiol 2018; 200:847-857. [PMID: 29423563 DOI: 10.1007/s00203-018-1489-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/26/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
Abstract
Rhodopila globiformis: is the most acidophilic anaerobic anoxygenic phototrophic purple bacterium and was isolated from a warm acidic sulfur spring in Yellowstone Park. Its genome is larger than genomes of other phototrophic purple bacteria, containing 7248 Mb with a G + C content of 67.1% and 6749 protein coding and 53 RNA genes. The genome revealed some previously unknown properties such as the presence of two sets of structural genes pufLMC for the photosynthetic reaction center genes and two types of nitrogenases (Mo-Fe and V-Fe nitrogenase), capabilities of autotrophic carbon dioxide fixation and denitrification using nitrite. Rhodopila globiformis assimilates sulfate and utilizes the C1 carbon substrates CO and methanol and a number of organic compounds, in particular, sugars and aromatic compounds. It is among the few purple bacteria containing a large number of pyrroloquinoline quinone-dependent dehydrogenases. It has extended capacities to resist stress by heavy metals, demonstrates different resistance mechanisms to antibiotics, and employs several toxin/antitoxin systems.
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Affiliation(s)
- Johannes F Imhoff
- GEOMAR Helmholtz Center for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
| | - Tanja Rahn
- GEOMAR Helmholtz Center for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Sven Künzel
- Max Planck Institut für Evolutionsbiologie, 24306, Plön, Germany
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10
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Luque-Almagro VM, Cabello P, Sáez LP, Olaya-Abril A, Moreno-Vivián C, Roldán MD. Exploring anaerobic environments for cyanide and cyano-derivatives microbial degradation. Appl Microbiol Biotechnol 2017; 102:1067-1074. [PMID: 29209795 PMCID: PMC5778177 DOI: 10.1007/s00253-017-8678-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 11/25/2022]
Abstract
Cyanide is one of the most toxic chemicals for living organisms described so far. Its toxicity is mainly based on the high affinity that cyanide presents toward metals, provoking inhibition of essential metalloenzymes. Cyanide and its cyano-derivatives are produced in a large scale by many industrial activities related to recovering of precious metals in mining and jewelry, coke production, steel hardening, synthesis of organic chemicals, and food processing industries. As consequence, cyanide-containing wastes are accumulated in the environment becoming a risk to human health and ecosystems. Cyanide and related compounds, like nitriles and thiocyanate, are degraded aerobically by numerous bacteria, and therefore, biodegradation has been offered as a clean and cheap strategy to deal with these industrial wastes. Anaerobic biological treatments are often preferred options for wastewater biodegradation. However, at present very little is known about anaerobic degradation of these hazardous compounds. This review is focused on microbial degradation of cyanide and related compounds under anaerobiosis, exploring their potential application in bioremediation of industrial cyanide-containing wastes.
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Affiliation(s)
- Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, Edificio Celestino Mutis, Campus de Rabanales, 14071, Córdoba, Spain
| | - Lara P Sáez
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain.
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11
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Shit M, Bera S, Maity S, Maji S, Weyhermüller T, Ghosh P. Oxidovanadium Complexes of 2,2′‐Bipyridine, 1,10 Phenanthroline, and
p
‐Nitro‐
o
‐aminophenol – Radical versus Nonradical States. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201501246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Madhusudan Shit
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India, http://www.pghosh.in
| | - Sachinath Bera
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India, http://www.pghosh.in
| | - Suvendu Maity
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India, http://www.pghosh.in
| | - Subrata Maji
- Department of Chemistry, Bangabasi College, No.19, Rajkumar Chakraborty Sarani, Baithakkhana, Kolkata 700009, India
| | - Thomas Weyhermüller
- Max‐Planck‐Institut für Chemische Energiekonversion, Stiftstrasse 34–36, 45470 Mülheim an der Ruhr, Germany
| | - Prasanta Ghosh
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata 700103, India, http://www.pghosh.in
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12
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Abstract
Vanadium is special in at least two respects: on the one hand, the tetrahedral anion vanadate(v) is similar to the phosphate anion; vanadate can thus interact with various physiological substrates that are otherwise functionalized by phosphate. On the other hand, the transition metal vanadium can easily expand its sphere beyond tetrahedral coordination, and switch between the oxidation states +v, +iv and +iii in a physiological environment. The similarity between vanadate and phosphate may account for the antidiabetic potential of vanadium compounds with carrier ligands such as maltolate and picolinate, and also for vanadium's mediation in cardiovascular and neuronal defects. Other potential medicinal applications of more complex vanadium coordination compounds, for example in the treatment of parasitic tropical diseases, may also be rooted in the specific properties of the ligand sphere. The ease of the change in the oxidation state of vanadium is employed by prokarya (bacteria and cyanobacteria) as well as by eukarya (algae and fungi) in respiratory and enzymatic functions. Macroalgae (seaweeds), fungi, lichens and Streptomyces bacteria have available haloperoxidases, and hence enzymes that enable the 2-electron oxidation of halide X(-) with peroxide, catalyzed by a Lewis-acidic V(V) center. The X(+) species thus formed can be employed to oxidatively halogenate organic substrates, a fact with implications also for the chemical processes in the atmosphere. Vanadium-dependent nitrogenases in bacteria (Azotobacter) and cyanobacteria (Anabaena) convert N2 + H(+) to NH4(+) + H2, but are also receptive for alternative substrates such as CO and C2H2. Among the enigmas to be solved with respect to the utilization of vanadium in nature is the accumulation of V(III) by some sea squirts and fan worms, as well as the purport of the nonoxido V(IV) compound amavadin in the fly agaric.
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Affiliation(s)
- Dieter Rehder
- Chemistry Department, University of Hamburg, 20146 Hamburg, Germany.
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13
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Chen CY, Chen ML, Chen HB, Wang H, Cramer SP, Zhou ZH. α-Hydroxy coordination of mononuclear vanadyl citrate, malate and S-citramalate with N-heterocycle ligand, implying a new protonation pathway of iron-vanadium cofactor in nitrogenase. J Inorg Biochem 2014; 141:114-120. [PMID: 25240212 PMCID: PMC5065718 DOI: 10.1016/j.jinorgbio.2014.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/04/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
Unlike the most of α-alkoxy coordination in α-hydroxycarboxylates to vanadium, novel α-hydroxy coordination to vanadium(IV) has been observed for a series of chiral and achiral monomeric α-hydroxycarboxylato vanadyl complexes [VO(H2cit)(bpy)]·2H2O (1), [VO(Hmal)(bpy)]·H2O (2), [VO(H2cit)(phen)]·1.5H2O (3), [VO(Hmal)(phen)]·H2O (4), and [(Δ)VO(S-Hcitmal)(bpy)]·2H2O (5), [VO(H2cit)(phen)]2·6.5H2O (6), which were isolated from the reactions of vanadyl sulfate with α-hydroxycarboxylates and N-heterocycle ligands in acidic solution. The complexes feature a tridentate citrate, malate or citramalate that chelates to vanadium atom through their α-hydroxy, α-carboxy and β-carboxy groups; while the other β-carboxylic acidic group of citrate is free to participate strong hydrogen bonds with lattice water molecule. The neutral α-hydroxy group also forms strong intermolecular hydrogen bonds with water molecule and the negatively-charged α-carboxy group in the environment. The inclusion of a hydrogen ion in α-alkoxy group results in the formation of a series of neutral complexes with one less positive charge. There are two different configurations of citrate with respect to the trans-position of axial oxo group, where the complex with trans-hydroxy configuration seems more stable with less hindrance. The average bond distances of V-Ohydroxy and V-Oα-carboxy are 2.196 and 2.003Å respectively, which are comparable to the VO distance (2.15Å) of homocitrate in FeV-cofactor of V-nitrogenase. A new structural model is suggested for R-homocitrato iron vanadium cofactor as VFe7S9C(R-Hhomocit) (H4homocit=homocitric acid) with one more proton in homocitrate ligand.
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Affiliation(s)
- Can-Yu Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 310036, China
| | - Mao-Long Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hong-Bin Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States.
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; Department of Chemistry, University of California, Davis, CA 95616, United States.
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14
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Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 2014; 114:4041-62. [PMID: 24467365 PMCID: PMC4012840 DOI: 10.1021/cr400641x] [Citation(s) in RCA: 979] [Impact Index Per Article: 97.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brian M Hoffman
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
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15
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Mancuso L, Jürjens G, Hermane J, Harmrolfs K, Eichner S, Fohrer J, Collisi W, Sasse F, Kirschning A. Bioreduction of aryl azides during mutasynthesis of new ansamitocins. Org Lett 2013; 15:4442-5. [PMID: 23981134 DOI: 10.1021/ol401989e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Supplementing a culture of a mutant strain of Actinosynnema pretiosum that is unable to biosynthesize aminohydroxy benzoic acid (AHBA), with 3-azido-5-hydroxy-benzoic acid and 3-azido-5-amino-benzoic acid, unexpectedly yielded anilino ansamitocins instead of the expected azido derivatives. This is the first example of the bioreduction of organic azides. The unique nature of these results was demonstrated when 3-azido-5-amino-benzoic acid was fed to the corresponding AHBA blocked mutant of Streptomyces hygroscopicus, the geldanamycin producer. This mutasynthetic experiment yielded the fully processed azido derivative of geldanamycin.
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Affiliation(s)
- Lena Mancuso
- Institut für Organische Chemie und Biomolekulares Wikstoffzentrum (BMWZ) der Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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16
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Seefeldt LC, Yang ZY, Duval S, Dean DR. Nitrogenase reduction of carbon-containing compounds. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1102-11. [PMID: 23597875 DOI: 10.1016/j.bbabio.2013.04.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 04/03/2013] [Accepted: 04/08/2013] [Indexed: 10/27/2022]
Abstract
Nitrogenase is an enzyme found in many bacteria and archaea that catalyzes biological dinitrogen fixation, the reduction of N2 to NH3, accounting for the major input of fixed nitrogen into the biogeochemical N cycle. In addition to reducing N2 and protons, nitrogenase can reduce a number of small, non-physiological substrates. Among these alternative substrates are included a wide array of carbon-containing compounds. These compounds have provided unique insights into aspects of the nitrogenase mechanism. Recently, it was shown that carbon monoxide (CO) and carbon dioxide (CO2) can also be reduced by nitrogenase to yield hydrocarbons, opening new insights into the mechanism of small molecule activation and reduction by this complex enzyme as well as providing clues for the design of novel molecular catalysts. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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Chikwana VM, Stec B, Lee BWK, de Crécy-Lagard V, Iwata-Reuyl D, Swairjo MA. Structural basis of biological nitrile reduction. J Biol Chem 2012; 287:30560-70. [PMID: 22787148 DOI: 10.1074/jbc.m112.388538] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme QueF catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ(0)) to 7-aminomethyl-7-deazaguanine (preQ(1)), the only nitrile reduction reaction known in biology. We describe here two crystal structures of Bacillus subtilis QueF, one of the wild-type enzyme in complex with the substrate preQ(0), trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the C55A mutant in complex with the substrate preQ(0) bound noncovalently. The QueF enzyme forms an asymmetric tunnel-fold homodecamer of two head-to-head facing pentameric subunits, harboring 10 active sites at the intersubunit interfaces. In both structures, a preQ(0) molecule is bound at eight sites, and in the wild-type enzyme, it forms a thioimide covalent linkage to the catalytic residue Cys-55. Both structural and transient kinetic data show that preQ(0) binding, not thioimide formation, induces a large conformational change in and closure of the active site. Based on these data, we propose a mechanism for the activation of the Cys-55 nucleophile and subsequent hydride transfer.
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Affiliation(s)
- Vimbai M Chikwana
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
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Roth LE, Tezcan FA. ATP-uncoupled, six-electron photoreduction of hydrogen cyanide to methane by the molybdenum-iron protein. J Am Chem Soc 2012; 134:8416-9. [PMID: 22564208 DOI: 10.1021/ja303265m] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A detailed study of the eight-electron/eight-proton catalytic reaction of nitrogenase has been hampered by the fact that electron and proton flow in this system is controlled by ATP-dependent protein-protein interactions. Recent studies have shown that it is possible to circumvent the dependence on ATP through the use of potent small-molecule reductants or light-driven electron injection, but success has been limited to two-electron reductions of hydrazine, acetylene, or protons. Here we show that a variant of the molybdenum-iron protein labeled with a Ru-photosensitizer can support the light-driven, six-electron catalytic reduction of hydrogen cyanide into methane and likely also ammonia. Our findings suggest that the efficiency of this light-driven system is limited by the initial one- or two-electron reduction of the catalytic cofactor (FeMoco) to enable substrate binding, but the subsequent electron-transfer steps into the FeMoco-bound substrate proceed efficiently.
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Affiliation(s)
- Lauren E Roth
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, 92093-0356, United States
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Abstract
Steady-state assays of nitrogenases share at least five requirements: an anaerobic environment, a consistent source of magnesium adenosine triphosphate (MgATP), a suitable source of reductant, a buffer system compatible with the product-quantification protocol to be used, and the desired substrate. The assay is initiated by injection of the component protein(s) of the enzyme or MgATP and terminated by injection of either acid or a solution of Na(2)EDTA. The various nitrogenases catalyze the reduction of a wide variety of substrates. This chapter outlines the methods used to analyze the products of nitrogenase-catalyzed reactions involving nitrogen-nitrogen bonds, nitrogen-oxygen bonds, carbon-nitrogen bonds, carbon-carbon bonds, carbon-oxygen bonds, carbon-sulfur bonds, and hydrogen only. The usefulness of measurements of residual amounts of other components of nitrogenase assays is also discussed.
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Affiliation(s)
- William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA.
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McGuinness ET. Some Molecular Moments of the Hadean and Archaean Aeons: A Retrospective Overview from the Interfacing Years of the Second to Third Millennia. Chem Rev 2010; 110:5191-215. [DOI: 10.1021/cr050061l] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Eugene T. McGuinness
- Department of Chemistry & Biochemistry, Seton Hall University, South Orange, New Jersey 07079-2690
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Sosa-Torres ME, Kroneck PMH. Interaction of Cyanide with Enzymes Containing Vanadium, Manganese, Non-Heme Iron, and Zinc. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Since the early discovery of Prussian Blue, cyano transition metal complexes have played a fundamental role in coordination chemistry. They represent important compounds with fascinating chemical and physical properties which turn them into valuable tools for both chemists and biologists. HCN as a precursor in prebiotic chemistry has gained interest in view of its polymers being involved in the formation of amino acids, purines, and orotic acid, a biosynthetic precursor of uracil. Clearly, the rapid formation of adenine by aqueous polymerization of HCN is one of the key discoveries in these experiments. The cyanide anion is usually toxic for most aerobic organisms because of its inhibitory effects on respiratory enzymes, but as a substrate it is an important source of carbon and nitrogen for microorganisms, fungi and plants. Most interestingly, the cyanide anion is a ligand of important metal-dependent biomolecules, such as the hydrogenases and the cobalt site in vitamin B12.
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Affiliation(s)
- Martha E. Sosa-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria Coyoacán, 04510, D.F. México México
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Bröcker MJ, Virus S, Ganskow S, Heathcote P, Heinz DW, Schubert WD, Jahn D, Moser J. ATP-driven reduction by dark-operative protochlorophyllide oxidoreductase from Chlorobium tepidum mechanistically resembles nitrogenase catalysis. J Biol Chem 2008; 283:10559-67. [PMID: 18252716 DOI: 10.1074/jbc.m708010200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During chlorophyll and bacteriochlorophyll biosynthesis in gymnosperms, algae, and photosynthetic bacteria, dark-operative protochlorophyllide oxidoreductase (DPOR) reduces ring D of aromatic protochlorophyllide stereospecifically to produce chlorophyllide. We describe the heterologous overproduction of DPOR subunits BchN, BchB, and BchL from Chlorobium tepidum in Escherichia coli allowing their purification to apparent homogeneity. The catalytic activity was found to be 3.15 nmol min(-1) mg(-1) with K(m) values of 6.1 microm for protochlorophyllide, 13.5 microm for ATP, and 52.7 microm for the reductant dithionite. To identify residues important in DPOR function, 21 enzyme variants were generated by site-directed mutagenesis and investigated for their metal content, spectroscopic features, and catalytic activity. Two cysteine residues (Cys(97) and Cys(131)) of homodimeric BchL(2) are found to coordinate an intersubunit [4Fe-4S] cluster, essential for low potential electron transfer to (BchNB)(2) as part of the reduction of the protochlorophyllide substrate. Similarly, Lys(10) and Leu(126) are crucial to ATP-driven electron transfer from BchL(2). The activation energy of DPOR electron transfer is 22.2 kJ mol(-1) indicating a requirement for 4 ATP per catalytic cycle. At the amino acid level, BchL is 33% identical to the nitrogenase subunit NifH allowing a first tentative structural model to be proposed. In (BchNB)(2), we find that four cysteine residues, three from BchN (Cys(21), Cys(46), and Cys(103)) and one from BchB (Cys(94)), coordinate a second inter-subunit [4Fe-4S] cluster required for catalysis. No evidence for any type of molybdenum-containing cofactor was found, indicating that the DPOR subunit BchN clearly differs from the homologous nitrogenase subunit NifD. Based on the available data we propose an enzymatic mechanism of DPOR.
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Affiliation(s)
- Markus J Bröcker
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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