1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
2
|
Schwartz SL, Rangel LT, Payette JG, Fournier GP. A Proterozoic microbial origin of extant cyanide-hydrolyzing enzyme diversity. Front Microbiol 2023; 14:1130310. [PMID: 37065136 PMCID: PMC10098168 DOI: 10.3389/fmicb.2023.1130310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
In addition to its role as a toxic environmental contaminant, cyanide has been hypothesized to play a key role in prebiotic chemistry and early biogeochemical evolution. While cyanide-hydrolyzing enzymes have been studied and engineered for bioremediation, the extant diversity of these enzymes remains underexplored. Additionally, the age and evolution of microbial cyanide metabolisms is poorly constrained. Here we provide comprehensive phylogenetic and molecular clock analyses of the distribution and evolution of the Class I nitrilases, thiocyanate hydrolases, and nitrile hydratases. Molecular clock analyses indicate that bacterial cyanide-reducing nitrilases were present by the Paleo- to Mesoproterozoic, and were subsequently horizontally transferred into eukaryotes. These results present a broad diversity of microbial enzymes that could be optimized for cyanide bioremediation.
Collapse
Affiliation(s)
- Sarah L. Schwartz
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- *Correspondence: Sarah L. Schwartz,
| | - L. Thiberio Rangel
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jack G. Payette
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gregory P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
3
|
MacArdle SG, Rees DC. Solvent Deuterium Isotope Effects of Substrate Reduction by Nitrogenase from Azotobacter vinelandii. J Am Chem Soc 2022; 144:21125-21135. [DOI: 10.1021/jacs.2c07574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Siobhán G. MacArdle
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Douglas C. Rees
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| |
Collapse
|
4
|
Abstract
Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N2) to ammonia (NH3). The N2 reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N2, nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO2) to hydrocarbons. However, it remains an open question whether these ‘side reactivities’ play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron‐only nitrogenase. The isozymes differ in their metal content, structure, and substrate‐dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO2 to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.
Collapse
Affiliation(s)
- Niels N Oehlmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| |
Collapse
|
5
|
Manoj KM, Bazhin N. The murburn precepts for aerobic respiration and redox homeostasis. Progress in Biophysics and Molecular Biology 2021; 167:104-120. [DOI: 10.1016/j.pbiomolbio.2021.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/13/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022]
|
6
|
Leite-Mondin M, DiLegge MJ, Manter DK, Weir TL, Silva-Filho MC, Vivanco JM. The gut microbiota composition of Trichoplusia ni is altered by diet and may influence its polyphagous behavior. Sci Rep 2021; 11:5786. [PMID: 33707556 DOI: 10.1038/s41598-021-85057-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/15/2021] [Indexed: 12/25/2022] Open
Abstract
Insects are known plant pests, and some of them such as Trichoplusia ni feed on a variety of crops. In this study, Trichoplusia ni was fed distinct diets of leaves of Arabidopsis thaliana or Solanum lycopersicum as well as an artificial diet. After four generations, the microbial composition of the insect gut was evaluated to determine if the diet influenced the structure and function of the microbial communities. The population fed with A. thaliana had higher proportions of Shinella, Terribacillus and Propionibacterium, and these genera are known to have tolerance to glucosinolate activity, which is produced by A. thaliana to deter insects. The population fed with S. lycopersicum expressed increased relative abundances of the Agrobacterium and Rhizobium genera. These microbial members can degrade alkaloids, which are produced by S. lycopersicum. All five of these genera were also present in the respective leaves of either A. thaliana or S. lycopersicum, suggesting that these microbes are acquired by the insects from the diet itself. This study describes a potential mechanism used by generalist insects to become habituated to their available diet based on acquisition of phytochemical degrading gut bacteria.
Collapse
|
7
|
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
| |
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- Michael Rohde
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| | - Katharina Grunau
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yasuhiro Ohki
- Department of Chemsitry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| |
Collapse
|
11
|
Manoj KM, Ramasamy S, Parashar A, Gideon DA, Soman V, Jacob VD, Pakshirajan K. Acute toxicity of cyanide in aerobic respiration: Theoretical and experimental support for murburn explanation. Biomol Concepts 2020; 11:32-56. [PMID: 32187011 DOI: 10.1515/bmc-2020-0004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/19/2020] [Indexed: 12/30/2022] Open
Abstract
The inefficiency of cyanide/HCN (CN) binding with heme proteins (under physiological regimes) is demonstrated with an assessment of thermodynamics, kinetics, and inhibition constants. The acute onset of toxicity and CN's mg/Kg LD50 (μM lethal concentration) suggests that the classical hemeFe binding-based inhibition rationale is untenable to account for the toxicity of CN. In vitro mechanistic probing of CN-mediated inhibition of hemeFe reductionist systems was explored as a murburn model for mitochondrial oxidative phosphorylation (mOxPhos). The effect of CN in haloperoxidase catalyzed chlorine moiety transfer to small organics was considered as an analogous probe for phosphate group transfer in mOxPhos. Similarly, inclusion of CN in peroxidase-catalase mediated one-electron oxidation of small organics was used to explore electron transfer outcomes in mOxPhos, leading to water formation. The free energy correlations from a Hammett study and IC50/Hill slopes analyses and comparison with ligands ( CO/ H 2 S/ N 3 - ) $\left( {\text{CO}}/{{{{\text{H}}_{2}}\text{S}}/{\text{N}_{3}^{\text{-}}}\;}\; \right)$ provide insights into the involvement of diffusible radicals and proton-equilibriums, explaining analogous outcomes in mOxPhos chemistry. Further, we demonstrate that superoxide (diffusible reactive oxygen species, DROS) enables in vitro ATP synthesis from ADP+phosphate, and show that this reaction is inhibited by CN. Therefore, practically instantaneous CN ion-radical interactions with DROS in matrix catalytically disrupt mOxPhos, explaining the acute lethal effect of CN.
Collapse
Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu: The Science & Ethics Foundation Snehatheeram, Kulappully, Shoranur-2 (PO), Kerala, India-679122
| | - Surjith Ramasamy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India-781039
| | - Abhinav Parashar
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, India-522213
| | - Daniel Andrew Gideon
- Department of Biotechnology, Bishop Heber College, Tiruchirappalli, Tamil Nadu, India-620017
| | - Vidhu Soman
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India-110016
| | - Vivian David Jacob
- Satyamjayatu: The Science & Ethics Foundation Snehatheeram, Kulappully, Shoranur-2 (PO), Kerala, India-679122
| | - Kannan Pakshirajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India-781039
| |
Collapse
|
12
|
Abstract
Nitrogenase is the enzyme that catalyzes biological N2 reduction to NH3. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO2, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.
Collapse
Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Derek F Harris
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Abstract
This study aims at investigating the iron cyanide (CN) degradation potential of two natural bacterial isolates with the purpose of their application in iron CN phytoremediation. The strains were isolated from contaminated soil and incubated over 4 months with 50 mg L-1 CN (as ferrocyanide) as the sole iron and nitrogen source. Unlike previous reports, the study provides control for bacterial growth, biotic and abiotic CN losses. Bacterial growth, CN, ammonium, and nitrate concentrations were monitored regularly. Both strains grew less rapid with iron CN compared with the positive control. However, the growth was diauxic. The CN concentration in the media decreased with 20% and 25% respectively, while that in the sterile controls remained stable. Ammonium was detected in the media of both strains implying that a fraction of the initially applied ferrocyanide has been converted. The nitrogen lost from the system evened out with that in the cells at the end of the experiments. These results showed that the investigated strains were undoubtedly able to grow on iron CN as an alternative nitrogen source, but contrary to some previous findings, the iron CN utilization is much slower and takes place only after complete exhaustion of the cellular nitrogen reserves.
Collapse
Affiliation(s)
- Tsvetelina Dimitrova
- Chair of Soil Protection and Recultivation, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Frank Repmann
- Chair of Soil Protection and Recultivation, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Dirk Freese
- Chair of Soil Protection and Recultivation, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| |
Collapse
|
15
|
Park JM, Trevor Sewell B, Benedik MJ. Cyanide bioremediation: the potential of engineered nitrilases. Appl Microbiol Biotechnol 2017; 101:3029-3042. [PMID: 28265723 DOI: 10.1007/s00253-017-8204-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
Abstract
The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.
Collapse
Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | - B Trevor Sewell
- Structural Biology Research Unit, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA.
| |
Collapse
|
16
|
Katz FEH, Shi X, Owens CP, Joseph S, Tezcan FA. Determination of nucleoside triphosphatase activities from measurement of true inorganic phosphate in the presence of labile phosphate compounds. Anal Biochem 2017; 520:62-7. [PMID: 28017740 DOI: 10.1016/j.ab.2016.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/10/2016] [Accepted: 12/14/2016] [Indexed: 11/24/2022]
Abstract
One of the most common assays for nucleoside triphosphatase (NTPase) activity entails the quantification of inorganic phosphate (Pi) as a colored phosphomolybdate complex at low pH. While this assay is very sensitive, it is not selective for Pi in the presence of labile organic phosphate compounds (OPCs). Since NTPase activity assays typically require a large excess of OPCs, such as nucleotides, selectivity for Pi in the presence of OPCs is often critical in evaluating enzyme activity. Here we present an improved method for the measurement of enzymatic nucleotide hydrolysis as Pi released, which achieves selectivity for Pi in the presence of OPCs while also avoiding the costs and hazards inherent in other methods for measuring nucleotide hydrolysis. We apply this method to the measurement of ATP hydrolysis by nitrogenase and GTP hydrolysis by elongation factor G (EF-G) in order to demonstrate the broad applicability of our method for the determination of nucleotide hydrolysis in the presence of interfering OPCs.
Collapse
|
17
|
Affiliation(s)
- Jonathan Rittle
- Division of Chemistry and Chemical Engineering California Institute of Technology USA
| | - Jonas C. Peters
- Division of Chemistry and Chemical Engineering California Institute of Technology USA
| |
Collapse
|
18
|
Abstract
Nitrogenase enzymes mediate the six-electron reductive cleavage of cyanide to CH4 and NH3 . Herein we demonstrate for the first time the liberation of CH4 and NH3 from a well-defined iron cyanide coordination complex, [SiP(iPr) 3 ]Fe(CN) (where [SiP(iPr) 3 ] represents a tris(phosphine)silyl ligand), on exposure to proton and electron equivalents. [SiP(iPr) 3 ]Fe(CN) additionally serves as a useful entry point to rare examples of terminally-bound Fe(CNH) and Fe(CNH2 ) species that, in accord with preliminary mechanistic studies, are plausible intermediates of the cyanide reductive protonation to generate CH4 and NH3 . Comparative studies with a related [SiP(iPr) 3 ]Fe(CNMe2 ) complex suggests the possibility of multiple, competing mechanisms for cyanide activation and reduction.
Collapse
Affiliation(s)
- Jonathan Rittle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, USA
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, USA.
| |
Collapse
|
19
|
Affiliation(s)
- Faith E. H. Katz
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| | - Cedric P. Owens
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| | - F. A. Tezcan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| |
Collapse
|
20
|
Spatzal T, Perez KA, Howard JB, Rees DC. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor. eLife 2015; 4:e11620. [PMID: 26673079 PMCID: PMC4755756 DOI: 10.7554/elife.11620] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/15/2015] [Indexed: 12/05/2022] Open
Abstract
Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32-1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis.
Collapse
Affiliation(s)
- Thomas Spatzal
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Kathryn A Perez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - James B Howard
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Douglas C Rees
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| |
Collapse
|
21
|
Hammer TJ, Bowers MD. Gut microbes may facilitate insect herbivory of chemically defended plants. Oecologia 2015; 179:1-14. [DOI: 10.1007/s00442-015-3327-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/16/2015] [Indexed: 12/17/2022]
|
22
|
Legras JL, Chuzel G, Arnaud A, Galzy P. Natural nitriles and their metabolism. World J Microbiol Biotechnol 2014; 6:83-108. [PMID: 24429979 DOI: 10.1007/bf01200927] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/1989] [Accepted: 10/15/1989] [Indexed: 11/29/2022]
Abstract
The present work reviews the numerous nitrile compounds that have been isolated from plants and animals. Two kinds of potentially toxic molecules are widespread, namely the cyanogenic glycosides and cyanollpids. Many other aromatic and allphatic nitriles are synthesized to a lesser extent. Different studies on the synthesis and degradation of these cyanogenic compounds are also reviewed to emphasize the potential use of different microorganisms for the detoxification of food and foodstuff.
Collapse
Affiliation(s)
- J L Legras
- ENSA-INRA, Place Viala, 34060, Montpellier Cedex, France
| | | | | | | |
Collapse
|
23
|
Seefeldt LC, Yang ZY, Duval S, Dean DR. Nitrogenase reduction of carbon-containing compounds. Biochim Biophys Acta 2013; 1827:1102-11. [PMID: 23597875 DOI: 10.1016/j.bbabio.2013.04.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
| | | | | | | |
Collapse
|
24
|
|
25
|
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.
Collapse
Affiliation(s)
- Lauren E Roth
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, 92093-0356, United States
| | | |
Collapse
|
26
|
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.
Collapse
Affiliation(s)
- William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA.
| | | |
Collapse
|
27
|
Nicolet Y, Martin L, Tron C, Fontecilla-Camps JC. A glycyl free radical as the precursor in the synthesis of carbon monoxide and cyanide by the [FeFe]-hydrogenase maturase HydG. FEBS Lett 2010; 584:4197-202. [PMID: 20837009 DOI: 10.1016/j.febslet.2010.09.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 09/03/2010] [Indexed: 11/29/2022]
Abstract
HydG uses tyrosine to synthesize the CN(-)/CO ligands of [FeFe]-hydrogenase active site. We have mutated two of the [4Fe-4S]-cluster cysteine ligands of the HydG C-terminal domain (CTD) to serine. The double mutant can still synthesize CN(-) but not CO. In a mutant lacking the CTD both CN(-) and CO synthesis are abolished. Like in ThiH, the initial steps of CN(-) synthesis are carried out in the TIM-barrel domain of HydG but some component(s) of the CTD are later needed. The mutants indicate that CO synthesis is metal-based and occurs in the CTD. We postulate that CN(-)/CO synthesis is initiated by H(2)N-*CH-CO(2)(-). Fragmentation of this radical into H(2)N-*CH(2) and CO(2) or H(2)C=NH and *CO(2)(-) provides plausible precursors for CN(-)/CO synthesis.
Collapse
Affiliation(s)
- Yvain Nicolet
- Laboratoire de Cristallographie et de Cristallogenèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Université Joseph Fourier, Grenoble, France
| | | | | | | |
Collapse
|
28
|
Ebbs SD, Kosma DK, Nielson EH, Machingura M, Baker AJM, Woodrow IE. Nitrogen supply and cyanide concentration influence the enrichment of nitrogen from cyanide in wheat (Triticum aestivum L.) and sorghum (Sorghum bicolor L.). Plant Cell Environ 2010; 33:1152-60. [PMID: 20199620 DOI: 10.1111/j.1365-3040.2010.02136.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cyanide assimilation by the beta-cyanoalanine pathway produces asparagine, aspartate and ammonium, allowing cyanide to serve as alternate or supplemental source of nitrogen. Experiments with wheat and sorghum examined the enrichment of (15)N from cyanide as a function of external cyanide concentration in the presence or absence of nitrate and/or ammonium. Cyanogenic nitrogen became enriched in plant tissues following exposure to (15)N-cyanide concentrations from 5 to 200 microm, but when exposure occurred in the absence of nitrate and ammonium, (15)N enrichment increased significantly in sorghum shoots at solution cyanide concentrations of > or =50 microm and in wheat roots at 200 microm cyanide. In an experiment with sorghum using (13)C(15)N, there was also a significant difference in the tissue (13)C:(15)N ratio, suggestive of differential metabolism and transport of carbon and nitrogen under nitrogen-free conditions. A reciprocal (15)N labelling study using KC(15)N and (15)NH(4)(+) and wheat demonstrated an interaction between cyanide and ammonium in roots in which increasing solution ammonium concentrations decreased the enrichment from 100 microm cyanide. In contrast, with increasing solution cyanide concentrations there was an increase in the enrichment from ammonium. The results suggest increased transport and assimilation of cyanide in response to decreased nitrogen supply and perhaps to ammonium supply.
Collapse
Affiliation(s)
- Stephen D Ebbs
- Department of Plant Biology and Center for Ecology, Southern Illinois University Carbondale, Carbondale, Illinois 62901-6509, USA.
| | | | | | | | | | | |
Collapse
|
29
|
Abstract
The analytical potential of the reaction of ammonia with o-phthalaldehyde mercaptoethanol reagent at pH 7 (an atypical fluorescence) has already been demonstrated. This, coupled with additional findings reported here, has led to an ammonia determination well suited to nitrogenase studies. As a result, large numbers of samples can be rapidly analyzed by high-pressure liquid chromatrography methods under mild conditions and without prior microdiffusion. Neither sodium dithionite (or other components of the usual nitrogenase assay), nor alternative substrates (cyanide, azide, methyl isonitrile), nor their products (methylamine, dimethylamine, hydrazine) interfere. High-pressure liquid chromatography showed that the fluorescent "product" of the o-phthalaldehyde mercaptoethanol reagent-ammonia reaction was, in fact, more than just a single compound. Despite this, once the proper solvent composition was found, high-pressure liquid chromatography with a small inexpensive C(18) "guard" column proved quite fast and reproducible for this measurement. Fluorescence response to ammonia was linear to at least 40 nmol/ml. A previous problem, long-term stability of the fluorescence, was solved by running the reactions in the dark. Background ammonia in the buffer could be substantially reduced by an analogous o-phthalaldehyde mercaptoethanol reagent reaction, using t-butyl mercaptan, and solvent extraction.
Collapse
Affiliation(s)
- J L Corbin
- Charles F. Kettering Research Laboratory, Yellow Springs, Ohio 45387
| |
Collapse
|
30
|
Kaewkannetra P, Imai T, Garcia-Garcia FJ, Chiu TY. Cyanide removal from cassava mill wastewater using Azotobactor vinelandii TISTR 1094 with mixed microorganisms in activated sludge treatment system. J Hazard Mater 2009; 172:224-228. [PMID: 19632039 DOI: 10.1016/j.jhazmat.2009.06.162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/13/2009] [Accepted: 06/30/2009] [Indexed: 05/28/2023]
Abstract
Cassava mill wastewater has a high organic and cyanide content and is an important economic product of traditional and rural low technology agro-industry in many parts of the world. However, the wastewater is toxic and can pose serious threat to the environment and aquatic life in the receiving waters. The ability of Azotobactor vinelandii TISTR 1094, a N2-fixing bacterium, to grow and remove cyanide in cassava wastewater was evaluated. Results revealed that the cells in the exponential phase reduce the level of cyanide more rapidly than when the cells are at their stationary growth phase. The rate of cyanide removal by A. vinelandii depends on the initial cyanide concentration. As the initial cyanide concentration increased, removal rate increased and cyanide removal of up to 65.3% was achieved. In the subsequent pilot scale trial involving an activated sludge system, the introduction of A. vinelandii into the system resulted in cyanide removals of up to 90%. This represented an improvement of 20% when compared to the activated sludge system which did not incorporate the strain.
Collapse
Affiliation(s)
- P Kaewkannetra
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | | | | |
Collapse
|
31
|
Basile LJ, Willson RC, Sewell BT, Benedik MJ. Genome mining of cyanide-degrading nitrilases from filamentous fungi. Appl Microbiol Biotechnol 2008; 80:427-35. [DOI: 10.1007/s00253-008-1559-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 05/28/2008] [Accepted: 05/30/2008] [Indexed: 10/21/2022]
|
32
|
Yu Y, Sadique AR, Smith JM, Dugan TR, Cowley RE, Brennessel WW, Flaschenriem CJ, Bill E, Cundari TR, Holland PL. The reactivity patterns of low-coordinate iron-hydride complexes. J Am Chem Soc 2008; 130:6624-38. [PMID: 18444648 PMCID: PMC2474859 DOI: 10.1021/ja710669w] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report a survey of the reactivity of the first isolable iron-hydride complexes with a coordination number less than 5. The high-spin iron(II) complexes [(beta-diketiminate)Fe(mu-H)] 2 react rapidly with representative cyanide, isocyanide, alkyne, N 2, alkene, diazene, azide, CO 2, carbodiimide, and Brønsted acid containing substrates. The reaction outcomes fall into three categories: (1) addition of Fe-H across a multiple bond of the substrate, (2) reductive elimination of H 2 to form iron(I) products, and (3) protonation of the hydride to form iron(II) products. The products include imide, isocyanide, vinyl, alkyl, azide, triazenido, benzo[ c]cinnoline, amidinate, formate, and hydroxo complexes. These results expand the range of known bond transformations at iron complexes. Additionally, they give insight into the elementary transformations that may be possible at the iron-molybdenum cofactor of nitrogenases, which may have hydride ligands on high-spin, low-coordinate metal atoms.
Collapse
Affiliation(s)
- Ying Yu
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Azwana R. Sadique
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Jeremy M. Smith
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Thomas R. Dugan
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Ryan E. Cowley
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | | | | | - Eckhard Bill
- Max-Planck-Institut für Bioanorganische Chemie, D-45470 Mülheim an der Ruhr, Germany
| | - Thomas R. Cundari
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| |
Collapse
|
33
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Markus J Bröcker
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Fisher K, Dilworth MJ, Newton WE. Azotobacter vinelandii vanadium nitrogenase: formaldehyde is a product of catalyzed HCN reduction, and excess ammonia arises directly from catalyzed azide reduction. Biochemistry 2006; 45:4190-8. [PMID: 16566593 PMCID: PMC4296739 DOI: 10.1021/bi0514109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Mo-nitrogenase-catalyzed reduction of both cyanide and azide results in the production of excess NH3, which is an amount of NH3 over and above that expected to be formed from the well-recognized reactions. Several suggestions about the possible sources of excess NH3 have been made, but previous attempts to characterize these reactions have met with either limited (or no) success or controversy. Because V-nitrogenase has a propensity to release partially reduced intermediates, e.g., N2H4 during N2 reduction, it was selected to probe the reduction of cyanide and azide. Sensitive assay procedures were developed and employed to monitor the production of either HCHO or CH3OH (its further two-electron-reduced product) from HCN. Like Mo-nitrogenase, V-nitrogenase suffered electron-flux inhibition by CN- (but was much less sensitive than Mo-nitrogenase), but unlike the case for Mo-nitrogenase, MgATP hydrolysis was also inhibited by CN-. V-Nitrogenase also released more of the four-electron-reduced intermediate, CH3NH2, than did Mo-nitrogenase. At high NaCN concentrations, V-nitrogenase directed a significant percentage of electron flux into excess NH3, and under these conditions, substantial amounts of HCHO, but no CH3OH, were detected for the first time. With azide, in contrast to the case for Mo-nitrogenase, both total electron flux and MgATP hydrolysis with V-nitrogenase were inhibited. V-Nitrogenase, unlike Mo-nitrogenase, showed no preference between the two-electron reduction to N2-plus-NH3 and the six-electron reduction to N2H4-plus-NH3. V-Nitrogenase formed more excess NH3, but reduction of the N2 produced by the two-electron reduction of N3(-) was not its source. Rather, it was formed directly by the eight-electron reduction of N3(-). Unlike Mo-nitrogenase, CO could not completely eliminate either cyanide or azide reduction by V-nitrogenase. CO did, however, eliminate the inhibition of both electron flux and MgATP hydrolysis by CN-, but not that caused by azide. These different responses to CO suggest different sites or modes of interaction for these two substrates with V-nitrogenase.
Collapse
Affiliation(s)
| | | | - William E. Newton
- Corresponding author W.E. Newton (Tel: 540-231-8431; FAX: 540-231-9070; ) to whom proofs should be sent
| |
Collapse
|
35
|
Wilson PE, Nyborg AC, Kenealey J, Lowery TJ, Crawford K, King CR, Engan AJ, Johnson JL, Watt GD. Evidence for a synergistic salt-protein interaction -- complex patterns of activation vs. inhibition of nitrogenase by salt. Biophys Chem 2006; 122:184-94. [PMID: 16603308 DOI: 10.1016/j.bpc.2006.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 03/16/2006] [Accepted: 03/19/2006] [Indexed: 11/26/2022]
Abstract
The molybdenum nitrogenase enzyme system, comprised of the MoFe protein and the Fe protein, catalyzes the reduction of atmospheric N(2) to NH(3). Interactions between these two proteins and between Fe protein and nucleotides (MgADP and MgATP) are crucial to catalysis. It is well established that salts are inhibitors of nitrogenase catalysis that target these interactions. However, the implications of salt effects are often overlooked. We have reexamined salt effects in light of a comprehensive framework for nitrogenase interactions to offer an in-depth analysis of the sources of salt inhibition and underlying apparent cooperativity. More importantly, we have identified patterns of salt activation of nitrogenase that correspond to at least two mechanisms. One of these mechanisms is that charge screening of MoFe protein-Fe protein interactions in the nitrogenase complex accelerates the rate of nitrogenase complex dissociation, which is the rate-limiting step of catalysis. This kind of salt activation operates under conditions of high catalytic activity and low salt concentrations that may resemble those found in vivo. While simple kinetic arguments are strong evidence for this kind of salt activation, further confirmation was sought by demonstrating that tight complexes that have previously displayed little or no activity due to the inability of Fe protein to dissociate from the complex are activated by the presence of salt. This occurs for the combination Azotobacter vinelandii MoFe protein with: (a) the L127Delta Fe protein; and (b) Clostridium pasteurianum Fe protein. The curvature of activation vs. salt implies a synergistic salt-protein interaction.
Collapse
Affiliation(s)
- Phillip E Wilson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Maskos Z, Fisher K, Sørlie M, Newton WE, Hales BJ. Variant MoFe proteins of Azotobacter vinelandii: effects of carbon monoxide on electron paramagnetic resonance spectra generated during enzyme turnover. J Biol Inorg Chem 2005; 10:394-406. [PMID: 15887041 DOI: 10.1007/s00775-005-0648-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 04/08/2005] [Indexed: 10/25/2022]
Abstract
The resting state of wild-type nitrogenase MoFe protein exhibits an S=3/2 electron paramagnetic resonance (EPR) signal originating from the FeMo cofactor, the enzyme's active site. When nitrogenase turns over under CO, this signal disappears and one (sometimes two) of three new EPR signals, which also arise from the FeMo cofactor, appears, depending on the CO concentration. The appearance and properties of these CO-inducible EPR signals, which were also generated with variant MoFe proteins (alphaR96Q, alphaR96K, alphaQ191K, alphaR359K, alphaR96K/alphaR359K, alphaR277C, alphaR277H, and DeltanifV) that are impacted around the FeMo cofactor, have been investigated. No new CO-induced EPR signals arise from any variant, suggesting that no new CO-binding sites are produced by the substitutions. All variant proteins, except alphaR277H, produce the lo-CO signal; all, except alphaQ191K, produce the hi(5)-CO signal; but only two (alphaR96Q and DeltanifV) exhibit the hi-CO signal. FeMo cofactor's environment clearly dictates which CO-induced EPR signals are generated; however, none of these EPR signals correlate with CO inhibition of H(2) evolution observed with some of these variants. CO inhibition of H(2) evolution is, therefore, due to CO binding to a different site(s) from those responsible for the CO-induced EPR signals. Some resting-state variants have overlapping S=3/2 EPR signals, whose intensities simultaneously decrease under turnover conditions, indicating that all FeMo cofactor conformations are catalytically active. Moreover, these variants produce a similar number of hi(5)-CO signals after turnover under CO to the number of resting-state S=3/2 signals. The FeMo cofactor associated with the hi(5)-CO signal likely contains two bridging CO molecules.
Collapse
Affiliation(s)
- Zofia Maskos
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | | | | | | |
Collapse
|
37
|
Almeida SS, Guedes da Silva MC, Jerzykiewicz LB, Sobota P, Pombeiro AJ. Cyanide as a versatile Lewis base ligand at a dinitrogen-binding iron(II) centre: mono- and heteronuclear adducts. Inorganica Chim Acta 2003. [DOI: 10.1016/s0020-1693(03)00249-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
38
|
Abstract
Electrochemical behaviour of various metallo cyano adducts of trans-[FeH(CN)(dppe)2], viz. the dinuclear complexes [FeH(dppe)2(μ-CN)PdCl2(PPh3)], [FeH(dppe)2(μ-CN)NiCl2(PCy3)], and trinuclear [{FeH(dppe)2(μ-CN)}2(ReOCl3)], [{FeH(dppe)2(μ-CN)}2PtCl(Ph)] and [{FeX(dppe)2(μ-CN)}2WCl3(OH)] (X = Cl or OH, dppe = 1,2-diphenylphosphinoethane, PCy3 = P(C6H11)3), as well as the benzoylisocyanide mononuclear adduct trans-[FeH(CNCOPh)- (dppe)2], is reported. All of them exhibit FeII/FeIII-based oxidations (which are reversible, except for trans-[FeH(CNCOPh)(dppe)2]). The metallocyanide bridges C≡N-Re-N≡C and C≡N-W-N≡C in [{FeH(dppe)2(μ-CN)}2(ReOCl3)] and [{FeX(dppe)2(μ-CN)}2WCl3(OH)], respectively, allow electronic communication between the iron centres, with possible generation of mixed-valence FeII/FeIII complexes whose comproportionation constant could be estimated in the former case. From the values of the measured oxidation potentials, the electrochemical PL and EL ligand parameters have been estimated for the metallocyanide ligands that were shown to behave as stronger net electron donors than organoisocyanides, although weaker than cyanide itself. Ligand-centred reduction processes were also observed to lead, in the cases of complexes trans-[FeH(CNCOPh)(dppe)2] (CNCOPh-based reduction) and [FeH(dppe)2(μ-CN)PdCl2(PPh3)] (PdII-based reduction in the CNPdCl2(PPh3)- metallocyanide ligand), to the dissociation of the adduct, with regeneration of the parent cyano complex trans-[FeH(CN)(dppe)2], thus reflecting the reductive decrease of the electrophilic (or Lewis acidic) character of the benzoyl and {PdCl2(PPh3)} groups.
Collapse
|
39
|
|
40
|
|
41
|
|
42
|
da Silva MFCG, da Silva JJRF, Pombeiro AJL, Pellinghelli MA, Tiripicchio A. Deprotonation reactions of the aminocarbyne complex trans-[ReCl(CNH2)(dppe)2][BF4](dppe = Ph2PCH2CH2PPh2). Synthesis and properties of the cyano-complexes trans-[Re(CN)L(dppe)2](L = NCR, N2, CO or CCHPh) and crystal structure of trans-[Re(CN)(NCMe)(dppe)2]PriOH. ACTA ACUST UNITED AC 1996. [DOI: 10.1039/dt9960002763] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
43
|
|
44
|
Lemos MN, da Silva MC, Pombeiro AJ. Electron-transfer activation of the aminocarbyne and the hydrogen isocyanide complexes trans-[ReCl(CNHn)(Ph2PCH2CH2PPh2)2][BF4]n−1 (n=2 or 1). Interconversion of coordinated CNH2 and CNH. Inorganica Chim Acta 1994. [DOI: 10.1016/0020-1693(94)04064-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
45
|
Richards AJ, Lowe DJ, Richards RL, Thomson AJ, Smith BE. Electron-paramagnetic-resonance and magnetic-circular-dichroism studies of the binding of cyanide and thiols to the thiols to the iron-molybdenum cofactor from Klebsiella pneumoniae nitrogenase. Biochem J 1994; 297 ( Pt 2):373-8. [PMID: 8297344 PMCID: PMC1137839 DOI: 10.1042/bj2970373] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
FeMoco, a low-M(r) metal cluster of probable composition Fe7MoS9 complexed with homocitrate, has been extracted with N-methylformamide from the MoFe protein of the nitrogenase enzyme from Klebsiella pneumoniae. The binding of cyanide and thiols to the FeMoco cluster in its paramagnetic S = 3/2 oxidation level has been studied by low-temperature e.p.r. and magnetic-circular-dichroism (m.c.d.) spectroscopies. Cyanide binds to isolated FeMoco at more than one site, and causes changes in the g values form g = 4.6, 3.2, 2.0 to g = 4.29, 3.82, 2.02 E.p.r. competition studies indicate that one cyanide can be displaced by thiolate from one type of site. The form of the low-temperature m.c.d. spectrum is little changed by ligand binding, thus the basic cluster structure remains intact. However, when benzenethiol is bound, a new intense band (lambda 387 nm) is observed, indicating the generation of an increased ligand-to-cluster charge-transfer interaction.
Collapse
Affiliation(s)
- A J Richards
- School of Chemical Sciences, University of East Anglia, Norwich U.K
| | | | | | | | | |
Collapse
|
46
|
|
47
|
Wolle D, Kim C, Dean D, Howard J. Ionic interactions in the nitrogenase complex. Properties of Fe-protein containing substitutions for Arg-100. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50576-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
48
|
Hills A, Hughes DL, Macdonald CJ, Mohammed MY, Pickett CJ. Transformation of a methyleneamide ligand at molybdenum: electrochemical oxidation to a cyanide, reactions with elemental oxygen, sulphur or selenium and X-ray crystal structures of trans-[Mo(CN)Cl(dppe)2]·MeOH and trans-[Mo(NCS)Cl(dppe)2]; electroreduction of the cyanide to an aminocarbyne, trans-[Mo(CNH2)Cl(dppe)2](dppe = Ph2PCH2CH2PPh2). ACTA ACUST UNITED AC 1991. [DOI: 10.1039/dt9910000121] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
49
|
Deits TL, Howard JB. Effect of salts on Azotobacter vinelandii nitrogenase activities. Inhibition of iron chelation and substrate reduction. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39673-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
50
|
Lowe DJ, Fisher K, Thorneley RN, Vaughn SA, Burgess BK. Kinetics and mechanism of the reaction of cyanide with molybdenum nitrogenase from Azotobacter vinelandii. Biochemistry 1989; 28:8460-6. [PMID: 2605195 DOI: 10.1021/bi00447a028] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The steady-state kinetic behavior of the six-electron reduction of N2 by nitrogenase is known to differ markedly from the six-electron reduction of cyanide in two ways. First, on extrapolation to infinite concentration of cyanide, the H2 evolution reaction is almost completely suppressed whereas at extrapolated infinite concentration of N2, H2 evolution continues. Second, as the ratio of the Fe protein to the MoFe protein increases, the reduction of N2 is favored over H2 evolution, whereas the reduction of cyanide becomes less favored relative to H2 evolution. We have extended these steady-state experiments with Azotobacter vinelandii nitrogenase to include a third observation, that the six-electron reduction of N2 is favored over H2 evolution at high total protein concentrations whereas cyanide reduction is less favored over H2 evolution at high total protein concentrations. All three steady-state observations can be explained by a model whereby cyanide is proposed to bind to a redox state of the MoFe protein more oxidized than that reactive toward H2 evolution and N2 reduction. To test this model, we have examined the pre-steady-state kinetic behavior of both cyanide reduction by A. vinelandii nitrogenase and cyanide inhibition of total electron flow through nitrogenase. The data show that in the presence or absence of cyanide there is a short lag of 100 ms before H2 is detected, followed by a linear phase of H2 evolution lasting for about 3 s, during which time no effects of cyanide are observable. After 3 s electron flow is finally inhibited by cyanide, and the cyanide reduction product CH4 is finally formed.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- D J Lowe
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
| | | | | | | | | |
Collapse
|