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Journal of Biological Inorganic... Mar 2015Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with... (Review)
Review
Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.
Topics: Azotobacter vinelandii; Bacteriochlorophylls; Catalysis; Molybdenum; Nitrogen; Nitrogen Fixation; Nitrogenase; Structure-Activity Relationship
PubMed: 25491285
DOI: 10.1007/s00775-014-1225-3 -
Accounts of Chemical Research Dec 2019The fixation of atmospheric dinitrogen to ammonia by industrial technologies (such as the Haber Bosch process) has revolutionized humankind. In contrast to industrial... (Review)
Review
The fixation of atmospheric dinitrogen to ammonia by industrial technologies (such as the Haber Bosch process) has revolutionized humankind. In contrast to industrial technologies, a single enzyme is known for its ability to reduce or "fix" dinitrogen: nitrogenase. Nitrogenase is a complex oxidoreductase enzymatic system that includes a catalytic protein (where dinitrogen is reduced) and an electron-transferring reductase protein (termed the Fe protein) that delivers the electrons necessary for dinitrogen fixation. The catalytic protein most commonly contains a FeMo cofactor (called the MoFe protein), but it can also contain a VFe or FeFe cofactor. Besides their ability to fix dinitrogen to ammonia, these nitrogenases can also reduce substrates such as carbon dioxide to formate. Interestingly, the VFE nitrogenase can also form carbon-carbon bonds. The vast majority of research surrounding nitrogenase employs the Fe protein to transfer electrons, which is also associated with the rate-limiting step of nitrogenase catalysis and also requires the hydrolysis of adenosine triphosphate. Thus, there is significant interest in artificially transferring electrons to the catalytic nitrogenase proteins. In this Account, we review nitrogenase electrocatalysis whereby electrons are delivered to nitrogenase from electrodes. We first describe the use of an electron mediator (cobaltocene) to transfer electrons from electrodes to the MoFe protein. The reduction of protons to molecular hydrogen was realized, in addition to azide and nitrite reduction to ammonia. Bypassing the rate-limiting step within the Fe protein, we also describe how this approach was used to interrogate the rate-limiting step of the MoFe protein: metal-hydride protonolysis at the FeMo-co. This Account next reviews the use of cobaltocene to mediate electron transfer to the VFe protein, where the reduction of carbon dioxide and the formation of carbon-carbon bonds (yielding the formation of ethene and propene) was realized. This approach also found success in mediating electron transfer to the FeFe catalytic protein, which exhibited improved carbon dioxide reduction in comparison to the MoFe protein. In the final example of mediated electron transfer to the catalytic protein, this Account also reviews recent work where the coupling of infrared spectroscopy with electrochemistry enabled the potential-dependent binding of carbon monoxide to the FeMo-co to be studied. As an alternative to mediated electron transfer, recent work that has sought to transfer electrons to the catalytic proteins in the absence of electron mediators (by direct electron transfer) is also reviewed. This approach has subsequently enabled a thermodynamic landscape to be proposed for the cofactors of the catalytic proteins. Finally, this Account also describes nitrogenase electrocatalysis whereby electrons are first transferred from an electrode to the Fe protein, before being transferred to the MoFe protein alongside the hydrolysis of adenosine triphosphate. In this way, increased quantities of ammonia can be electrocatalytically produced from dinitrogen fixation. We discuss how this has led to the further upgrade of electrocatalytically produced ammonia, in combination with additional enzymes (diaphorase, alanine dehydrogenase, and transaminase), to selective production of chiral amine intermediates for pharmaceuticals. This Account concludes by discussing current and future research challenges in the field of electrocatalytic nitrogen fixation by nitrogenase.
Topics: Biocatalysis; Chemistry Techniques, Synthetic; Electrochemistry; Nitrogenase
PubMed: 31800207
DOI: 10.1021/acs.accounts.9b00494 -
Biochimica Et Biophysica Acta 2013Nitrogenase contains two unique metalloclusters: the P-cluster and the M-cluster. The assembly processes of P- and M-clusters are arguably the most complicated processes... (Review)
Review
Nitrogenase contains two unique metalloclusters: the P-cluster and the M-cluster. The assembly processes of P- and M-clusters are arguably the most complicated processes in bioinorganic chemistry. There is considerable interest in decoding the biosynthetic mechanisms of the P- and M-clusters, because these clusters are not only biologically important, but also chemically unprecedented. Understanding the assembly mechanisms of these unique metalloclusters is crucial for understanding the structure-function relationship of nitrogenase. Here, we review the recent advances in this research area, with an emphasis on our work that provide important insights into the biosynthetic pathways of these high-nuclearity metal centers. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Topics: Models, Molecular; Nitrogenase; Protein Conformation
PubMed: 23232096
DOI: 10.1016/j.bbabio.2012.12.001 -
Chemical Reviews Jun 2020Nitrogenase is the only enzyme capable of reducing N to NH. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase,... (Review)
Review
Nitrogenase is the only enzyme capable of reducing N to NH. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.
Topics: Adenosine Triphosphate; Biocatalysis; Electrochemical Techniques; Electron Transport; Hydrolysis; Models, Molecular; Nitrogenase; Photochemical Processes
PubMed: 31999100
DOI: 10.1021/acs.chemrev.9b00663 -
Chemistry, An Asian Journal Jul 2017The cofactor of nitrogenase is the largest and most intricate metal cluster known in nature. Its reactivity, mode of action and even the precise binding site of... (Review)
Review
The cofactor of nitrogenase is the largest and most intricate metal cluster known in nature. Its reactivity, mode of action and even the precise binding site of substrate remain a matter of debate. For decades, synthetic chemists have taken inspiration from the exceptional structural, electronic and catalytic features of the cofactor and have tried to either mimic the unique topology of the entire site, or to extract its functional principles and build them into novel catalysts that achieve the same-or very similar-astounding transformations. We review some of the available model chemistry as it represents the various approaches that have been taken from studying the cofactor, to eventually summarize the current state of knowledge on catalysis by nitrogenase and highlight the mutually beneficial role of model chemistry and enzymology in bioinorganic chemistry.
Topics: Models, Chemical; Molecular Structure; Nitrogenase; Organometallic Compounds
PubMed: 28425208
DOI: 10.1002/asia.201700478 -
Molecules (Basel, Switzerland) Dec 2023Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N into bioavailable ammonium, an essential prerequisite for all organismic life. The... (Review)
Review
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
Topics: Nitrogenase; Nitrogen Fixation; Catalysis; Molybdenum; Nitrogen
PubMed: 38138449
DOI: 10.3390/molecules28247959 -
Chemical Reviews Jun 2020The reduction of dinitrogen to ammonia by nitrogenase reflects a complex choreography involving two component proteins, MgATP and reductant. At center stage of this... (Review)
Review
The reduction of dinitrogen to ammonia by nitrogenase reflects a complex choreography involving two component proteins, MgATP and reductant. At center stage of this process resides the active site cofactor, a complex metallocluster organized around a trigonal prismatic arrangement of iron sites surrounding an interstitial carbon. As a consequence of the choreography, electrons and protons are delivered to the active site for transfer to the bound N. While the detailed mechanism for the substrate reduction remains enigmatic, recent developments highlight the role of hydrides and the privileged role for two irons of the trigonal prism in the binding of exogenous ligands. Outstanding questions concern the precise nature of the intermediates between N and NH, and whether the cofactor undergoes significant rearrangement during turnover; resolution of these issues will require the convergence of biochemistry, structure, spectroscopy, computation, and model chemistry.
Topics: Ammonia; Crystallization; Metals, Heavy; Models, Molecular; Nitrogen; Nitrogenase; Protein Conformation
PubMed: 32538623
DOI: 10.1021/acs.chemrev.0c00067 -
Molecules (Basel, Switzerland) Dec 2023Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the... (Review)
Review
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
Topics: Nitrogenase; Cryoelectron Microscopy; Hydrogen; Iron; Sulfur; Oxidation-Reduction
PubMed: 38138444
DOI: 10.3390/molecules28247952 -
Annual Review of Biochemistry 1976
Review
Topics: Adenosine Triphosphate; Amino Acids; Bacteria; Electron Spin Resonance Spectroscopy; Electron Transport; Hydrogen; Iron; Kinetics; Molecular Weight; Molybdenum; Nitrogenase; Protein Conformation; Species Specificity
PubMed: 183600
DOI: 10.1146/annurev.bi.45.070176.002205 -
Essays in Biochemistry May 2017The versatile enzyme system nitrogenase accomplishes the challenging reduction of Nand other substrates through the use of two main metalloclusters. For molybdenum... (Review)
Review
The versatile enzyme system nitrogenase accomplishes the challenging reduction of Nand other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [FeS]-core P-cluster and a [MoFeSC-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N, and both originate from [FeS] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [FeS] clusters on NifDK called the P*-cluster. An accessory protein NifZ aids in P-cluster fusion, and reductive coupling is facilitated by NifH in a stepwise manner to form P-cluster on each half of NifDK. For M-cluster biosynthesis, two [FeS] clusters on NifB are coupled with a carbon atom in a radical-SAM dependent process, and concomitant addition of a 'ninth' sulfur atom generates the [FeSC]-core L-cluster. On the scaffold protein NifEN, L-cluster is matured to M-cluster by the addition of Mo and homocitrate provided by NifH. Finally, matured M-cluster in NifEN is directly transferred to NifDK, where a conformational change locks the cofactor in place. Mechanistic insights into these fascinating biosynthetic processes are detailed in this chapter.
Topics: Bacterial Proteins; Molybdoferredoxin; Nitrogenase; Oxidoreductases
PubMed: 28487403
DOI: 10.1042/EBC20160071