Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor

Spatzal, Thomas; Aksoyoglu, Müge; Zhang, Limei; Andrade, Susana L. A.; Schleicher, Erik; Weber, Stefan; Rees, Douglas C.; Einsle, Oliver

doi:10.1126/science.1214025

Cited by 793 publications

(924 citation statements)

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“…The initial structure is based on the crystal structure of MoFe protein from Azotobacter vinelandii at an atomic resolution of 1.0 Å (PDB code: 3U7Q) 6 . Modifications were made to the basic structure: two calcium ions at the interface of subunits were changed to Fe(II) ions, according to the discovery of these sites as iron ions 41 .…”

Section: Model Preparation and Solvationmentioning

confidence: 99%

“…In this article, we describe QM/MM modelling of the MoFe protein, starting from the high-resolution crystal structure (PDB code: 3U7Q 6 ). We utilize multiple-sized QM regions and achieve convergence of the FeMoco geometric structure with respect to QM-region size and also demonstrate some convergence for redox properties.…”

Section: Introductionmentioning

confidence: 99%

“…The MoFe protein is an α 2 β 2 heterotetramer and contains two metal-sulfur clusters in each heterodimer: the P-cluster (an Fe 8 S 7 cluster believed to shuttle electrons to the active site) and the FeMo cofactor (FeMoco). FeMoco is an unusual ironmolybdenum-sulfur cluster (MoFe 7 S 9 C) that contains an interstitial atom that was revealed to be a carbon a few years ago 6,7 . It includes a homocitrate ligand and is anchored to the protein via histidine and cysteine residues.…”

Section: Introductionmentioning

confidence: 99%

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QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

2017

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Nitrogenase is one of the most fascinating enzymes in nature, being responsible for all biological nitrogen reduction. Despite decades of research it is among the enzymes in bioinorganic chemistry whose mechanism is the most poorly understood. The MoFe protein of nitrogenase contains an iron-molybdenum-sulfur cluster, FeMoco, where N 2 reduction takes place. The resting state of FeMoco has been characterized by crystallography, multiple spectroscopic techniques and theory (broken-symmetry density functional theory) and all heavy atoms are now characterized. The cofactor charge, however, has been controversial, the electronic structure has proved enigmatic and little is known about the mechanism. While many computational studies have been performed on FeMoco, few have taken the protein environment properly into account. In this study, we put forward QM/MM models of the MoFe protein from Azotobacter vinelandii, centered on FeMoco. By a detailed analysis of the FeMoco geometry and comparing to the atomic resolution crystal structure we conclude that only the [MoFe 7 S 9 C] 1-charge is a possible resting state charge. Further we find that, of the 3 lowest energy broken-symmetry solutions of FeMoco the BS7-235 spin isomer (where 235 refers to Fe atoms that are "spin-down") is the only one that can be reconciled with experiment. This is revealed by a comparison of the metal-metal distances in the experimental crystal structure, a rare case of spin-coupling phenomena being visible through the molecular structure. This could be interpreted as the enzyme deliberately stabilizing a specific electronic state of the cofactor, possibly for tuning specific reactivity on specific metal atoms. Finally, we show that the alkoxide group on the Mo-bound homocitrate must be protonated under resting state conditions; the presence of which has implications regarding the nature of FeMoco redox states as well as for potential substrate reduction mechanisms.3

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Section: Model Preparation and Solvationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

2017

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“…Structural models of the Mcluster (A) and the Fe 6 RHH compound (B), and the overlay of the two structures (C) in top (left) and side (right) views. PDB entry 3U7Q [12] and data from ref. …”

Section: Introductionmentioning

confidence: 99%

“…[11][12][13] This unique metallocluster has attracted the attention of synthetic chemists and chemical biologists alike and prompted a joint search between them for a synthetic mimic of the M-cluster that could be combined with an appropriate protein scaffold into a functional enzyme. One synthetic compound has come into sight as a potential candidate for this line of investigation.…”

Section: Introductionmentioning

confidence: 99%

Combining a Nitrogenase Scaffold and a Synthetic Compound into an Artificial Enzyme

et al. 2015

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Nitrogenase catalyzes substrate reduction at its cofactor center ([(Cit)MoFe 7 S 9 C] n− ; designated M-cluster). Here, we report the formation of an artificial, nitrogenase-mimicking enzyme upon insertion of a synthetic model complex ([Fe 6 S 9 (SEt) 2 ] 4− ; designated Fe 6 RHH ) into the catalytic component of nitrogenase (designated NifDK). Two Fe 6 RHH clusters were inserted into NifDK, rendering the resultant protein (designated NifDK Fe ) in a similar conformation to that upon insertion of native M-clusters. NifDK Fe could work together with the reductase component of nitrogenase to reduce C 2 H 2 in an ATP-dependent reaction. It could also act as an enzyme on its own in the presence of Eu(II) DTPA, displaying a strong activity in C 2 H 2 reduction while demonstrating an ability to reduce CN − to C1-C3 hydrocarbons in an ATP-independent manner.

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Nitrogen Fixation

Newton

2015

Kirk-Othmer Encyclopedia of Chemical Technology

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About 80% of the Earth's atmosphere is made up of nitrogen gas (N 2 ), but nitrogen is most often the limiting nutrient for agricultural productivity, because neither plants nor animals can use it directly. It must first be fixed into either ammonium or nitrate. Only the simplest life forms, bacteria and archaea, can produce ammonium from N 2 using the enzyme called nitrogenase. N 2 is also fixed by nonbiological processes, which contribute equally to the total annual fixation rate. In fact, without commercial fertilizers, the human population could not be supported. This article first describes the major industrial processes and their shortcomings, emphasizing the dominant Haber‐Bosch process. Then, an overview of the various biological nitrogen‐fixing systems, both free‐living and symbiotic organisms, focusing on the agriculturally important legume– Rhizobium symbiosis is provided. Nitrogenase is detailed and analyzed next with sections on its evolution, biosynthesis, composition and structure, regulation, and catalytic mechanism, the last of which is now beginning to be understood in some detail. The penultimate section describes attempts to duplicate either the reactivity or the structure of nitrogenase in chemical systems, some of which have achieved limited catalytic capability. Finally, the last section attempts to highlight both the important strides made and the problems that remain. These include limiting losses of applied fertilizer to ground water and atmosphere; careful matching of inoculant with cultivar; reducing fossil fuel energy inputs to fertilizer production; manipulating plant colonization and symbiosis development to produce new pairings; and simplifying the biological process for transfer to other organisms.

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Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor

Abstract: Structural data show that the light atom at the center of the nitrogenase active site cofactor is a carbon.

Cited by 793 publications

References 6 publications

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

Combining a Nitrogenase Scaffold and a Synthetic Compound into an Artificial Enzyme

Nitrogen Fixation

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