Structural Models of the [Fe<sub>4</sub>S<sub>4</sub>] Clusters of Homologous Nitrogenase Fe Proteins

Blank, Michael; Lee, Chi Chung; Hu, Yilin; Hodgson, Keith O.; Hedman, Britt; Ribbe, Markus W.

doi:10.1021/ic200636k

Cited by 34 publications

(47 citation statements)

References 35 publications

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“…More recently, Blank et al . have suggested a similar distortion for the reduced state 10 . However, the samples for EXAFS studies almost always include at least 10-20% glycerol or similar glassing agent, which is known to affect Fe protein properties.…”

Section: Introductionmentioning

confidence: 78%

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Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

Mitra

George

Guo³

et al. 2013

J. Am. Chem. Soc.

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Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm−1 decrease in Fe-S stretching frequencies with each added electron. The “oxidized” [4Fe-4S]2+ state spectrum is consistent with and extends previous resonance Raman spectra. For the “reduced” [4Fe-4S]1+ state in Fe protein, and for any “all-ferrous” [4Fe-4S]0 cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å−1 indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.

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Section: Introductionmentioning

confidence: 78%

“…11 and recently by Blank et al . 10 . Our data are similar, except that a decade in progress of synchrotron radiation sources and detectors allowed us to take spectra over a wider range: out to k = 16 or 21 Å −1 as opposed to 14 Å −1 or less in previous studies.…”

Section: Resultsmentioning

confidence: 99%

Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

Mitra

George

Guo³

et al. 2013

J. Am. Chem. Soc.

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“…In A. vinelandii, the Fe proteins have relatively high sequence identity, with VnfH at~90% and AnfH at~60% compared to NifH [8], and VnfH and AnfH have conserved cysteine residues indicative of [FeS] cluster binding. The dithionite-reduced Fe proteins all display a characteristic EPR spectrum composed of a mixture of S = 1/2 and S = 3/2 resonances [44,45], indicating that a similar type of [Fe 4 S 4 ] cluster is present in each system. In support of this notion, analysis of the NifH, VnfH, and AnfH by XAS has demonstrated that the [FeS] clusters in each protein have a very similar structure.…”

Section: Features Of the Fe Proteinmentioning

confidence: 99%

The Fe Protein: An Unsung Hero of Nitrogenase

Jasniewski

Sickerman

et al. 2018

Inorganics

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Although the nitrogen-fixing enzyme nitrogenase critically requires both a reductase component (Fe protein) and a catalytic component, considerably more work has focused on the latter species. Properties of the catalytic component, which contains two highly complex metallocofactors and catalyzes the reduction of N 2 into ammonia, understandably making it the "star" of nitrogenase. However, as its obligate redox partner, the Fe protein is a workhorse with multiple supporting roles in both cofactor maturation and catalysis. In particular, the nitrogenase Fe protein utilizes nucleotide binding and hydrolysis in concert with electron transfer to accomplish several tasks of critical importance. Aside from the ATP-coupled transfer of electrons to the catalytic component during substrate reduction, the Fe protein also functions in a maturase and insertase capacity to facilitate the biosynthesis of the two-catalytic component metallocofactors: fusion of the [Fe 8 S 7 ] P-cluster and insertion of Mo and homocitrate to form the matured [(homocitrate)MoFe 7 S 9 C] M-cluster. These and key structural-functional relationships of the indispensable Fe protein and its complex with the catalytic component will be covered in this review.

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“…The structures of the clusters shown in (a) and (b) are based on crystallographic data, [11-13, 15, 16] while the structures of the clusters shown in (c) and (d) are based on XAS/EXAFS data. [48][49][50][51] PYMOL was used to create the structural models in this figure (PDB IDs: 1N2C, 1M1N, 3U7Q). HC: hydrocarbons.…”

Section: Nitrogenase and Carbon: Reductive C à C Coupling By Nitrogenasementioning

confidence: 99%

Nitrogenases—A Tale of Carbon Atom(s)

Ribbe

2016

Angew Chem Int Ed

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Named after its ability to catalyze the reduction of nitrogen to ammonia, nitrogenase has a surprising rapport with carbon-both through the interstitial carbide that resides in the central cavity of its cofactor and through its ability to catalyze the reductive carbon-carbon coupling of small carbon compounds into hydrocarbon products. Recently, a radical-SAM-dependent pathway was revealed for the insertion of carbide, which signifies a novel biosynthetic route to complex bridged metalloclusters. Moreover, a sulfur-displacement mechanism was proposed for the activation of carbon monoxide by nitrogenase, which suggests an essential role of the interstitial carbide in maintaining the stability while permitting a certain flexibility of the cofactor structure during substrate turnover.

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Structural Models of the [Fe₄S₄] Clusters of Homologous Nitrogenase Fe Proteins

Cited by 34 publications

References 35 publications

Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

The Fe Protein: An Unsung Hero of Nitrogenase

Nitrogenases—A Tale of Carbon Atom(s)

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Structural Models of the [Fe4S4] Clusters of Homologous Nitrogenase Fe Proteins

Cited by 34 publications

References 35 publications

Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

The Fe Protein: An Unsung Hero of Nitrogenase

Nitrogenases—A Tale of Carbon Atom(s)

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Structural Models of the [Fe₄S₄] Clusters of Homologous Nitrogenase Fe Proteins