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Comparative Electronic Structures of Nitrogenase Femoco and Fevco† Cite This: Dalton Trans., 2017, 46, 2445 Julian A

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Comparative Electronic Structures of Nitrogenase Femoco and Fevco† Cite This: Dalton Trans., 2017, 46, 2445 Julian A Showcasing collaborative research from the Max Planck As featured in: Institute for Chemical Energy Conversion, the University of Washington, and the University of Freiburg. Volume 46 Number 8 28 February 2017 Pages 2389–2738 Dalton Comparative electronic structures of nitrogenase FeMoco and Transactions An international journal of inorganic chemistry FeVco rsc.li/dalton The electronic structures of the nitrogenase active sites, FeMoco and FeVco, have been investigated by a parallel study of the holoenzymes with synthetic cubane cluster models. Using high-resolution X-ray spectroscopies coupled with density functional theory calculations, key diff erences between FeMoco and FeVco have been identifi ed, rationalizing the isozymes’ ISSN 1477-9226 PAPER Dong-Sheng Li, Qichun Zhang et al. Ag-NPs embedded in two novel Zn3 /Zn5 -cluster-based metal–organic diff erential affi nity for various substrates. frameworks for catalytic reduction of 2/3/4-nitrophenol See Oliver Einsle, Julie A. Kovacs, Serena DeBeer et al. , Dalton Trans. , 2017, 46 , 2445. rsc.li/dalton Registered charity number: 207890 Dalton Transactions View Article Online PAPER View Journal | View Issue Comparative electronic structures of nitrogenase FeMoco and FeVco† Cite this: Dalton Trans., 2017, 46, 2445 Julian A. Rees,a,b Ragnar Bjornsson,a,c Joanna K. Kowalska,a Frederico A. Lima,a,d Julia Schlesier,e Daniel Sippel,e Thomas Weyhermüller,a Oliver Einsle,*e Julie A. Kovacs*b and Serena DeBeer*a,f An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron–sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron–heterometal bonds, which are found to be weaker in FeVco. Received 12th January 2017, Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through Accepted 25th January 2017 highly covalent Fe–C bonding. The implications of these conclusions are discussed in light of the differ- Creative Commons Attribution 3.0 Unported Licence. DOI: 10.1039/c7dt00128b ential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible func- rsc.li/dalton tional roles for both the heterometal and the interstitial carbide are detailed. Introduction of spectra obtained using element-specific techniques such as 57Fe Mössbauer and X-ray spectroscopies. Thus, the exact The nitrogenase enzymes catalyze the reduction of atmo- electronic structure of FeMoco remains an area of active – spheric dinitrogen. Of the three classes of nitrogenases, de- investigation.4 8 lineated by the elemental composition of their active site In contrast, the vanadium-dependent nitrogenase is a less This article is licensed under a ffi cofactors, the molybdenum-dependent nitrogenases are the e cient N2 reduction catalyst at ambient temperatures, requir- most active under ambient conditions.1 They are also the most ing more ATP and additional reducing equivalents (Table S1†). well-studied; a combination of crystallographic2 and spectro- However, its activity is comparably unaffected by decreased scopic2,3 studies have provided the complete atomic structure temperatures.9 Furthermore, it has been shown that the Open Access Article. Published on 02 February 2017. Downloaded 9/27/2021 12:24:14 AM. of the MoFe7S9Ciron–molybdenum cofactor, (FeMoco) as vanadium nitrogenase exhibits a unique ability to promote the shown in Fig. 1A. The FeMoco is located in the MoFe protein, reduction of CO to short-chain hydrocarbons (Table S1†).10 – – which also contains an Fe8S7 cluster termed the P-cluster This reductive C C bond coupling is akin to Fischer Tropsch (Fig. 1B). While both of these unique iron–sulfur clusters are chemistry, but utilizes protons and electrons in place of H2. essential for the function of nitrogenase, the presence of 15 The relative inability of the molybdenum nitrogenase to total iron atoms in the clusters complicates the interpretation perform the same chemistry (CO is a reversible inhibitor of molybdenum nitrogenase11) poses significant questions regarding the structural and/or electronic differences under- lying the disparate reactivity of these two isozymes. aMax Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany. E-mail: [email protected]; We have recently provided the first direct evidence for an 12 Tel: +49 208 306 3605 interstitial carbide in the iron–vanadium cofactor (FeVco), bDepartment of Chemistry, University of Washington, Box 351700, Seattle, establishing the structural homology of FeMoco and FeVco WA 98195-1700, USA. E-mail: [email protected] (the so-called M-clusters, where M = Mo or V). A subsequent, cScience Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland independent study confirmed our findings and also reported dCentro Nacional de Pesquisa em Energia e Materiais Brazilian Synchrotron Light 13 Laboratory - LNLS Rua Giuseppe Máximo Scolfaro, 10.000 13083-970 Campinas SP, the binding of CO to the resting state of FeVco. The latter Brazil result is of significant interest because CO coordination to eInstitute for Biochemistry and BIOSS Centre for Biological Signalling Studies, Albert FeMoco only occurs under turnover conditions. This suggests Ludwigs University Freiburg, Germany. E-mail: [email protected] that despite the similar geometric structures of the M-clusters, fDepartment of Chemistry and Chemical Biology, Cornell University, Ithaca, they have sufficiently different electronic structures so as to NY 14853, USA †Electronic supplementary information (ESI) available: Additional figures and impact their ability to bind substrate. It is possible that these tables, computational data and information. See DOI: 10.1039/c7dt00128b changes in the electronic structure also engender the differ- This journal is © The Royal Society of Chemistry 2017 Dalton Trans.,2017,46, 2445–2455 | 2445 View Article Online Paper Dalton Transactions in M-cluster oxidation states, as well as differences in intra- cluster bonding and covalency. The role of these electronic structural differences in tuning substrate binding affinities is discussed. Experimental Sample preparation The MoFe2 and VFe15 proteins were expressed and purified as previously described, and samples for X-ray spectroscopic measurements were also prepared following published proto- cols.12 FeMoco was extracted from MoFe protein by treatment with N-methylformamide (NMF) and dithiothreitol (DTT), following the protocol of Shah and Brill.16,17 The extraction of FeMoco was performed using 1 mL of NMF for 25 mg of protein, and used under strict exclusion of dioxygen, without further concentration. The final concentration of cofactor is estimated to be ∼0.2 mM. An aliquot of the NMF and DTT solution of extracted cofactor was placed in a Delrin cell with a38μm Kapton tape window, and immediately frozen in liquid N2. 18 Creative Commons Attribution 3.0 Unported Licence. The model compounds (Et4N)[(Tp)MoFe3S4Cl3] and (Me N)[VFe S Cl (DMF)]19 were synthesized as previously Fig. 1 Structural representations of FeMoco (A) and the P-cluster (B) 4 3 4 3 from Azotobacter vinelandii nitrogenase, adapted from PDB 3U7Q, and reported, and handled under inert atmosphere. Samples were the synthetic cubane molybdenum and vanadium iron–sulfur cluster prepared by grinding solid compound into a fine powder in a 18 19 models (Et4N)[(Tp)MoFe3S4Cl3] (C) and (Me4N)[VFe3S4Cl3(DMF)3] (D) mortar and pestle. The powders were then pressed into 1 mm used in this study. Tp = tris(pyrazolyl)borate, DMF = dimethylformamide. thick Al spacers and sealed with 38 μm Kapton tape. For non- Color scheme for atoms: Fe = orange, S = yellow, C = gray, Mo = green, resonant XES measurements, the solid samples were measured V = purple, N = blue, O = red, Cl = light green, B = pink. Inorganic sulfides are shown as spheres, cysteinate residues are shown as sticks, without dilution, and for HERFD XAS measurements samples and hydrogen atoms and counterions have been omitted for clarity. were diluted ∼1 : 10 by mass with BN to minimize self- This article is licensed under a absorption. Data collection ences in reactivity towards native and non-native substrates Open Access Article. Published on 02 February 2017. Downloaded 9/27/2021 12:24:14 AM. X-ray spectroscopic measurements were conducted at beamline detailed above. ID-26 at the European Synchrotron Radiation Facility (ESRF), To address these questions, the present work examines the France, and at beamline C-1 at the Cornell High Energy comparative electronic structures of the M-clusters in the Synchrotron Source (CHESS), NY, USA. For all experiments, the intact MoFe and VFe proteins. A combination of high-energy flight path of the emitted X-rays was filled with He gas to mini- resolution fluorescence detected (HERFD) X-ray absorption mize signal attenuation. Samples were maintained at cryogenic spectroscopy (XAS) at the Kα (2p → 1s) and Kβ (3p → 1s) emis- temperatures, using a continuous flow liquid He cryostat at sion lines, as well as non-resonant Kβ X-ray emission spec- 10 K at ESRF and a He displex cryostat at 40 K at CHESS. For troscopy (XES) is utilized in order to obtain detailed insight all experiments, the monochromatic incident energy was cali- into the electronic structural differences in the protein active brated to the first inflection point of an iron foil (7111.2 eV), sites. By comparing the present data to previously published and the XES spectrometers were calibrated using the Kβ emis- 3,14 Δ data on both a P-cluster-only variant of nitrogenase ( nifB), sion features of Fe2O3 (Kβ′ = 7045.2 eV, Kβ1,3 = 7060.6 eV, Kβ″ = β as well as isolated FeMoco, we are able to ascertain which 7092.0 eV, K 2,5 = 7107.2 eV). spectral features correspond to the M-cluster vs. the P-cluster. Non-resonant Fe Kβ XES measurements were performed at Further insight into the role of the heterometal in tuning the both ESRF and CHESS.
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