Mechanism of Mo-Dependent Nitrogenase

Yang, Zhiyong; Danyal, Karamatullah; Seefeldt, Lance C.

doi:10.1007/978-1-61779-194-9_2

Cited by 40 publications

(28 citation statements)

References 162 publications

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“…Potential proton donor/acceptors are within hydrogen-bonding distance of the ␤Ser 188 hydroxyl group (an ordered water molecule) and the ␣Cys 88 backbone amide (␣Glu 153 side chain). Sequential hydride formation has been postulated as part of the catalytic cycle (21); therefore, the single redox P 1ϩ /P N couple fits well into the most recent proposed deficit-spending mechanism. Additionally, previous spectroscopic studies have also shown residues around the distal side of the P-cluster cubane (relative to FeMo-co) to be involved in PCET (17).…”

Section: Structure Of Nitrogenase P-cluster Intermediatesupporting

confidence: 71%

Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase

Keable

Zadvornyy

Johnson

et al. 2018

Journal of Biological Chemistry

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Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N) to ammonia (NH) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum-iron protein (MoFe protein) that contains the iron-molybdenum cofactor (FeMo-co) sites where N is reduced to NH The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the transition from the all-ferrous resting (P) state to the two-electron oxidized P state is accompanied by protein serine hydroxyl and backbone amide ligation to iron. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P, P, and P) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination, implicating that the P state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states.

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Section: Structure Of Nitrogenase P-cluster Intermediatesupporting

confidence: 71%

Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase

Keable

Zadvornyy

Johnson

et al. 2018

Journal of Biological Chemistry

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“…This proton wire and its surrounds are strictly conserved in all high-quality crystal structures [31]. Density functional calculations have The chemical mechanism through which this enzyme reduces the extremely strong N-N bond under mild conditions has been long studied but is still enigmatic [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26]. A distinctive characteristic of the hydrogenating reactions effected at FeMo-co is the large number of protons plus electrons required [9]: The stoichiometry of the physiological reaction of nitrogenase is close to N2 + An H atom bound to S3B can migrate to other Fe and S atoms of FeMo-co: see Figure 2b.…”

Section: Introductionmentioning

confidence: 99%

Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry

Dance

2019

Inorganics

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The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.

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“…Actually, the reduction of N 2 is activated by the electrons which are delivered from either ferredoxins or flavodoxins to the MoFe-protein, where the catalytic process is mediated by way of the Fe-protein [16]. The formation of the Fe-protein and MoFe-protein complex is beneficial to the intermolecular electrons' transfer which is driven by the MgATP hydrolysis and will dissociate to restart and accumulate the necessary electrons needed for N 2 reduction when the hydrolysis and the transfer are complete [26,27]. Moreover, through the associated Fe-protein conformational changes, a stepwise mechanism is anticipated to prolong the lifetime of the Fe-protein-MoFe-protein complex which, in turn, could orchestrate the sequence of intra-complex electron-transfer required for substrate reduction [28].…”

Section: Reduction Mechanism Of N 2 To Nhmentioning

confidence: 99%

Progress in Synthesizing Analogues of Nitrogenase Metalloclusters for Catalytic Reduction of Nitrogen to Ammonia

Yang

2019

Catalysts

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Ammonia (NH3) has played an essential role in meeting the increasing demand for food and the worldwide need for nitrogen (N2) fertilizer since 1913. Unfortunately, the traditional Haber–Bosch process for producing NH3 from N2 is a high energy-consumption process with approximately 1.9 metric tons of fossil CO2 being released per metric ton of NH3 produced. As a very challenging target, any ideal NH3 production process reducing fossil energy consumption and environmental pollution would be welcomed. Catalytic NH3 synthesis is an attractive and promising alternative approach. Therefore, developing efficient catalysts for synthesizing NH3 from N2 under ambient conditions would create a significant opportunity to directly provide nitrogenous fertilizers in agricultural fields as needed in a distributed manner. In this paper, the literature on alternative, available, and sustainable NH3 production processes in terms of the scientific aspects of the spatial structures of nitrogenase metalloclusters, the mechanism of reducing N2 to NH3 catalyzed by nitrogenase, the synthetic analogues of nitrogenase metalloclusters, and the opportunities for continued research are reviewed.

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Mechanism of Mo-Dependent Nitrogenase

Cited by 40 publications

References 162 publications

Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase

Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase

Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry

Progress in Synthesizing Analogues of Nitrogenase Metalloclusters for Catalytic Reduction of Nitrogen to Ammonia

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