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

Keable, S.M.; Zadvornyy, Oleg A.; Johnson, Lewis E.; Ginovska, Bojana; Rasmussen, Andrew J.; Danyal, Karamatullah; Eilers, Brian J.; Prussia, Gregory A.; LeVan, Axl X.; Raugei, Simone; Seefeldt, Lance C.; Peters, John W.

doi:10.1074/jbc.ra118.002435

Cited by 49 publications

(75 citation statements)

References 40 publications

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“…We have extended the quantum-refinement approach to allow for multiple conformations in the QM systems. Below, we first describe the implementation of this approach with dual conformations and then illustrate its performance for the Pcluster in two crystal structures of nitrogenase: PDB entries 3u7q (Spatzal et al, 2011) and 6cpk (Keable et al, 2018).…”

Section: Resultsmentioning

confidence: 99%

“…1b). These have been shown to be the proper protonation states of the Pcluster (Keable et al, 2018;. Thereby, the net charge of the QM system is À4 in all three states, because the addition of an electron is compensated by the deprotonation of SerD188 or CysC88.…”

Section: Qm Calculationsmentioning

confidence: 96%

“…The two-electron oxidation of the P-cluster from P N to P 2+ is accompanied by the deprotonation of two protein residues: the OG atom of SerD188 and the backbone N atom of CysC88 (Spatzal et al, 2011;Keable et al, 2018). The deprotonated groups coordinate to the Fe6 and Fe5 ions, causing the movement of these two ions away from the S1 ion, cleaving the Fe5-S1 and Fe6-S1 bonds and giving rise to a distorted structure of the second cubane in the P-cluster in the P 2+ state.…”

Section: Performance Of Comqumx-2qm For Pdb Entry 3u7qmentioning

confidence: 99%

“…Quantum refinement is a powerful technique for detecting the presence of multiple conformations, characterized by the fact that no single structural interpretation fits the crystallographic data satisfactorily (Sö derhjelm & Ryde, 2006;Rulíšek & Ryde, 2006;Cao & Ryde, 2020). For example, we have shown that a recent crystal structure of the putative one-electron oxidized state (P 1+ ) of the P-cluster in nitrogenase (Keable et al, 2018) actually contains a mixture of one-and two-electron oxidized states . This means that the structural details (for example Fe-Fe and Fe-S bond lengths) of the crystal structure cannot be trusted, even after quantum refinement, because the structure is a mixture of two oxidation states, giving distances that are weighted averages.…”

Section: Introductionmentioning

confidence: 99%

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Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

Cao

Ryde

2020

Acta Cryst Sect D Struct Biol

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X-ray crystallography is the main source of atomistic information on the structure of proteins. Normal crystal structures are obtained as a compromise between the X-ray scattering data and a set of empirical restraints that ensure chemically reasonable bond lengths and angles. However, such restraints are not always available or accurate for nonstandard parts of the structure, for example substrates, inhibitors and metal sites. The method of quantum refinement, in which these empirical restraints are replaced by quantum-mechanical (QM) calculations, has previously been suggested for small but interesting parts of the protein. Here, this approach is extended to allow for multiple conformations in the QM region by performing separate QM calculations for each conformation. This approach is shown to work properly and leads to improved structures in terms of electron-density maps and real-space difference density Z-scores. It is also shown that the quality of the structures can be gauged using QM strain energies. The approach, called ComQumX-2QM, is applied to the P-cluster in two different crystal structures of the enzyme nitrogenase, i.e. an Fe8S7Cys6 cluster, used for electron transfer. One structure is at a very high resolution (1.0 Å) and shows a mixture of two different oxidation states, the fully reduced PN state (Fe8 2+, 20%) and the doubly oxidized P2+ state (80%). In the original crystal structure the coordinates differed for only two iron ions, but here it is shown that the two states also show differences in other atoms of up to 0.7 Å. The second structure is at a more modest resolution, 2.1 Å, and was originally suggested to show only the one-electron oxidized state, P1+. Here, it is shown that it is rather a 50/50% mixture of the P1+ and P2+ states and that many of the Fe—Fe and Fe—S distances in the original structure were quite inaccurate (by up to 0.8 Å). This shows that the new ComQumX-2QM approach can be used to sort out what is actually seen in crystal structures with dual conformations and to give locally improved coordinates.

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Section: Resultsmentioning

confidence: 99%

Section: Qm Calculationsmentioning

confidence: 96%

Section: Performance Of Comqumx-2qm For Pdb Entry 3u7qmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

Cao

Ryde

2020

Acta Cryst Sect D Struct Biol

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“…Next, the peripheric Fe‐protein hydrolyzes MgATP to offer the necessary energy/electrons for the following multiple proton–electron transfer (PET) processes toward ammonia generation . During these dinitrogen reduction processes, the Fe–protein scaffold around the cofactor serves as a coordination buffer sphere by H‐bonding and redox‐active moieties, enabling steady progress of the PET process at a low energy barrier (see Figure c). Above all, the active centers capable of adsorbing dinitrogen, such as transition metals Fe and Mo, coupled with efficient electron transfer pathways from electrocatalysts to the antibonding π* orbitals of dinitrogen, are particularly crucial for NN bond cleavage in NRR using electrocatalysts.…”

Section: Fundamental Comprehension On Dinitrogen Electroreductionmentioning

confidence: 99%

Atomic Modulation, Structural Design, and Systematic Optimization for Efficient Electrochemical Nitrogen Reduction

et al. 2020

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Ammonia (NH3) is a pivotal precursor in fertilizer production and a potential energy carrier. Currently, ammonia production worldwide relies on the traditional Haber–Bosch process, which consumes massive energy and has a large carbon footprint. Recently, electrochemical dinitrogen reduction to ammonia under ambient conditions has attracted considerable interest owing to its advantages of flexibility and environmental friendliness. However, the biggest challenge in dinitrogen electroreduction, i.e., the low efficiency and selectivity caused by poor specificity of electrocatalysts/electrolytic systems, still needs to be overcome. Although substantial progress has been made in recent years, acquiring most available electrocatalysts still relies on low efficiency trial‐and‐error methods. It is thus imperative to establish some critical guiding principles for nitrogen electroreduction toward a rational design and accelerated development of this field. Herein, a basic understanding of dinitrogen electroreduction processes and the inherent relationships between adsorbates and catalysts from fundamental theory are described, followed by an outline of the crucial principles for designing efficient electrocatalysts/electrocatalytic systems derived from a systematic evaluation of the latest significant achievements. Finally, the future research directions and prospects of this field are given, with a special emphasis on the opportunities available by following the guiding principles.

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Nitrogenase: Metal Cluster Models

Ohta

2019

Encyclopedia of Inorganic and Bioinorganic Chemistry

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Nitrogenases are metalloenzymes that are involved in the biological fixation of nitrogen. Nitrogenases contain the following metal–sulfur clusters: the [Fe 4 S 4 ] cluster, the P‐cluster, and one of the FeMo‐cofactor, the FeV‐cofactor, or the FeFe‐cofactor. At present, structures of all clusters except for that of the FeFe‐cofactor have been determined by X‐ray diffraction studies of nitrogenases. The metal–sulfur clusters in nitrogenases have remained challenging synthetic targets due to their unique structural features. In addition, the elucidation of the properties of the cluster models, including their structural, spectroscopic, magnetic, and electronic characteristics, as well as their reactivity may further our understanding of the properties and functionality of nitrogenases. This article reviews hitherto reported structural models of nitrogenase metalloclusters. Although the synthesis of reliable structural models of the FeMo‐cofactor and the FeV‐cofactor remains challenging, high‐precision structural models have already been obtained for the [Fe 4 S 4 ] cluster and the P‐cluster, which has allowed systematic investigations into their structures and redox properties. This article also summarizes the current state‐of‐the‐art regarding the functional modeling of nitrogenases with metal–sulfur clusters, which includes the reduction of hydrazine to ammonia and of C 1 ‐substrates to hydrocarbons, and N 2 ‐binding. Moreover, the reactivity of nitrogenase with a structural model inserted instead of the FeMo‐cofactor has recently been reported.

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

Cited by 49 publications

References 40 publications

Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

Atomic Modulation, Structural Design, and Systematic Optimization for Efficient Electrochemical Nitrogen Reduction

Nitrogenase: Metal Cluster Models

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