Structural consequences of turnover-induced homocitrate loss in nitrogenase

Rebeccah A. Warmack (), Ailiena O. Maggiolo, Andres Orta, Belinda B. Wenke, James B. Howard and Douglas C. Rees ()
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Rebeccah A. Warmack: California Institute of Technology
Ailiena O. Maggiolo: California Institute of Technology
Andres Orta: California Institute of Technology
Belinda B. Wenke: California Institute of Technology
James B. Howard: University of Minnesota
Douglas C. Rees: California Institute of Technology

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: Abstract Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein – a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA – that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.

Date: 2023
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DOI: 10.1038/s41467-023-36636-4

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