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bioRxiv · 10.1101/2025.09.09.675011

Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Kashyap, R.·Deere, T. M.·Dhamad, A.·Chanderban, M.·Tokmina-Lukaszewska, M.·Bothner, B.·Lessner, D. J.·Antony, E.
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Abstract

Nitrogenases are metalloenzymes that catalyze the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle. While bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases remain unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a 3.2 [A] cryo-electron microscopy structure of a native nitrogenase-PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an unprecedented assembly of three NifDK heterotetramers bridged by six NifI1,2 heterotrimeric PII complexes, which sterically block NifH association and lock the enzyme in an inactive state. The PII complexes display asymmetric binding of ADP and 2-oxoglutarate, coupling nitrogenase inhibition directly to cellular energy and nitrogen status. Addition of 2-oxoglutarate and ATP releases the NifI complexes, stimulating a threefold increase in NifDK activity in vitro. This higher-order architecture uncovers a previously unrecognized regulatory strategy in methanogens, in which PII proteins drive nitrogenase oligomerization to control activity. The discovery that nitrogenase activity may be modulated through direct assembly into higher-order structures opens new avenues for exploring nitrogenase evolution, regulation, and biotechnological applications. One sentence summaryDiscovery of a nitrogenase-PII protein supercomplex in methanogens, uncovering a metabolite-gated assembly mechanism for nitrogenase inhibition.

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Kashyap, R., Deere, T. M., Dhamad, A., Chanderban, M., Tokmina-Lukaszewska, M., Bothner, B., Lessner, D. J., Antony, E.. 2025-09-10. Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex. https://doi.org/10.1101/2025.09.09.675011

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