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

Nitrogenases are metalloenzymes that catalyse the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle1,2. Although bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases have remained unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a cryo-electron microscopy structure of a native nitrogenase-PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an 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 show 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 identifies a regulatory strategy in methanogens in which PII proteins drive nitrogenase oligomerization to control activity. The finding that nitrogenase activity may be modulated through direct assembly into higher-order structures indicates future directions for the exploration of nitrogenase evolution, regulation and biotechnological applications.