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

Published: 10/07/2026, 12:00 AM

Nature (2026) Cite this article 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. This is a preview of subscription content, access via your institution Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription Prices may be subject to local taxes which are calculated during checkout The single-particle cryo-EM maps and models have been deposited into the Protein Data Bank and Electron Microscopy Data Bank with the following accession codes: state 1 (D*KKD*) PDB 11UY and EMD-76071; state 2 (DKKD*) PDB 11SX and EMD-76025; state 3 (PII–DKKD*) PDB 11MY and EMD-75852; state 4 (supercomplex (C1 symmetry), (PII–DKKD–PII)3 PDB 9P1X and EMD-71144; state 4 (supercomplex (C3 symmetry), (PII–DKKD–PII)3 PDB 12AH and EMD-70378; state 5 (D#KKD*) PDB 11ZK and EMD-76217; and supercomplex (PII–DKKD–PII)3 from strictly anoxic grids PDB 37CY and EMD-78079. Source data are provided with this paper. Peters, J. W., Fisher, K. & Dean, D. R. Nitrogenase structure and function: a biochemical-genetic perspective. Annu. Rev. Microbiol. 49, 335–366 https://doi.org/10.1146/annurev.mi.49.100195.002003 (1995). Article CAS PubMed Google Scholar Seefeldt, L. C., Hoffman, B. M. & Dean, D. R. Mechanism of Mo-dependent nitrogenase. Annu. Rev. Biochem. 78, 701–722 https://doi.org/10.1146/annurev.biochem.78.070907.103812 (2009).