8DBX

CryoEM structure of partially oxidized MoFe-protein on ultrathin carbon

Summary for 8DBX

• Entry DOI: 10.2210/pdb8dbx/pdb
• EMDB information: 27316 27317
• Descriptor: Nitrogenase molybdenum-iron protein alpha chain, Nitrogenase molybdenum-iron protein beta chain, iron-sulfur-molybdenum cluster with interstitial carbon, ... (8 entities in total)
• Functional Keywords: nitrogenase, metalloenzyme, metal binding protein, oxidoreductase
• Biological source: Azotobacter vinelandii; More
• Total number of polymer chains: 4
• Total formula weight: 234581.60

Authors

Warmack, R.A.,Rees, D.C. (deposition date: 2022-06-14, release date: 2023-03-08, Last modification date: 2024-06-12)

Primary citation

Warmack, R.A.,Maggiolo, A.O.,Orta, A.,Wenke, B.B.,Howard, J.B.,Rees, D.C.
Structural consequences of turnover-induced homocitrate loss in nitrogenase.
Nat Commun, 14:1091-1091, 2023

PubMed 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.

PubMed: 36841829
DOI: 10.1038/s41467-023-36636-4

Experimental method

ELECTRON MICROSCOPY (1.92 Å)