Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Structural consequences of turnover-induced homocitrate loss in nitrogenase.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 1091, Year 2023
Publish date	Feb 25, 2023
Authors	Rebeccah A Warmack / Ailiena O Maggiolo / Andres Orta / Belinda B Wenke / James B Howard / Douglas C Rees /
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 ...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.
External links	Nat Commun / PubMed:36841829 / PubMed Central
Methods	EM (single particle)
Resolution	1.92 - 2.71 Å
Structure data	26957 8crs EMDB-26957, PDB-8crs: CryoEM Structure of nitrogenase MoFe-protein in detergent Method: EM (single particle) / Resolution: 2.04 Å 27316 8dbx EMDB-27316, PDB-8dbx: CryoEM structure of partially oxidized MoFe-protein on ultrathin carbon Method: EM (single particle) / Resolution: 1.92 Å 28272 8enl EMDB-28272, PDB-8enl: CryoEM structure of the high pH turnover-inactivated nitrogenase MoFe-protein Method: EM (single particle) / Resolution: 2.37 Å 28273 8enm EMDB-28273, PDB-8enm: CryoEM structure of the high pH nitrogenase MoFe-protein under non-turnover conditions Method: EM (single particle) / Resolution: 2.14 Å 28274 8enn EMDB-28274, PDB-8enn: Homocitrate-deficient nitrogenase MoFe-protein from Azotobacter vinelandii nifV knockout Method: EM (single particle) / Resolution: 2.58 Å 28275 8eno EMDB-28275, PDB-8eno: Homocitrate-deficient nitrogenase MoFe-protein from A. vinelandii nifV knockout in complex with NafT Method: EM (single particle) / Resolution: 2.71 Å
Chemicals	ChemComp-ICS: iron-sulfur-molybdenum cluster with interstitial carbon ChemComp-HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID ChemComp-1N7: CHAPSO / detergentYM ChemComp-CLF: FE(8)-S(7) CLUSTER ChemComp-FE: Unknown entry ChemComp-HOH: WATER ChemComp-1CL: FE(8)-S(7) CLUSTER, OXIDIZED ChemComp-UNX: Unknown entry ChemComp-CIT*: CITRIC ACID
Source	azotobacter vinelandii (bacteria) azotobacter vinelandii dj (bacteria)
Keywords	METAL BINDING PROTEIN / OXIDOREDUCTASE / Nitrogenase / metalloenzyme / nitrogen fixation / reductase / MoFe