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Structure paper

TitleStructural consequences of turnover-induced homocitrate loss in nitrogenase.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 1091, Year 2023
Publish dateFeb 25, 2023
AuthorsRebeccah A Warmack / Ailiena O Maggiolo / Andres Orta / Belinda B Wenke / James B Howard / Douglas C Rees /
PubMed AbstractNitrogenase 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 linksNat Commun / PubMed:36841829 / PubMed Central
MethodsEM (single particle)
Resolution1.92 - 2.71 Å
Structure data

EMDB-26957, PDB-8crs:
CryoEM Structure of nitrogenase MoFe-protein in detergent
Method: EM (single particle) / Resolution: 2.04 Å

EMDB-27316, PDB-8dbx:
CryoEM structure of partially oxidized MoFe-protein on ultrathin carbon
Method: EM (single particle) / Resolution: 1.92 Å

EMDB-28272, PDB-8enl:
CryoEM structure of the high pH turnover-inactivated nitrogenase MoFe-protein
Method: EM (single particle) / Resolution: 2.37 Å

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

EMDB-28274, PDB-8enn:
Homocitrate-deficient nitrogenase MoFe-protein from Azotobacter vinelandii nifV knockout
Method: EM (single particle) / Resolution: 2.58 Å

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 / detergent*YM

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)
KeywordsMETAL BINDING PROTEIN / OXIDOREDUCTASE / Nitrogenase / metalloenzyme / nitrogen fixation / reductase / MoFe

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