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Structure paper

TitleStructural evolution of nitrogenase states under alkaline turnover.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 10472, Year 2024
Publish dateDec 2, 2024
AuthorsRebeccah A Warmack / Douglas C Rees /
PubMed AbstractBiological nitrogen fixation, performed by the enzyme nitrogenase, supplies nearly 50% of the bioavailable nitrogen pool on Earth, yet the structural nature of the enzyme intermediates involved in ...Biological nitrogen fixation, performed by the enzyme nitrogenase, supplies nearly 50% of the bioavailable nitrogen pool on Earth, yet the structural nature of the enzyme intermediates involved in this cycle remains ambiguous. Here we present four high resolution cryoEM structures of the nitrogenase MoFe-protein, sampled along a time course of alkaline reaction mixtures under an acetylene atmosphere. This series of structures reveals a sequence of salient changes including perturbations to the inorganic framework of the FeMo-cofactor; depletion of the homocitrate moiety; diminished density around the S2B belt sulfur of the FeMo-cofactor; rearrangements of cluster-adjacent side chains; and the asymmetric displacement of the FeMo-cofactor. We further demonstrate that the nitrogenase associated factor T protein can recognize and bind an alkaline inactivated MoFe-protein in vitro. These time-resolved structures provide experimental support for the displacement of S2B and distortions of the FeMo-cofactor at the E-E intermediates of the substrate reduction mechanism, prior to nitrogen binding, highlighting cluster rearrangements potentially relevant to nitrogen fixation by biological and synthetic clusters.
External linksNat Commun / PubMed:39622820 / PubMed Central
MethodsEM (single particle)
Resolution1.92 - 2.33 Å
Structure data

45626

9cjb

EMDB-45626, PDB-9cjb:
CryoEM structure of nitrogenase MoFe-protein 60 minute time point under alkaline turnover
Method: EM (single particle) / Resolution: 1.97 Å

45627

9cjc

EMDB-45627, PDB-9cjc:
CryoEM structure of nitrogenase MoFe-protein 20 minute time point under alkaline turnover
Method: EM (single particle) / Resolution: 2.04 Å

45628

9cjd

EMDB-45628, PDB-9cjd:
CryoEM structure of nitrogenase MoFe-protein 5 minute time point under alkaline turnover
Method: EM (single particle) / Resolution: 1.92 Å

45629

9cje

EMDB-45629, PDB-9cje:
CryoEM structure of nitrogenase MoFe-protein 20 second time point under alkaline turnover
Method: EM (single particle) / Resolution: 2.22 Å

45630

9cjf

EMDB-45630, PDB-9cjf:
CryoEM structure of alkaline-inactivated nitrogenase MoFe-protein in complex with NafT
Method: EM (single particle) / Resolution: 2.33 Å

Chemicals

ChemComp-ICS:
iron-sulfur-molybdenum cluster with interstitial carbon

ChemComp-CLF:
FE(8)-S(7) CLUSTER

ChemComp-FE:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-HCA:
3-HYDROXY-3-CARBOXY-ADIPIC ACID

ChemComp-1N7:
CHAPSO / detergent*YM

Source
  • azotobacter vinelandii (bacteria)
KeywordsMETAL BINDING PROTEIN / Oxidoreductase

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