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Structure paper

TitleStructural basis for the conformational protection of nitrogenase from O.
Journal, issue, pagesNature, Vol. 637, Issue 8047, Page 991-997, Year 2025
Publish dateJan 8, 2025
AuthorsSarah M Narehood / Brian D Cook / Suppachai Srisantitham / Vanessa H Eng / Angela A Shiau / Kelly L McGuire / R David Britt / Mark A Herzik / F Akif Tezcan /
PubMed AbstractThe low reduction potentials required for the reduction of dinitrogen (N) render metal-based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O). Such O sensitivity ...The low reduction potentials required for the reduction of dinitrogen (N) render metal-based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O). Such O sensitivity represents a major conundrum for the enzyme nitrogenase, as a large fraction of nitrogen-fixing organisms are either obligate aerobes or closely associated with O-respiring organisms to support the high energy demand of catalytic N reduction. To counter O damage to nitrogenase, diazotrophs use O scavengers, exploit compartmentalization or maintain high respiration rates to minimize intracellular O concentrations. A last line of damage control is provided by the 'conformational protection' mechanism, in which a [2Fe:2S] ferredoxin-family protein termed FeSII (ref. ) is activated under O stress to form an O-resistant complex with the nitrogenase component proteins. Despite previous insights, the molecular basis for the conformational O protection of nitrogenase and the mechanism of FeSII activation are not understood. Here we report the structural characterization of the Azotobacter vinelandii FeSII-nitrogenase complex by cryo-electron microscopy. Our studies reveal a core complex consisting of two molybdenum-iron proteins (MoFePs), two iron proteins (FePs) and one FeSII homodimer, which polymerize into extended filaments. In this three-protein complex, FeSII mediates an extensive network of interactions with MoFeP and FeP to position their iron-sulphur clusters in catalytically inactive but O-protected states. The architecture of the FeSII-nitrogenase complex is confirmed by solution studies, which further indicate that the activation of FeSII involves an oxidation-induced conformational change.
External linksNature / PubMed:39779844 / PubMed Central
MethodsEM (single particle)
Resolution2.27 - 3.94 Å
Structure data

45923

9ctz

EMDB-45923, PDB-9ctz:
Azotobacter vinelandii MoFeP (C2 symmetry)
Method: EM (single particle) / Resolution: 2.67 Å

45924

9cu0

EMDB-45924, PDB-9cu0:
Azotobacter vinelandii 1:1:1 MoFeP:FeP:FeSII-Complex (C1 symmetry)
Method: EM (single particle) / Resolution: 3.94 Å

45925

9cu1

EMDB-45925, PDB-9cu1:
Azotobacter vinelandii filamentous 2:2:1 MoFeP:FeP:FeSII-Complex (termini; C1 symmetry)
Method: EM (single particle) / Resolution: 2.83 Å

45926

9cu2

EMDB-45926, PDB-9cu2:
Azotobacter vinelandii filamentous 2:2:1 MoFeP:FeP:FeSII-Complex (C2 symmetry)
Method: EM (single particle) / Resolution: 2.27 Å

Chemicals

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

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

ChemComp-FE:
Unknown entry

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

ChemComp-HOH:
WATER

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

Source
  • azotobacter vinelandii (bacteria)
KeywordsMETAL BINDING PROTEIN / Nitrogenase / FeMoCo / nitrogen / P-cluster

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