5KOJ image
Deposition Date 2016-06-30
Release Date 2016-09-14
Last Version Date 2024-03-06
Entry Detail
PDB ID:
5KOJ
Keywords:
Title:
Nitrogenase MoFeP protein in the IDS oxidized state
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.59 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Nitrogenase protein alpha chain
Gene (Uniprot):nifD
Chain IDs:A, C
Chain Length:499
Number of Molecules:2
Biological Source:Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5)
Polymer Type:polypeptide(L)
Molecule:Nitrogenase FeMo beta subunit protein NifK
Gene (Uniprot):nifK
Chain IDs:B, D
Chain Length:511
Number of Molecules:2
Biological Source:Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5)
Primary Citation
Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer.
J.Am.Chem.Soc. 138 10124 10127 (2016)
PMID: 27487256 DOI: 10.1021/jacs.6b06783

Abstact

The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.

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Primary Citation of related structures