7BI7

An Unexpected P-Cluster like Intermediate En Route to the Nitrogenase FeMo-co

Summary for 7BI7

• Entry DOI: 10.2210/pdb7bi7/pdb
• Descriptor: FeMo cofactor biosynthesis protein NifB, IRON/SULFUR CLUSTER, FE(8)-S(7) CLUSTER, ... (7 entities in total)
• Functional Keywords: nitrogenase, radical sam enzyme, iron-molybdenum cofactor biosynthesis, metal binding protein
• Biological source: Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
• Total number of polymer chains: 2
• Total formula weight: 67291.20

Authors

Jenner, L.P.,Cherrier, M.V.,Amara, P.,Rubio, L.M.,Nicolet, Y. (deposition date: 2021-01-12, release date: 2021-03-10, Last modification date: 2024-11-06)

Primary citation

Jenner, L.P.,Cherrier, M.V.,Amara, P.,Rubio, L.M.,Nicolet, Y.
An unexpected P-cluster like intermediate en route to the nitrogenase FeMo-co.
Chem Sci, 12:5269-5274, 2021

PubMed Abstract: The nitrogenase MoFe protein contains two different FeS centers, the P-cluster and the iron-molybdenum cofactor (FeMo-co). The former is a [FeS] center responsible for conveying electrons to the latter, a [MoFeSC-()-homocitrate] species, where N reduction takes place. NifB is arguably the key enzyme in FeMo-co assembly as it catalyzes the fusion of two [FeS] clusters and the insertion of carbide and sulfide ions to build NifB-co, a [FeSC] precursor to FeMo-co. Recently, two crystal structures of NifB proteins were reported, one containing two out of three [FeS] clusters coordinated by the protein which is likely to correspond to an early stage of the reaction mechanism. The other one was fully complemented with the three [FeS] clusters (RS, K1 and K2), but was obtained at lower resolution and a satisfactory model was not obtained. Here we report improved processing of this crystallographic data. At odds with what was previously reported, this structure contains a unique [FeS] cluster, likely to be a NifB-co precursor resulting from the fusion of K1- and K2-clusters. Strikingly, this new [FeS] cluster has both a structure and coordination sphere geometry reminiscent of the fully reduced P-cluster (P-state) with an additional μ-bridging sulfide ion pointing toward the RS cluster. Comparison of available NifB structures further unveils the plasticity of this protein and suggests how ligand reorganization would accommodate cluster loading and fusion in the time-course of NifB-co synthesis.

PubMed: 34168778
DOI: 10.1039/d1sc00289a

Experimental method

X-RAY DIFFRACTION (3 Å)