PDBsum entry 6cdk

Oxidoreductase

PDB id: 6cdk

Contents

Protein chains

467 a.a.

522 a.a.

Ligands

HCA-ICS ×2

CLF ×2

Metals

_FE ×2

Waters ×741

PDB id:

6cdk

Name:

Oxidoreductase

Title:

Characterization of the p1+ intermediate state of nitrogenase p- cluster

Structure:

Nitrogenase molybdenum-iron protein alpha chain. Chain: a, c. Synonym: dinitrogenase, nitrogenase component i. Nitrogenase molybdenum-iron protein beta chain. Chain: b, d. Synonym: dinitrogenase, nitrogenase component i. Ec: 1.18.6.1

Source:

Azotobacter vinelandii. Organism_taxid: 354. Organism_taxid: 354

Resolution:

2.10Å R-factor: 0.233 R-free: 0.263

Authors:

S.M.Keable,O.A.Zadvornyy,A.J.Rasmussen,K.Danyal,B.J.Eilers, G.A.Prussia,A.X.Levan,L.C.Seefeldt,J.W.Peters

Key ref:

S.M.Keable et al. (2018). Structural characterization of the P¹⁺ intermediate state of the P-cluster of nitrogenase. J Biol Chem, 293, 9629-9635. PubMed id: 29720402 DOI: 10.1074/jbc.RA118.002435

Date:

08-Feb-18 Release date: 09-May-18

Supersedes:

5ijy

Protein chains

P07328  (NIFD_AZOVI) -  Nitrogenase molybdenum-iron protein alpha chain from Azotobacter vinelandii

Seq: 492 a.a.

Struc: 467 a.a.

Protein chains

P07329  (NIFK_AZOVI) -  Nitrogenase molybdenum-iron protein beta chain from Azotobacter vinelandii

Seq: 523 a.a.

Struc: 522 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.1.18.6.1 - nitrogenase.
• Pathway: Nitrogenase
• Reaction: N2 + 8 reduced [2Fe-2S]-[ferredoxin] + 16 ATP + 16 H2O = H2 + 8 oxidized [2Fe-2S]-[ferredoxin] + 2 NH4⁺ + 16 ADP + 16 phosphate + 6 H⁺
• Cofactor: Iron-sulfur; Vanadium cation or Mo cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.RA118.002435

J Biol Chem 293:9629-9635 (2018)

PubMed id: 29720402

Structural characterization of the P¹⁺ intermediate state of the P-cluster of nitrogenase.

S.M.Keable, O.A.Zadvornyy, L.E.Johnson, B.Ginovska, A.J.Rasmussen, K.Danyal, B.J.Eilers, G.A.Prussia, A.X.LeVan, S.Raugei, L.C.Seefeldt, J.W.Peters.

ABSTRACT

Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N₂) to ammonia (NH₃) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum-iron protein (MoFe protein) that contains the iron-molybdenum cofactor (FeMo-co) sites where N₂ is reduced to NH₃ The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the transition from the all-ferrous resting (P^N) state to the two-electron oxidized P²⁺ state is accompanied by protein serine hydroxyl and backbone amide ligation to iron. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P²⁺, P¹⁺, and P^N) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination, implicating that the P¹⁺ state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P²⁺ states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states.