PDBsum entry 6n4m

Oxidoreductase

PDB id: 6n4m

Contents

Protein chain

283 a.a.

Ligands

ADP

SF4

Metals

_MG

Waters ×115

PDB id:

6n4m

Name:

Oxidoreductase

Title:

Ids-oxidized adp-bound form of the nitrogenase fe-protein from a. Vinelandii

Structure:

Nitrogenase iron protein 1. Chain: a. Synonym: nitrogenase fe protein 1,nitrogenase component ii, nitrogenase reductase. Ec: 1.18.6.1

Source:

Azotobacter vinelandii. Organism_taxid: 354

Resolution:

1.58Å R-factor: 0.165 R-free: 0.188

Authors:

B.B.Wenke,T.Spatzal,D.C.Rees

Key ref:

B.B.Wenke et al. (2019). Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]^2+/1+/0 States of the Nitrogenase Fe-Protein. Angew Chem Int Ed Engl, 58, 3894-3897. PubMed id: 30698901 DOI: 10.1002/anie.201813966

Date:

19-Nov-18 Release date: 13-Feb-19

Protein chain

P00459  (NIFH1_AZOVI) -  Nitrogenase iron protein 1 from Azotobacter vinelandii

Seq: 290 a.a.

Struc: 283 a.a.

Enzyme reactions

• Enzyme class: 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⁺

N2 + 8 × reduced [2Fe-2S]-[ferredoxin] + 16 × ATP + 16 × H2O = H2 (Bound ligand (Het Group name = ADP) corresponds exactly) + 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: 10.1002/anie.201813966

Angew Chem Int Ed Engl 58:3894-3897 (2019)

PubMed id: 30698901

Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]^2+/1+/0 States of the Nitrogenase Fe-Protein.

B.B.Wenke, T.Spatzal, D.C.Rees.

ABSTRACT

The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+, and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-Å resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]¹⁺ state, our analysis identifies a solvent exposed, delocalized Fe^2.5+ pair and a buried Fe²⁺ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S]⁰ and [4Fe:4S]²⁺ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe²⁺ and valence delocalized Fe^2.5+ , respectively.