PDBsum entry 1de0

Oxidoreductase

PDB id: 1de0

Contents

Protein chains

289 a.a. *

Ligands

SF4

Waters ×224

* Residue conservation analysis

PDB id:

1de0

Name:

Oxidoreductase

Title:

Modulating the midpoint potential of the [4fe-4s] cluster of the nitrogenase fe protein

Structure:

Nitrogenase iron protein. Chain: a, b. Mutation: yes

Source:

Azotobacter vinelandii. Organism_taxid: 354

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.221 R-free: 0.281

Authors:

S.B.Jang,L.C.Seefeldt,J.W.Peters

Key ref:

S.B.Jang et al. (2000). Modulating the midpoint potential of the [4Fe-4S] cluster of the nitrogenase Fe protein. Biochemistry, 39, 641-648. PubMed id: 10651628 DOI: 10.1021/bi991694v

Date:

12-Nov-99 Release date: 09-Feb-00

Protein chains

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

Seq: 290 a.a.

Struc: 289 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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⁺
• Cofactor: Iron-sulfur; Vanadium cation or Mo cation

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

reference

DOI no: 10.1021/bi991694v

Biochemistry 39:641-648 (2000)

PubMed id: 10651628

Modulating the midpoint potential of the [4Fe-4S] cluster of the nitrogenase Fe protein.

S.B.Jang, L.C.Seefeldt, J.W.Peters.

ABSTRACT

Protein-bound [FeS] clusters function widely in biological electron-transfer reactions, where their midpoint potentials control both the kinetics and thermodynamics of these reactions. The polarity of the protein environment around [FeS] clusters appears to contribute largely to modulating their midpoint potentials, with local protein dipoles and water dipoles largely defining the polarity. The function of the [4Fe-4S] cluster containing Fe protein in nitrogenase catalysis is, at least in part, to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. Phenylalanine at position 135 is located near the [4Fe-4S] cluster of nitrogenase Fe protein and has been suggested by amino acid substitution studies to participate in defining both the midpoint potential and the nucleotide-induced changes in the [4Fe-4S] cluster. In the present study, the crystal structure of the Azotobacter vinelandii nitrogenase Fe protein variant having phenylalanine at position 135 substituted by tryptophan has been determined by X-ray diffraction methods and refined to 2.4 A resolution. A comparison of available Fe protein structures not only provides a structural basis for the more positive midpoint potential observed in the tryptophan substituted variant but also suggests a possible general mechanism by which the midpoint potential could be controlled by nucleotide interactions and nitrogenase complex formation.