PDBsum entry 1xdb

Oxidoreductase

PDB id: 1xdb

Contents

Protein chains

289 a.a. *

Ligands

SF4

* Residue conservation analysis

PDB id:

1xdb

Name:

Oxidoreductase

Title:

Crystal structure of the nitrogenase fe protein asp129glu

Structure:

Nitrogenase iron protein 1. Chain: a, b. Synonym: nitrogenase fe protein, nitrogenase component ii, nitrogenase reductase. Engineered: yes. Mutation: yes

Source:

Azotobacter vinelandii. Organism_taxid: 354. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.227 R-free: 0.299

Authors:

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

Key ref:

S.B.Jang et al. (2004). Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii. J Biol Inorg Chem, 9, 1028-1033. PubMed id: 15549494

Date:

05-Sep-04 Release date: 01-Mar-05

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

J Biol Inorg Chem 9:1028-1033 (2004)

PubMed id: 15549494

Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii.

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

ABSTRACT

The structures of nitrogenase Fe proteins with defined amino acid substitutions in the previously implicated nucleotide-dependent signal transduction pathways termed switch I and switch II have been determined by X-ray diffraction methods. In the Fe protein of nitrogenase the nucleotide-dependent switch regions are responsible for communication between the sites responsible for nucleotide binding and hydrolysis and the [4Fe-4S] cluster of the Fe protein and the docking interface that interacts with the MoFe protein upon macromolecular complex formation. In this study the structural characterization of the Azotobacter vinelandii nitrogenase Fe protein with Asp at position 39 substituted by Asn in MgADP-bound and nucleotide-free states provides an explanation for the experimental observation that the altered Fe proteins form a trapped complex subsequent to a single electron transfer event. The structures reveal that the substitution allows the formation of a hydrogen bond between the switch I Asn39 and the switch II Asp125. In the structure of the native enzyme the analogous interaction between the side chains of Asp39 and Asp125 is precluded due to electrostatic repulsion. These results suggest that the electrostatic repulsion between Asp39 and Asp125 is important for dissociation of the Fe protein:MoFe protein complex during catalysis. In a separate study, the structural characterization of the Fe protein with Asp129 substituted by Glu provides the structural basis for the observation that the Glu129-substituted variant in the absence of bound nucleotides has biochemical properties in common with the native Fe protein with bound MgADP. Interactions of the longer Glu side chain with the phosphate binding loop (P-loop) results in a similar conformation of the switch II region as the conformation that results from the binding of the phosphate of ADP to the P-loop.