Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum

Schlessman, J. L., Woo, D., Joshua-Tor, L., Howard, J. B., Rees, D. C. (1998) Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. Journal of Molecular Biology, 280 (4). pp. 669-685. ISSN 00222836 (ISSN)

URL: https://www.ncbi.nlm.nih.gov/pubmed/9677296
DOI: 10.1006/jmbi.1998.1898

Abstract

The nitrogenase iron (Fe) protein performs multiple functions during biological nitrogen fixation, including mediating the mechanistically essential coupling between ATP hydrolysis and electron transfer to the nitrogenase molybdenum iron (MoFe) protein during substrate reduction, and participating in the biosynthesis and insertion of the FeMo-cofactor into the MoFe-protein. To establish a structural framework for addressing the diverse functions of Fe-protein, crystal structures of the Fe-proteins from Azotobacter vinelandii and Clostridium pasteurianum have been determined at resolutions of 2.2 Å and 1.93 Å, respectively. These two Fe-proteins are among the more diverse in terms of amino acid sequence and biochemical properties. As described initially for the A. vinelandii Fe-protein in a different crystal form at 2.9 Å resolution, each subunit of the dimeric Fe-protein adopts a polypeptide fold related to other mononucleotide-binding proteins such as G-proteins, with the two subunits bridged by a 4Fe:4S cluster. The overall similarities in the subunit fold and dimer arrangement observed in the structures of the A. vinelandii and C. pasteurianum Fe-proteins indicate that they are representative of the conformation of free Fe-protein that is not in complex with nucleotide or the MoFe-protein. Residues in the cluster and nucleotide-binding sites are linked by a network of conserved hydrogen bonds, salt-bridges and water molecules that may conformationally couple these regions. Significant variability is observed in localized regions, especially near the 4Fe:4S cluster and the MoFe-protein binding surface, that change conformation upon formation of the ADP·AlF4- stabilized complex with the MoFe-protein. A core of 140 conserved residues is identified in an alignment of 59 Fe-protein sequences that may be useful for the identification of homologous proteins with functions comparable to that of Fe-protein in non-nitrogen fixing systems.

Item Type: Paper
Uncontrolled Keywords: Iron-sulfur proteins Macromolecular structure Metalloproteins Nitrogen fixation Nucleotide-binding proteins guanine nucleotide binding protein iron sulfur protein nitrogenase protein subunit amino acid sequence article azotobacter vinelandii clostridium pasteurianum conformational transition crystal structure hydrogen bond nonhuman nucleotide sequence priority journal protein conformation protein folding unindexed sequence Bacterial Proteins Clostridium Dimerization Models, Molecular Molecular Sequence Data Nucleotides Oxidoreductases Sequence Alignment Sequence Homology Amino Acid Bacteria (microorganisms) Posibacteria
Subjects: Investigative techniques and equipment > X-Ray Diffraction
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein structure rendering
Investigative techniques and equipment > x ray crystallography
CSHL Authors:
Communities: CSHL labs > Joshua-Tor lab
Depositing User: CSHL Librarian
Date Deposited: 20 Mar 2012 20:57
Last Modified: 07 Sep 2017 13:34
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Dataset ID:
URI: http://repository.cshl.edu/id/eprint/25502

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