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The structure of the yeast nadh dehydrogenase (ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates

Academic Article
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Overview

authors

  • Iwata, M.
  • Lee, Y.
  • Yamashita, T.
  • Yagi, Takao
  • Iwata, S.
  • Cameron, A. D.
  • Maher, M. J.

publication date

  • September 2012

journal

  • Proceedings of the National Academy of Sciences of the United States of America  Journal

abstract

  • Bioenergy is efficiently produced in the mitochondria by the respiratory system consisting of complexes I-V. In various organisms, complex I can be replaced by the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the transfer of an electron from NADH via FAD to quinone, without proton pumping. The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the matrix. A number of studies have investigated the potential use of Ndi1 as a therapeutic agent against complex I disorders, and the NDH-2 enzymes have emerged as potential therapeutic targets for treatments against the causative agents of malaria and tuberculosis. Here we present the crystal structures of Ndi1 in its substrate-free, NAD(+)- and ubiquinone- (UQ2) complexed states. The structures reveal that Ndi1 is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure. Crucially, the structures of the Ndi1-NAD(+) and Ndi1-UQ2 complexes show overlapping binding sites for the NAD(+) and quinone substrates.

subject areas

  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • Cytoplasm
  • Dimerization
  • Electron Transport Complex I
  • Electrons
  • Escherichia coli
  • Lipids
  • Molecular Conformation
  • Mutation
  • Protein Structure, Tertiary
  • Protons
  • Quinones
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Static Electricity
  • Water
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Research

keywords

  • alternative complex I
  • structural biology
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Identity

PubMed Central ID

  • PMC3458368

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.1210059109

PubMed ID

  • 22949654
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Additional Document Info

start page

  • 15247

end page

  • 15252

volume

  • 109

issue

  • 38

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