Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Sep 18;109(38):15247-52.
doi: 10.1073/pnas.1210059109. Epub 2012 Sep 4.

The Structure of the Yeast NADH Dehydrogenase (Ndi1) Reveals Overlapping Binding Sites for Water- And Lipid-Soluble Substrates

Affiliations
Free PMC article

The Structure of the Yeast NADH Dehydrogenase (Ndi1) Reveals Overlapping Binding Sites for Water- And Lipid-Soluble Substrates

Momi Iwata et al. Proc Natl Acad Sci U S A. .
Free PMC article

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.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Crystal structure of Ndi1. (A) Cartoon representation of the Ndi1 monomer. The FAD-binding, NADH-binding, and membrane-anchor domains are colored green, lilac, and pink, respectively. The FAD (yellow) cofactor is represented as sticks. (B) The Ndi1 dimer. Both monomers are represented as cartoons, with molecule A in pale cyan and molecule B in gray. The FAD cofactors are shown as yellow spheres. Transparent surface representations of both monomers are also shown. The interaction surface between monomers is extensive at ∼9% of the surface area of each monomer. (C) Monomer B only from the representation in B is shown alone, with the regions of surface that interact with monomer A in the dimer highlighted: residues 103–116, blue; residues 145–165, red; residues 198–219 green; residues 489–513, pink.
Fig. 2.
Fig. 2.
Ndi1 surface electrostatic charge and hydrophobic membrane-anchor domain. The Ndi1 dimer is viewed from above (A and B) and below (C and D) the membrane plane. (A and C) Cartoon representations of the dimeric structure, with molecule A in pale cyan and molecule B in light gray. The FAD cofactors are highlighted as yellow spheres. (B and D) The electrostatic surface of the dimer, with surfaces of negative potential in red, positive in blue, and uncharged in white. The surface that faces the membrane (D) presents a hydrophobic ridge for membrane insertion [indicated (ii)], which is bordered by regions of positive charge [indicated (i) and (iii)]. (E) The Ndi1 dimer viewed parallel to the membrane. Molecule A is represented in pale cyan and molecule B in light gray. The membrane-anchor domains are highlighted in pale pink, with hydrophobic residues shown as sticks. The membrane anchor domains form part of the dimer interface and present a number of aromatic side chains for insertion into the membrane (the approximate position of the membrane surface is indicated).
Fig. 3.
Fig. 3.
Ndi1 substrate channels. Clipped electrostatic surface representation of the Ndi1 dimer, showing the FAD-binding pocket (FAD cofactor shown as sticks with yellow carbon atoms) and the hydrophilic (occupied by NAD+, with blue carbon atoms) and hydrophobic (occupied by UQ2, with pink carbon atoms) channels, within the Ndi1 monomer.
Fig. 4.
Fig. 4.
UQ2- and NAD+-binding sites in the structure of Ndi1 are coincident. The structures of the Ndi1–NAD+ and Ndi1–UQ2 complexes are superposed. For simplicity, the polypeptide chain and the surface of only the Ndi1–NAD+ complex are represented in pale gray. The positions of the FAD cofactor (yellow carbon atoms), the NAD+ (blue carbon atoms), and UQ2 (pink carbon atoms) molecules are shown. In this superposition, the positions of the UQ2 moiety and the nicotinamide ring of the NAD+ molecule coincide.

Similar articles

See all similar articles

Cited by 34 articles

See all "Cited by" articles

Publication types

Feedback