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| | ==Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+== | | ==Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+== |
| - | <StructureSection load='4gap' size='340' side='right' caption='[[4gap]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='4gap' size='340' side='right'caption='[[4gap]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4gap]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4gap]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GAP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g9k|4g9k]], [[4gav|4gav]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gap OCA], [https://pdbe.org/4gap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gap RCSB], [https://www.ebi.ac.uk/pdbsum/4gap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gap ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NDI1, YML120C, YM7056.06C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(non-electrogenic) NADH:ubiquinone reductase (non-electrogenic)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.9 1.6.5.9] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gap OCA], [http://pdbe.org/4gap PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gap RCSB], [http://www.ebi.ac.uk/pdbsum/4gap PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gap ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NDI1_YEAST NDI1_YEAST]] Catalyzes the oxidation of NADH generated inside the Mitochondrion. | + | [https://www.uniprot.org/uniprot/NDI1_YEAST NDI1_YEAST] Catalyzes the oxidation of NADH generated inside the Mitochondrion. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | + | [[Category: Large Structures]] |
| - | [[Category: Cameron, A D]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Iwata, M]] | + | [[Category: Cameron AD]] |
| - | [[Category: Iwata, S]] | + | [[Category: Iwata M]] |
| - | [[Category: Lee, Y]] | + | [[Category: Iwata S]] |
| - | [[Category: Maher, M J]] | + | [[Category: Lee Y]] |
| - | [[Category: Yagi, T]] | + | [[Category: Maher MJ]] |
| - | [[Category: Yamashita, T]] | + | [[Category: Yagi T]] |
| - | [[Category: Membrane]]
| + | [[Category: Yamashita T]] |
| - | [[Category: Nucleotide-binding domain]]
| + | |
| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
NDI1_YEAST Catalyzes the oxidation of NADH generated inside the Mitochondrion.
Publication Abstract from PubMed
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.
The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.,Iwata M, Lee Y, Yamashita T, Yagi T, Iwata S, Cameron AD, Maher MJ Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15247-52. Epub 2012 Sep 4. PMID:22949654[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Iwata M, Lee Y, Yamashita T, Yagi T, Iwata S, Cameron AD, Maher MJ. The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates. Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15247-52. Epub 2012 Sep 4. PMID:22949654 doi:http://dx.doi.org/10.1073/pnas.1210059109
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