4gav

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==Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone==
==Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone==
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<StructureSection load='4gav' size='340' side='right' caption='[[4gav]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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<StructureSection load='4gav' size='340' side='right'caption='[[4gav]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gav]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GAV FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gav]] 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=4GAV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GAV FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=UQ2:UBIQUINONE-2'>UQ2</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g9k|4g9k]], [[4gap|4gap]]</td></tr>
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<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=UQ2:UBIQUINONE-2'>UQ2</scene></td></tr>
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<tr><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=4932 Saccharomyces cerevisiae])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gav OCA], [https://pdbe.org/4gav PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gav RCSB], [https://www.ebi.ac.uk/pdbsum/4gav PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gav ProSAT]</span></td></tr>
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<tr><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>
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</table>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gav OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gav RCSB], [http://www.ebi.ac.uk/pdbsum/4gav PDBsum]</span></td></tr>
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== Function ==
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<table>
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[https://www.uniprot.org/uniprot/NDI1_YEAST NDI1_YEAST] Catalyzes the oxidation of NADH generated inside the Mitochondrion.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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<ref>PMID:22949654</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Large Structures]]
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[[Category: Cameron, A D.]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Iwata, M.]]
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[[Category: Cameron AD]]
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[[Category: Iwata, S.]]
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[[Category: Iwata M]]
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[[Category: Lee, Y.]]
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[[Category: Iwata S]]
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[[Category: Maher, M J.]]
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[[Category: Lee Y]]
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[[Category: Yagi, T.]]
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[[Category: Maher MJ]]
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[[Category: Yamashita, T.]]
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[[Category: Yagi T]]
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[[Category: Membrane]]
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[[Category: Yamashita T]]
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[[Category: Nucleotide-binding domain]]
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[[Category: Oxidoreductase]]
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Current revision

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with quinone

PDB ID 4gav

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