This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4g9k

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structure of the Ndi1 protein from Saccharomyces cerevisiae

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4g9k"

@@ Line 1: / Line 1: @@
 ==Structure of the Ndi1 protein from Saccharomyces cerevisiae==
-<StructureSection load='4g9k' size='340' side='right' caption='[[4g9k]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='4g9k' size='340' side='right'caption='[[4g9k]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4g9k]] 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=4G9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G9K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4g9k]] 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=4G9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G9K 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></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gap|4gap]], [[4gav|4gav]]</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></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4g9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g9k OCA], [https://pdbe.org/4g9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g9k RCSB], [https://www.ebi.ac.uk/pdbsum/4g9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g9k ProSAT]</span></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=4g9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g9k OCA], [http://pdbe.org/4g9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g9k RCSB], [http://www.ebi.ac.uk/pdbsum/4g9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g9k ProSAT]</span></td></tr>
 </table>
 == 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;">
-== 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<ref>PMID:22949654</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4g9k" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </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: Nadh:quinone oxidoreductase]]
-[[Category: Oxidoreductase]]

4g9k

From Proteopedia

Current revision

Structure of the Ndi1 protein from Saccharomyces cerevisiae

Structural highlights

Function

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox