4gap - Revision history

OCA at 11:26, 1 March 2024

2024-03-01T11:26:28Z

← Older revision		Revision as of 11:26, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<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>		<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" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.9Å</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='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='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>
	</table>		</table>
	== Function ==		== Function ==
	[https://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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4gap" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:45, 26 October 2022

2022-10-26T06:45:43Z

← Older revision		Revision as of 06:45, 26 October 2022
Line 1:		Line 1:

	==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 ==
Line 25:		Line 22:
	__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~~]]

OCA at 18:36, 11 August 2016

2016-08-11T18:36:03Z

← Older revision		Revision as of 18:36, 11 August 2016
Line 1:		Line 1:

	==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/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. 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 [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>
	</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"><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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g9k\|4g9k]], [[4gav\|4gav]]</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=~~4932 Saccharomyces cerevisiae~~])</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='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://www.rcsb.org/pdb/explore.do?structureId=4gap RCSB], [http://www.ebi.ac.uk/pdbsum/4gap PDBsum]</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 ==
			[[http://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 ==
Line 17:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4gap" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Saccharomyces cerevisiae~~]]		[[Category: Baker's yeast]]
	[[Category: Cameron, A D]]		[[Category: Cameron, A D]]
	[[Category: Iwata, M]]		[[Category: Iwata, M]]

OCA at 13:17, 5 January 2015

2015-01-05T13:17:28Z

← Older revision		Revision as of 13:17, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gap]] 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=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 [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. 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>
	</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><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>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g9k\|4g9k]], [[4gav\|4gav]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g9k\|4g9k]], [[4gav\|4gav]]</td></tr>
	<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>		<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=4932 Saccharomyces cerevisiae])</td></tr>
	<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>		<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><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://www.rcsb.org/pdb/explore.do?structureId=4gap RCSB], [http://www.ebi.ac.uk/pdbsum/4gap PDBsum]</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://www.rcsb.org/pdb/explore.do?structureId=4gap RCSB], [http://www.ebi.ac.uk/pdbsum/4gap PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Cameron, A D.]]		[[Category: Cameron, A D]]
	[[Category: Iwata, M.]]		[[Category: Iwata, M]]
	[[Category: Iwata, S.]]		[[Category: Iwata, S]]
	[[Category: Lee, Y.]]		[[Category: Lee, Y]]
	[[Category: Maher, M J.]]		[[Category: Maher, M J]]
	[[Category: Yagi, T.]]		[[Category: Yagi, T]]
	[[Category: Yamashita, T.]]		[[Category: Yamashita, T]]
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Nucleotide-binding domain]]		[[Category: Nucleotide-binding domain]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:51, 9 July 2014

2014-07-09T07:51:03Z

← Older revision		Revision as of 07:51, 9 July 2014
Line 1:		Line 1:
	[[~~Image~~:~~4gap~~.~~png~~\|~~left~~\|~~200px~~]]		==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=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4gap]] 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=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>
			</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g9k\|4g9k]], [[4gav\|4gav]]</td></tr>
			<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>
			<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>
			<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=4gap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gap RCSB], [http://www.ebi.ac.uk/pdbsum/4gap PDBsum]</span></td></tr>
			<table>
			<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.

	~~{{STRUCTURE_4gap\| PDB=4gap \| SCENE= }}~~		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>

	~~===Structure~~ of the ~~Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22949654}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[4gap]] 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=4GAP OCA].~~		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Cameron, A D.]]		[[Category: Cameron, A D.]]

OCA at 06:17, 3 October 2012

2012-10-03T06:17:50Z

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	[[Image:4gap.~~jpg~~\|left\|200px]]		[[Image:4gap.png\|left\|200px]]

	{{STRUCTURE_4gap\| PDB=4gap \| SCENE= }}		{{STRUCTURE_4gap\| PDB=4gap \| SCENE= }}
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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+===

			{{ABSTRACT_PUBMED_22949654}}

	==About this Structure==		==About this Structure==

OCA at 05:42, 5 September 2012

2012-09-05T05:42:54Z

← Older revision		Revision as of 05:42, 5 September 2012
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	~~'''Unreleased structure'''~~		[[Image:4gap.jpg\|left\|200px]]

	~~The entry~~ 4gap ~~is ON HOLD~~		{{STRUCTURE_4gap\| PDB=4gap \| SCENE= }}

	~~Authors: Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.~~		===Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+===

	~~Description~~: ~~Monotopic membrane protein in complex with NAD+~~
			==About this Structure==
			[[4gap]] 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=4GAP OCA].
			[[Category: Saccharomyces cerevisiae]]
			[[Category: Cameron, A D.]]
			[[Category: Iwata, M.]]
			[[Category: Iwata, S.]]
			[[Category: Lee, Y.]]
			[[Category: Maher, M J.]]
			[[Category: Yagi, T.]]
			[[Category: Yamashita, T.]]
			[[Category: Membrane]]
			[[Category: Nucleotide-binding domain]]
			[[Category: Oxidoreductase]]

OCA at 05:32, 22 August 2012

2012-08-22T05:32:15Z

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	The entry 4gap is ON HOLD		The entry 4gap is ON HOLD

	Authors: Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A. D., Maher, M. J.		Authors: Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A.D., Maher, M.J.

	Description: Monotopic membrane protein in complex with NAD+.		Description: Monotopic membrane protein in complex with NAD+

OCA: Protected "4gap" [edit=sysop:move=sysop]

2012-08-01T05:32:59Z

Protected "4gap" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:32, 1 August 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4gap is ON HOLD Authors: Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A. D., Maher, M. J. Description: Monotopic membrane prote...

2012-08-01T05:32:58Z

New page: '''Unreleased structure''' The entry 4gap is ON HOLD Authors: Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A. D., Maher, M. J. Description: Monotopic membrane prote...

New page

'''Unreleased structure'''

The entry 4gap is ON HOLD

Authors: Iwata, M., Lee, Y., Yamashita, T., Yagi, T., Iwata, S., Cameron, A. D., Maher, M. J.

Description: Monotopic membrane protein in complex with NAD+.