2r4e - Revision history

OCA at 09:19, 21 February 2024

2024-02-21T09:19:46Z

← Older revision		Revision as of 09:19, 21 February 2024
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	<StructureSection load='2r4e' size='340' side='right'caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2r4e' size='340' side='right'caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</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]] 2.1Å</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [https://pdbe.org/2r4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [https://www.ebi.ac.uk/pdbsum/2r4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4e 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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [https://pdbe.org/2r4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [https://www.ebi.ac.uk/pdbsum/2r4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/GLPD_ECOLI GLPD_ECOLI]] Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses molecular oxygen or nitrate as electron acceptor.		[https://www.uniprot.org/uniprot/GLPD_ECOLI GLPD_ECOLI] Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses molecular oxygen or nitrate as electron acceptor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2r4e ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2r4e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Sn-glycerol-3-phosphate dehydrogenase (GlpD) is an essential membrane enzyme, functioning at the central junction of respiration, glycolysis, and phospholipid biosynthesis. Its critical role is indicated by the multitiered regulatory mechanisms that stringently controls its expression and function. Once expressed, GlpD activity is regulated through lipid-enzyme interactions in Escherichia coli. Here, we report seven previously undescribed structures of the fully active E. coli GlpD, up to 1.75 A resolution. In addition to elucidating the structure of the native enzyme, we have determined the structures of GlpD complexed with substrate analogues phosphoenolpyruvate, glyceric acid 2-phosphate, glyceraldehyde-3-phosphate, and product, dihydroxyacetone phosphate. These structural results reveal conformational states of the enzyme, delineating the residues involved in substrate binding and catalysis at the glycerol-3-phosphate site. Two probable mechanisms for catalyzing the dehydrogenation of glycerol-3-phosphate are envisioned, based on the conformational states of the complexes. To further correlate catalytic dehydrogenation to respiration, we have additionally determined the structures of GlpD bound with ubiquinone analogues menadione and 2-n-heptyl-4-hydroxyquinoline N-oxide, identifying a hydrophobic plateau that is likely the ubiquinone-binding site. These structures illuminate probable mechanisms of catalysis and suggest how GlpD shuttles electrons into the respiratory pathway. Glycerol metabolism has been implicated in insulin signaling and perturbations in glycerol uptake and catabolism are linked to obesity in humans. Homologs of GlpD are found in practically all organisms, from prokaryotes to humans, with >45% consensus protein sequences, signifying that these structural results on the prokaryotic enzyme may be readily applied to the eukaryotic GlpD enzymes.

	Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.,Yeh JI, Chinte U, Du S Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3280-5. Epub 2008 Feb 22. PMID:18296637<ref>PMID:18296637</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2r4e" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Glycerol-3-phosphate dehydrogenase 3D structures\|Glycerol-3-phosphate dehydrogenase 3D structures]]		*[[Glycerol-3-phosphate dehydrogenase 3D structures\|Glycerol-3-phosphate dehydrogenase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~		[[Category: Escherichia coli]]
	~~[[Category: Glycerol-3-phosphate dehydrogenase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chinte, U]]		[[Category: Chinte U]]
	[[Category: Du, S]]		[[Category: Du S]]
	[[Category: Yeh~~, J I]]~~		[[Category: Yeh JI]]
	~~[[Category: Fad]]~~
	~~[[Category: Flavoprotein]]~~
	~~[[Category: Glpd]]~~
	~~[[Category: Glycerol metabolism]]~~
	~~[[Category: Oxidoreductase~~]]

OCA at 04:13, 2 July 2021

2021-07-02T04:13:57Z

← Older revision		Revision as of 04:13, 2 July 2021
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	==Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP==		==Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP==
	<StructureSection load='2r4e' size='340' side='right' caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2r4e' size='340' side='right'caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [~~http~~://pdbe.org/2r4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4e 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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [https://pdbe.org/2r4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [https://www.ebi.ac.uk/pdbsum/2r4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/GLPD_ECOLI GLPD_ECOLI]] Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses molecular oxygen or nitrate as electron acceptor.		[[https://www.uniprot.org/uniprot/GLPD_ECOLI GLPD_ECOLI]] Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses molecular oxygen or nitrate as electron acceptor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r4/2r4e_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r4/2r4e_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 2r4e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2r4e" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Glycerol-3-phosphate dehydrogenase 3D structures\|Glycerol-3-phosphate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Glycerol-3-phosphate dehydrogenase]]		[[Category: Glycerol-3-phosphate dehydrogenase]]
			[[Category: Large Structures]]
	[[Category: Chinte, U]]		[[Category: Chinte, U]]
	[[Category: Du, S]]		[[Category: Du, S]]

OCA at 07:42, 25 October 2017

2017-10-25T07:42:35Z

← Older revision		Revision as of 07:42, 25 October 2017
Line 1:		Line 1:

	==Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP==		==Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP==
	<StructureSection load='2r4e' size='340' side='right' caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2r4e' size='340' side='right' caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://pdbe.org/2r4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e 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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://pdbe.org/2r4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2r4e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2r4e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2r4e" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Glycerol-3-Phosphate Dehydrogenase\|Glycerol-3-Phosphate Dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:47, 11 September 2015

2015-09-11T09:47:01Z

← Older revision		Revision as of 09:47, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2r4e' size='340' side='right' caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2r4e' size='340' side='right' caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e 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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://pdbe.org/2r4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2r4e" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Glycerol-3-phosphate dehydrogenase]]		[[Category: Glycerol-3-phosphate dehydrogenase]]
	[[Category: Chinte, U]]		[[Category: Chinte, U]]

OCA at 14:42, 25 December 2014

2014-12-25T14:42:43Z

← Older revision		Revision as of 14:42, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R4E FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e 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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/GLPD_ECOLI GLPD_ECOLI]] Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses molecular oxygen or nitrate as electron acceptor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Glycerol-3-phosphate dehydrogenase]]		[[Category: Glycerol-3-phosphate dehydrogenase]]
	[[Category: Chinte, U.]]		[[Category: Chinte, U]]
	[[Category: Du, S.]]		[[Category: Du, S]]
	[[Category: Yeh, J I.]]		[[Category: Yeh, J I]]
	[[Category: Fad]]		[[Category: Fad]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]

OCA at 09:37, 29 September 2014

2014-09-29T09:37:23Z

← Older revision		Revision as of 09:37, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2r4e~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP==
			<StructureSection load='2r4e' size='340' side='right' caption='[[2r4e]], [[Resolution\|resolution]] 2.10Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R4E FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=T3A:N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC+ACID'>T3A</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glpD, glyD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol-3-phosphate_dehydrogenase Glycerol-3-phosphate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.3 1.1.5.3] </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=2r4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r4e RCSB], [http://www.ebi.ac.uk/pdbsum/2r4e PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r4/2r4e_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Sn-glycerol-3-phosphate dehydrogenase (GlpD) is an essential membrane enzyme, functioning at the central junction of respiration, glycolysis, and phospholipid biosynthesis. Its critical role is indicated by the multitiered regulatory mechanisms that stringently controls its expression and function. Once expressed, GlpD activity is regulated through lipid-enzyme interactions in Escherichia coli. Here, we report seven previously undescribed structures of the fully active E. coli GlpD, up to 1.75 A resolution. In addition to elucidating the structure of the native enzyme, we have determined the structures of GlpD complexed with substrate analogues phosphoenolpyruvate, glyceric acid 2-phosphate, glyceraldehyde-3-phosphate, and product, dihydroxyacetone phosphate. These structural results reveal conformational states of the enzyme, delineating the residues involved in substrate binding and catalysis at the glycerol-3-phosphate site. Two probable mechanisms for catalyzing the dehydrogenation of glycerol-3-phosphate are envisioned, based on the conformational states of the complexes. To further correlate catalytic dehydrogenation to respiration, we have additionally determined the structures of GlpD bound with ubiquinone analogues menadione and 2-n-heptyl-4-hydroxyquinoline N-oxide, identifying a hydrophobic plateau that is likely the ubiquinone-binding site. These structures illuminate probable mechanisms of catalysis and suggest how GlpD shuttles electrons into the respiratory pathway. Glycerol metabolism has been implicated in insulin signaling and perturbations in glycerol uptake and catabolism are linked to obesity in humans. Homologs of GlpD are found in practically all organisms, from prokaryotes to humans, with >45% consensus protein sequences, signifying that these structural results on the prokaryotic enzyme may be readily applied to the eukaryotic GlpD enzymes.

	~~{{STRUCTURE_2r4e\| PDB=2r4e \| SCENE= }}~~		Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.,Yeh JI, Chinte U, Du S Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3280-5. Epub 2008 Feb 22. PMID:18296637<ref>PMID:18296637</ref>

	~~===Crystal structure~~ of ~~Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18296637}}~~

	~~==About this Structure==~~
	~~[[2r4e]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2R4E OCA].~~

	==See Also==		==See Also==
	*[[Glycerol-3-Phosphate Dehydrogenase\|Glycerol-3-Phosphate Dehydrogenase]]		*[[Glycerol-3-Phosphate Dehydrogenase\|Glycerol-3-Phosphate Dehydrogenase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018296637<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Glycerol-3-phosphate dehydrogenase]]		[[Category: Glycerol-3-phosphate dehydrogenase]]

OCA at 17:56, 20 October 2012

2012-10-20T17:56:38Z

← Older revision		Revision as of 17:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2r4e]] is a 2 chain structure ~~of [[Glycerol-3-Phosphate Dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA].		[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA].

	==See Also==		==See Also==

OCA at 02:29, 27 July 2012

2012-07-27T02:29:43Z

← Older revision		Revision as of 02:29, 27 July 2012
Line 1:		Line 1:
	[[Image:2r4e.png\|left\|200px]]		[[Image:2r4e.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2r4e", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2r4e\| PDB=2r4e \| SCENE= }}		{{STRUCTURE_2r4e\| PDB=2r4e \| SCENE= }}

	===Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP===		===Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18296637}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18296637 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18296637}}		{{ABSTRACT_PUBMED_18296637}}

	==About this Structure==		==About this Structure==
	[[2r4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA].		[[2r4e]] is a 2 chain structure of [[Glycerol-3-Phosphate Dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4E OCA].

	==See Also==		==See Also==
	*[[Glycerol-3-Phosphate Dehydrogenase]]		*[[Glycerol-3-Phosphate Dehydrogenase\|Glycerol-3-Phosphate Dehydrogenase]]

	==Reference==		==Reference==
Line 31:		Line 20:
	[[Category: Du, S.]]		[[Category: Du, S.]]
	[[Category: Yeh, J I.]]		[[Category: Yeh, J I.]]
			[[Category: Fad]]
			[[Category: Flavoprotein]]
			[[Category: Glpd]]
			[[Category: Glycerol metabolism]]
			[[Category: Oxidoreductase]]

OCA at 07:39, 28 June 2011

2011-06-28T07:39:53Z

← Older revision		Revision as of 07:39, 28 June 2011
Line 22:		Line 22:

	==See Also==		==See Also==
	*[[Glycerol 3-Phosphate Dehydrogenase]]		*[[Glycerol-3-Phosphate Dehydrogenase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18296637~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018296637</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Glycerol-3-phosphate dehydrogenase]]		[[Category: Glycerol-3-phosphate dehydrogenase]]

OCA: Protected "2r4e" [edit=sysop:move=sysop]

2011-03-16T07:28:10Z

Protected "2r4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:28, 16 March 2011
(No difference)