1q1n - Revision history

OCA at 08:12, 14 February 2024

OCA — Wed, 14 Feb 2024 08:12:30 GMT

←Older revision		Revision as of 08:12, 14 February 2024
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	<StructureSection load='1q1n' size='340' side='right'caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='1q1n' size='340' side='right'caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1n]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1piw\|1piw]], [[1ps0\|1ps0]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">YMR318C (ADH6) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])~~</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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [https://pdbe.org/1q1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [https://www.ebi.ac.uk/pdbsum/1q1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1n ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [~~http~~://pdbe.org/1q1n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q1n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ADH6_YEAST ADH6_YEAST]] NADP-dependent alcohol dehydrogenase with a broad substrate specificity.	+	[https://www.uniprot.org/uniprot/ADH6_YEAST ADH6_YEAST] NADP-dependent alcohol dehydrogenase with a broad substrate specificity.
	== 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=1q1n 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=1q1n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of Saccharomyces cerevisiae ScAdh6p has been solved using the anomalous signal from the two zinc atoms found per subunit, and it constitutes the first structure determined from a member of the cinnamyl alcohol dehydrogenase family. ScAdh6p subunits exhibit the general fold of the medium-chain dehydrogenases/reductases (MDR) but with distinct specific characteristics. In the three crystal structures solved (two trigonal and one monoclinic), ScAdh6p molecules appear to be structural heterodimers composed of one subunit in the apo and the second subunit in the holo conformation. Between the two conformations, the relative disposition of domains remains unchanged, while two loops, Cys250-Asn260 and Ile277-Lys292, experience large movements. The apo-apo structure is disfavoured because of steric impairment involving the loop Ile277-Lys292, while in the holo-holo conformation some of the hydrogen bonds between subunits would break apart. These suggest that the first NADPH molecule would bind to the enzyme much more tightly than the second. In addition, fluorimetric analysis of NADPH binding demonstrates that only one cofactor molecule binds per dimer. Therefore, ScAdh6p appears to function according to a half-of-the-sites reactivity mechanism, resulting from a pre-existing (prior to cofactor binding) tendency for the structural asymmetry in the dimer. The specificity of ScAdh6p towards NADPH is mainly due to the tripod-like interactions of the terminal phosphate group with Ser210, Arg211 and Lys215. The size and the shape of the substrate-binding pocket correlate well with the substrate specificity of ScAdh6p towards cinnamaldehyde and other aromatic compounds. The structural relationships of ScAdh6p with other MDR structures are analysed.
-
-	Apo and Holo structures of an NADPH-dependent cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae.,Valencia E, Larroy C, Ochoa WF, Pares X, Fita I, Biosca JA J Mol Biol. 2004 Aug 20;341(4):1049-62. PMID:15289102<ref>PMID:15289102</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1q1n" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]		*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Biosca~~, J A~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Fita, I]]	+	[[Category: Biosca JA]]
-	[[Category: Larroy, C]]	+	[[Category: Fita I]]
-	[[Category: Ochoa~~, W F~~]]	+	[[Category: Larroy C]]
-	[[Category: Pares, X]]	+	[[Category: Ochoa WF]]
-	[[Category: Valencia, E]]	+	[[Category: Pares X]]
-	~~[[Category: Adh topology]]~~	+	[[Category: Valencia E]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:41, 9 December 2020

OCA — Wed, 09 Dec 2020 07:41:06 GMT

←Older revision		Revision as of 07:41, 9 December 2020
Line 1:		Line 1:

	==APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE==		==APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE==
-	<StructureSection load='1q1n' size='340' side='right' caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='1q1n' size='340' side='right'caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1piw\|1piw]], [[1ps0\|1ps0]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://pdbe.org/1q1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1n ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://pdbe.org/1q1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1q1n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1q1n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Biosca, J A]]		[[Category: Biosca, J A]]
	[[Category: Fita, I]]		[[Category: Fita, I]]

OCA at 08:19, 24 February 2018

OCA — Sat, 24 Feb 2018 08:19:52 GMT

←Older revision		Revision as of 08:19, 24 February 2018
Line 1:		Line 1:
		+
	==APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE==		==APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE==
	<StructureSection load='1q1n' size='340' side='right' caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='1q1n' size='340' side='right' caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://pdbe.org/1q1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n 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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://pdbe.org/1q1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q1n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/1q1n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/1q1n_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>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1q1n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1q1n" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:50, 8 February 2016

OCA — Mon, 08 Feb 2016 18:50:12 GMT

←Older revision		Revision as of 18:50, 8 February 2016
Line 18:		Line 18:
	<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=1q1n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:24, 10 September 2015

OCA — Thu, 10 Sep 2015 14:24:50 GMT

←Older revision		Revision as of 14:24, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1q1n' size='340' side='right' caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='1q1n' size='340' side='right' caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q1n]] is a 1 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=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q1n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([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">YMR318C (ADH6) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n 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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://pdbe.org/1q1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n 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 1q1n" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Biosca, J A]]		[[Category: Biosca, J A]]
	[[Category: Fita, I]]		[[Category: Fita, I]]

OCA at 01:26, 25 December 2014

OCA — Thu, 25 Dec 2014 01:26:07 GMT

←Older revision		Revision as of 01:26, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q1n]] is a 1 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=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q1n]] is a 1 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=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([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">YMR318C (ADH6) ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n 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=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ADH6_YEAST ADH6_YEAST]] NADP-dependent alcohol dehydrogenase with a broad substrate specificity.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Biosca, J A.]]	+	[[Category: Biosca, J A]]
-	[[Category: Fita, I.]]	+	[[Category: Fita, I]]
-	[[Category: Larroy, C.]]	+	[[Category: Larroy, C]]
-	[[Category: Ochoa, W F.]]	+	[[Category: Ochoa, W F]]
-	[[Category: Pares, X.]]	+	[[Category: Pares, X]]
-	[[Category: Valencia, E.]]	+	[[Category: Valencia, E]]
	[[Category: Adh topology]]		[[Category: Adh topology]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 22:57, 28 September 2014

OCA — Sun, 28 Sep 2014 22:57:57 GMT

←Older revision		Revision as of 22:57, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1q1n.~~png~~\|~~left~~\|200px]]	+	==APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE==
		+	<StructureSection load='1q1n' size='340' side='right' caption='[[1q1n]], [[Resolution\|resolution]] 3.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q1n]] is a 1 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=1Q1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q1N FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1piw\|1piw]], [[1ps0\|1ps0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YMR318C (ADH6) ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q1n RCSB], [http://www.ebi.ac.uk/pdbsum/1q1n 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/q1/1q1n_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 ==
		+	The crystal structure of Saccharomyces cerevisiae ScAdh6p has been solved using the anomalous signal from the two zinc atoms found per subunit, and it constitutes the first structure determined from a member of the cinnamyl alcohol dehydrogenase family. ScAdh6p subunits exhibit the general fold of the medium-chain dehydrogenases/reductases (MDR) but with distinct specific characteristics. In the three crystal structures solved (two trigonal and one monoclinic), ScAdh6p molecules appear to be structural heterodimers composed of one subunit in the apo and the second subunit in the holo conformation. Between the two conformations, the relative disposition of domains remains unchanged, while two loops, Cys250-Asn260 and Ile277-Lys292, experience large movements. The apo-apo structure is disfavoured because of steric impairment involving the loop Ile277-Lys292, while in the holo-holo conformation some of the hydrogen bonds between subunits would break apart. These suggest that the first NADPH molecule would bind to the enzyme much more tightly than the second. In addition, fluorimetric analysis of NADPH binding demonstrates that only one cofactor molecule binds per dimer. Therefore, ScAdh6p appears to function according to a half-of-the-sites reactivity mechanism, resulting from a pre-existing (prior to cofactor binding) tendency for the structural asymmetry in the dimer. The specificity of ScAdh6p towards NADPH is mainly due to the tripod-like interactions of the terminal phosphate group with Ser210, Arg211 and Lys215. The size and the shape of the substrate-binding pocket correlate well with the substrate specificity of ScAdh6p towards cinnamaldehyde and other aromatic compounds. The structural relationships of ScAdh6p with other MDR structures are analysed.

-	~~{{STRUCTURE_1q1n\| PDB=1q1n \| SCENE= }}~~	+	Apo and Holo structures of an NADPH-dependent cinnamyl alcohol dehydrogenase from Saccharomyces cerevisiae.,Valencia E, Larroy C, Ochoa WF, Pares X, Fita I, Biosca JA J Mol Biol. 2004 Aug 20;341(4):1049-62. PMID:15289102<ref>PMID:15289102</ref>

-	~~===APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15289102}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1q1n]] is~~ a ~~1 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=1Q1N OCA].~~	+

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]		*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015289102<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Biosca, J A.]]		[[Category: Biosca, J A.]]

OCA at 11:07, 20 October 2012

OCA — Sat, 20 Oct 2012 11:07:21 GMT

←Older revision		Revision as of 11:07, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1q1n]] is a 1 chain structure ~~of [[Alcohol dehydrogenase]]~~ 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=1Q1N OCA].	+	[[1q1n]] is a 1 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=1Q1N OCA].

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

OCA: Protected "1q1n" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 04:19:13 GMT

Protected "1q1n" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 26 July 2012

OCA at 04:19, 26 July 2012

OCA — Thu, 26 Jul 2012 04:19:12 GMT

←Older revision		Revision as of 04:19, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1q1n.png\|left\|200px]]		[[Image:1q1n.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1q1n", 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_1q1n\| PDB=1q1n \| SCENE= }}		{{STRUCTURE_1q1n\| PDB=1q1n \| SCENE= }}

	===APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE===		===APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15289102}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15289102 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15289102}}		{{ABSTRACT_PUBMED_15289102}}

	==About this Structure==		==About this Structure==
-	~~1Q1N~~ is a 1 chain structure of 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=1Q1N OCA].	+	[[1q1n]] is a 1 chain structure of [[Alcohol dehydrogenase]] 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=1Q1N OCA].
		+
		+	==See Also==
		+	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15289102~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015289102</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Biosca, J A.]]		[[Category: Biosca, J A.]]
Line 32:		Line 23:
	[[Category: Valencia, E.]]		[[Category: Valencia, E.]]
	[[Category: Adh topology]]		[[Category: Adh topology]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 01:53:59 2009''~~	+