1yqd - Revision history

OCA at 08:59, 14 February 2024

OCA — Wed, 14 Feb 2024 08:59:03 GMT

←Older revision		Revision as of 08:59, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1yqd' size='340' side='right'caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1yqd' size='340' side='right'caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Poptm Poptm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Populus_tremuloides Populus tremuloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <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]] 1.65Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [https://pdbe.org/1yqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [https://www.ebi.ac.uk/pdbsum/1yqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqd 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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [https://pdbe.org/1yqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [https://www.ebi.ac.uk/pdbsum/1yqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q94G59_POPTM Q94G59_POPTM]
	== 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=1yqd 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=1yqd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.
-
-	Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.,Bomati EK, Noel JP Plant Cell. 2005 May;17(5):1598-611. Epub 2005 Apr 13. PMID:15829607<ref>PMID:15829607</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yqd" 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: Cinnamyl-alcohol dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Poptm~~]]	+	[[Category: Populus tremuloides]]
-	[[Category: Bomati~~, E K~~]]	+	[[Category: Bomati EK]]
-	[[Category: Noel~~, J P]]~~	+	[[Category: Noel JP]]
-	~~[[Category: Biosynthesis]]~~	+
-	~~[[Category: Lignin]]~~	+
-	~~[[Category: Medium-chain dehydrogense/reductase]]~~	+
-	~~[[Category: Monolignol]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Plant defense]]~~	+
-	~~[[Category: Substrate inhibition]]~~	+
-	~~[[Category: Zinc-dependent~~]]	+

OCA at 16:54, 20 October 2021

OCA — Wed, 20 Oct 2021 16:54:58 GMT

←Older revision		Revision as of 16:54, 20 October 2021
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	<StructureSection load='1yqd' size='340' side='right'caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1yqd' size='340' side='right'caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Poptm Poptm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Poptm Poptm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [~~http~~://pdbe.org/1yqd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yqd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqd 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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [https://pdbe.org/1yqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [https://www.ebi.ac.uk/pdbsum/1yqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 16:51, 29 January 2020

OCA — Wed, 29 Jan 2020 16:51:30 GMT

←Older revision		Revision as of 16:51, 29 January 2020
Line 1:		Line 1:

	==Sinapyl Alcohol Dehydrogenase complexed with NADP+==		==Sinapyl Alcohol Dehydrogenase complexed with NADP+==
-	<StructureSection load='1yqd' size='340' side='right' caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='1yqd' size='340' side='right'caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Poptm Poptm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Poptm Poptm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]	+	*[[Alcohol dehydrogenase 3D structures\|Alcohol dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Cinnamyl-alcohol dehydrogenase]]		[[Category: Cinnamyl-alcohol dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Poptm]]		[[Category: Poptm]]
	[[Category: Bomati, E K]]		[[Category: Bomati, E K]]

OCA at 06:37, 25 April 2018

OCA — Wed, 25 Apr 2018 06:37:24 GMT

←Older revision		Revision as of 06:37, 25 April 2018
Line 1:		Line 1:
		+
	==Sinapyl Alcohol Dehydrogenase complexed with NADP+==		==Sinapyl Alcohol Dehydrogenase complexed with NADP+==
	<StructureSection load='1yqd' size='340' side='right' caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1yqd' size='340' side='right' caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://pdbe.org/1yqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd 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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://pdbe.org/1yqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yq/1yqd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yq/1yqd_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>

OCA at 20:37, 7 February 2016

OCA — Sun, 07 Feb 2016 20:37:35 GMT

←Older revision		Revision as of 20:37, 7 February 2016
Line 15:		Line 15:
	<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=1yqd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:47, 10 September 2015

OCA — Thu, 10 Sep 2015 04:47:23 GMT

←Older revision		Revision as of 04:47, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1yqd' size='340' side='right' caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1yqd' size='340' side='right' caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Populus_tremuloides Populus tremuloides~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Poptm Poptm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd 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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://pdbe.org/1yqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1yqd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Cinnamyl-alcohol dehydrogenase]]		[[Category: Cinnamyl-alcohol dehydrogenase]]
-	[[Category: ~~Populus tremuloides~~]]	+	[[Category: Poptm]]
	[[Category: Bomati, E K]]		[[Category: Bomati, E K]]
	[[Category: Noel, J P]]		[[Category: Noel, J P]]

OCA at 10:11, 8 January 2015

OCA — Thu, 08 Jan 2015 10:11:24 GMT

←Older revision		Revision as of 10:11, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_tremuloides Populus tremuloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_tremuloides Populus tremuloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd 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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Cinnamyl-alcohol dehydrogenase]]		[[Category: Cinnamyl-alcohol dehydrogenase]]
	[[Category: Populus tremuloides]]		[[Category: Populus tremuloides]]
-	[[Category: Bomati, E K.]]	+	[[Category: Bomati, E K]]
-	[[Category: Noel, J P.]]	+	[[Category: Noel, J P]]
	[[Category: Biosynthesis]]		[[Category: Biosynthesis]]
	[[Category: Lignin]]		[[Category: Lignin]]

OCA at 20:15, 28 September 2014

OCA — Sun, 28 Sep 2014 20:15:15 GMT

←Older revision		Revision as of 20:15, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1yqd.~~png\|left~~\|200px]]	+	==Sinapyl Alcohol Dehydrogenase complexed with NADP+==
		+	<StructureSection load='1yqd' size='340' side='right' caption='[[1yqd]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_tremuloides Populus tremuloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YQD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] </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=1yqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yqd RCSB], [http://www.ebi.ac.uk/pdbsum/1yqd 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/yq/1yqd_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 ==
		+	We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

-	~~{{STRUCTURE_1yqd\| PDB=1yqd \| SCENE= }}~~	+	Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.,Bomati EK, Noel JP Plant Cell. 2005 May;17(5):1598-611. Epub 2005 Apr 13. PMID:15829607<ref>PMID:15829607</ref>

-	~~===Sinapyl Alcohol Dehydrogenase complexed with NADP+===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15829607}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yqd]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Populus_tremuloides Populus tremuloides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA].~~	+

	==See Also==		==See Also==
	*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]		*[[Alcohol dehydrogenase\|Alcohol dehydrogenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015829607<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cinnamyl-alcohol dehydrogenase]]		[[Category: Cinnamyl-alcohol dehydrogenase]]
	[[Category: Populus tremuloides]]		[[Category: Populus tremuloides]]

OCA at 07:48, 20 October 2012

OCA — Sat, 20 Oct 2012 07:48:03 GMT

←Older revision		Revision as of 07:48, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1yqd]] is a 2 chain structure ~~of [[Alcohol dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Populus_tremuloides Populus tremuloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA].	+	[[1yqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Populus_tremuloides Populus tremuloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQD OCA].

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

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

OCA — Wed, 25 Jul 2012 17:29:44 GMT

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

←Older revision

Revision as of 17:29, 25 July 2012