1yb7 - Revision history

OCA at 06:55, 23 August 2023

OCA — Wed, 23 Aug 2023 06:55:22 GMT

←Older revision		Revision as of 06:55, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1yb7' size='340' side='right'caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='1yb7' size='340' side='right'caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hevbr Hevbr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ICN:(S)~~-~~2-HYDROXY-2~~,~~3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.76Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; max-height: 3em;'>[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3981 HEVBR])</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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [https://pdbe.org/1yb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [https://www.ebi.ac.uk/pdbsum/1yb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yb7 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47]~~ </~~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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [~~http~~://pdbe.org/1yb7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yb7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yb7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HNL_HEVBR HNL_HEVBR]] Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin.	+	[https://www.uniprot.org/uniprot/HNL_HEVBR HNL_HEVBR] Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hevbr~~]]	+	[[Category: Hevea brasiliensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lyase]]~~	+	[[Category: Gartler G]]
-	[[Category: Gartler, G]]	+	[[Category: Gruber K]]
-	[[Category: Gruber, K]]	+	[[Category: Kratky C]]
-	[[Category: Kratky, C]]	+
-	~~[[Category: Alpha-beta hydrolase fold]]~~	+
-	~~[[Category: Catalytic triad]]~~	+
-	~~[[Category: Substrate complex~~]]	+

OCA at 08:42, 20 January 2021

OCA — Wed, 20 Jan 2021 08:42:55 GMT

←Older revision		Revision as of 08:42, 20 January 2021
Line 1:		Line 1:

	==Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile==		==Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile==
-	<StructureSection load='1yb7' size='340' side='right' caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='1yb7' size='340' side='right'caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevbr Hevbr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevbr Hevbr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://pdbe.org/1yb7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yb7 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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://pdbe.org/1yb7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yb7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yb/1yb7_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yb/1yb7_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 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Hevbr]]		[[Category: Hevbr]]
		+	[[Category: Large Structures]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Gartler, G]]		[[Category: Gartler, G]]

OCA at 13:24, 12 October 2017

OCA — Thu, 12 Oct 2017 13:24:07 GMT

←Older revision		Revision as of 13:24, 12 October 2017
Line 1:		Line 1:
		+
	==Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile==		==Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile==
	<StructureSection load='1yb7' size='340' side='right' caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='1yb7' size='340' side='right' caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://pdbe.org/1yb7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://pdbe.org/1yb7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yb7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:59, 8 February 2016

OCA — Mon, 08 Feb 2016 19:59:49 GMT

←Older revision		Revision as of 19:59, 8 February 2016
Line 19:		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=1yb7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:54, 10 September 2015

OCA — Thu, 10 Sep 2015 14:54:08 GMT

←Older revision		Revision as of 14:54, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1yb7' size='340' side='right' caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='1yb7' size='340' side='right' caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Hevea_brasiliensis Hevea brasiliensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevbr Hevbr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 ~~Hevea brasiliensis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 HEVBR])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Hydroxynitrilase Hydroxynitrilase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.37 4.1.2.37] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.46 and 4.1.2.47 4.1.2.46 and 4.1.2.47] </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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://pdbe.org/1yb7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1yb7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hevea brasiliensis~~]]	+	[[Category: Hevbr]]
-	[[Category: ~~Hydroxynitrilase~~]]	+	[[Category: Lyase]]
	[[Category: Gartler, G]]		[[Category: Gartler, G]]
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
Line 40:		Line 41:
	[[Category: Alpha-beta hydrolase fold]]		[[Category: Alpha-beta hydrolase fold]]
	[[Category: Catalytic triad]]		[[Category: Catalytic triad]]
-	[[Category: Lyase]]
	[[Category: Substrate complex]]		[[Category: Substrate complex]]

OCA at 01:48, 25 December 2014

OCA — Thu, 25 Dec 2014 01:48:54 GMT

←Older revision		Revision as of 01:48, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 Hevea brasiliensis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 Hevea brasiliensis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxynitrilase Hydroxynitrilase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.37 4.1.2.37] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxynitrilase Hydroxynitrilase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.37 4.1.2.37] </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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HNL_HEVBR HNL_HEVBR]] Involved in cyanogenesis, the release of HCN from injured tissues. Decomposes a varieties of (R) or (S) cyanohydrins into HCN and the corresponding aldehydes and ketones. The natural substrate of this enzyme is (S)-acetone cyanohydrin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Hevea brasiliensis]]		[[Category: Hevea brasiliensis]]
	[[Category: Hydroxynitrilase]]		[[Category: Hydroxynitrilase]]
-	[[Category: Gartler, G.]]	+	[[Category: Gartler, G]]
-	[[Category: Gruber, K.]]	+	[[Category: Gruber, K]]
-	[[Category: Kratky, C.]]	+	[[Category: Kratky, C]]
	[[Category: Alpha-beta hydrolase fold]]		[[Category: Alpha-beta hydrolase fold]]
	[[Category: Catalytic triad]]		[[Category: Catalytic triad]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Substrate complex]]		[[Category: Substrate complex]]

OCA at 21:25, 29 September 2014

OCA — Mon, 29 Sep 2014 21:25:13 GMT

←Older revision		Revision as of 21:25, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1yb7.~~png~~\|~~left~~\|200px]]	+	==Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile==
		+	<StructureSection load='1yb7' size='340' side='right' caption='[[1yb7]], [[Resolution\|resolution]] 1.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YB7 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICN:(S)-2-HYDROXY-2,3-DIMETHYLBUTANENITRILE'>ICN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qj4\|1qj4]], [[1yas\|1yas]], [[2yas\|2yas]], [[3yas\|3yas]], [[4yas\|4yas]], [[5yas\|5yas]], [[6yas\|6yas]], [[7yas\|7yas]], [[1sc9\|1sc9]], [[1sci\|1sci]], [[1sck\|1sck]], [[1scq\|1scq]], [[1yb6\|1yb6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HNL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3981 Hevea brasiliensis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydroxynitrilase Hydroxynitrilase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.37 4.1.2.37] </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=1yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yb7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yb7 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/yb/1yb7_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 hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis (HbHNL) is utilized as a biocatalyst in stereospecific syntheses of alpha-hydroxynitriles from aldehydes and methyl-ketones. The catalyzed reaction represents one of the few industrially relevant examples of enzyme mediated C-C coupling reactions. In this work, we determined the X-ray crystal structures (at 1.54 and 1.76 Angstroms resolution) of HbHNL complexes with two chiral substrates -- mandelonitrile and 2,3-dimethyl-2-hydroxy-butyronitrile -- by soaking and rapid freeze quenching techniques. This is the first structural observation of the complex between a HNL and chiral substrates. Consistent with the known selectivity of the enzyme, only the S-enantiomers of the two substrates were observed in the active site. The binding modes of the chiral substrates were identical to that observed for the biological substrate acetone cyanohydrin. This indicates that the transformation of these non-natural substrates follows the same mechanism. A large hydrophobic pocket was identified in the active site of HbHNL which accommodates the more voluminous substituents of the two substrates. A three-point binding mode of the substrates -- hydrophobic pocket, hydrogen bonds between the hydroxyl group and Ser80 and Thr11, electrostatic interaction of the cyano group with Lys236 -- offers a likely structural explanation for the enantioselectivity of the enzyme. The structural data rationalize the observed (S)-enantioselectivity and form the basis for modifying the stereospecificity through rational design. The structures also revealed the necessity of considerable flexibility of the sidechain of Trp128 in order to bind and transform larger substrates.

-	~~{{STRUCTURE_1yb7\| PDB=1yb7 \| SCENE= }}~~	+	Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis.,Gartler G, Kratky C, Gruber K J Biotechnol. 2007 Mar 30;129(1):87-97. Epub 2006 Dec 17. PMID:17250917<ref>PMID:17250917</ref>

-	~~===Hydroxynitrile lyase from hevea brasiliensis in complex with 2~~,~~3-dimethyl-2-hydroxy-butyronitrile===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17250917}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1yb7]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Hevea_brasiliensis Hevea brasiliensis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017250917<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Hevea brasiliensis]]		[[Category: Hevea brasiliensis]]
	[[Category: Hydroxynitrilase]]		[[Category: Hydroxynitrilase]]

OCA: Protected "1yb7" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:17:01 GMT

Protected "1yb7" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:17, 5 January 2013

OCA at 17:16, 5 January 2013

OCA — Sat, 05 Jan 2013 17:16:59 GMT

←Older revision		Revision as of 17:16, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1yb7.png\|left\|200px]]		[[Image:1yb7.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yb7", 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_1yb7\| PDB=1yb7 \| SCENE= }}		{{STRUCTURE_1yb7\| PDB=1yb7 \| SCENE= }}

	===Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile===		===Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17250917}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17250917 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17250917}}		{{ABSTRACT_PUBMED_17250917}}

	==About this Structure==		==About this Structure==
-	~~1YB7~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA].	+	[[1yb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17250917~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017250917</ref><references group="xtra"/>
	[[Category: Hevea brasiliensis]]		[[Category: Hevea brasiliensis]]
-	[[Category: ~~Transfered to EC 4 1.2 37~~]]	+	[[Category: Hydroxynitrilase]]
	[[Category: Gartler, G.]]		[[Category: Gartler, G.]]
	[[Category: Gruber, K.]]		[[Category: Gruber, K.]]
Line 31:		Line 19:
	[[Category: Alpha-beta hydrolase fold]]		[[Category: Alpha-beta hydrolase fold]]
	[[Category: Catalytic triad]]		[[Category: Catalytic triad]]
		+	[[Category: Lyase]]
	[[Category: Substrate complex]]		[[Category: Substrate complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:39:39 2009''

OCA at 00:39, 17 February 2009

OCA — Tue, 17 Feb 2009 00:39:40 GMT

←Older revision		Revision as of 00:39, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1YB7 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA].	+	1YB7 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB7 OCA].

	==Reference==		==Reference==
-	~~Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis., Gartler G, Kratky C, Gruber K, J Biotechnol. 2007 Mar 30;129(1):87-97. Epub 2006 Dec 17.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17250917 17250917]~~	+	<ref group="xtra">PMID:17250917</ref><references group="xtra"/>
	[[Category: Hevea brasiliensis]]		[[Category: Hevea brasiliensis]]
-	[[Category: Single protein]]
	[[Category: Transfered to EC 4 1.2 37]]		[[Category: Transfered to EC 4 1.2 37]]
	[[Category: Gartler, G.]]		[[Category: Gartler, G.]]
Line 34:		Line 33:
	[[Category: Substrate complex]]		[[Category: Substrate complex]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 06~~:21:~~12 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:39:39 2009''