1t6j - Revision history

OCA at 08:06, 15 November 2023

OCA — Wed, 15 Nov 2023 08:06:02 GMT

←Older revision		Revision as of 08:06, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='1t6j' size='340' side='right'caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1t6j' size='340' side='right'caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_6016 Cbs 6016~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CIN:4~~-~~CARBOXYCINNAMIC+ACID'>CIN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1t6p\|1t6p]]~~</~~div></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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [https://pdbe.org/1t6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [https://www.ebi.ac.uk/pdbsum/1t6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6j ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [~~http~~://pdbe.org/1t6j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t6j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PALY_RHOTO PALY_RHOTO]] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.<ref>PMID:5102931</ref>	+	[https://www.uniprot.org/uniprot/PALY_RHOTO PALY_RHOTO] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.<ref>PMID:5102931</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cbs 6016]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lyase~~]]	+	[[Category: Rhodotorula toruloides]]
-	[[Category: Calabrese~~, J C~~]]	+	[[Category: Calabrese JC]]
-	[[Category: Jordan~~, D B]]~~	+	[[Category: Jordan DB]]
-	~~[[Category: Cinnamate]]~~	+
-	~~[[Category: Mio]]~~	+
-	~~[[Category: Triple helix coiled coil~~]]	+

OCA at 11:43, 24 December 2020

OCA — Thu, 24 Dec 2020 11:43:35 GMT

←Older revision		Revision as of 11:43, 24 December 2020
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	==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==		==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
-	<StructureSection load='1t6j' size='340' side='right' caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1t6j' size='340' side='right'caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T6J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6p\|1t6p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t6p\|1t6p]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://pdbe.org/1t6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6j 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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://pdbe.org/1t6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6j_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 34:		Line 34:

	==See Also==		==See Also==
-	*[[Aminomutase\|Aminomutase]]	+	*[[Aminomutase 3D structures\|Aminomutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Cbs 6016]]		[[Category: Cbs 6016]]
		+	[[Category: Large Structures]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Calabrese, J C]]		[[Category: Calabrese, J C]]

OCA at 14:51, 12 October 2017

OCA — Thu, 12 Oct 2017 14:51:25 GMT

←Older revision		Revision as of 14:51, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==		==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
	<StructureSection load='1t6j' size='340' side='right' caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1t6j' size='340' side='right' caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://pdbe.org/1t6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j 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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://pdbe.org/1t6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 16:07, 7 February 2016

OCA — Sun, 07 Feb 2016 16:07:44 GMT

←Older revision		Revision as of 16:07, 7 February 2016
Line 20:		Line 20:
	<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=1t6j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1t6j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1t6j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminomutase\|Aminomutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:04, 10 September 2015

OCA — Thu, 10 Sep 2015 03:04:46 GMT

←Older revision		Revision as of 03:04, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1t6j' size='340' side='right' caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1t6j' size='340' side='right' caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodosporidium_toruloides Rhodosporidium toruloides~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6p\|1t6p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6p\|1t6p]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 ~~Rhodosporidium toruloides~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j 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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://pdbe.org/1t6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	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 1t6j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cbs 6016]]
	[[Category: Lyase]]		[[Category: Lyase]]
-	[[Category: Rhodosporidium toruloides]]
	[[Category: Calabrese, J C]]		[[Category: Calabrese, J C]]
	[[Category: Jordan, D B]]		[[Category: Jordan, D B]]

OCA at 16:31, 24 December 2014

OCA — Wed, 24 Dec 2014 16:31:13 GMT

←Older revision		Revision as of 16:31, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6J FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6p\|1t6p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6p\|1t6p]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 Rhodosporidium toruloides])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 Rhodosporidium toruloides])</td></tr>
-	<tr><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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j 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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PALY_RHOTO PALY_RHOTO]] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.<ref>PMID:5102931</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]
-	[[Category: Calabrese, J C.]]	+	[[Category: Calabrese, J C]]
-	[[Category: Jordan, D B.]]	+	[[Category: Jordan, D B]]
	[[Category: Cinnamate]]		[[Category: Cinnamate]]
-	[[Category: Lyase]]
	[[Category: Mio]]		[[Category: Mio]]
	[[Category: Triple helix coiled coil]]		[[Category: Triple helix coiled coil]]

OCA at 11:29, 3 October 2014

OCA — Fri, 03 Oct 2014 11:29:26 GMT

←Older revision		Revision as of 11:29, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1t6j\| PDB=1t6j \| SCENE= }}~~	+	==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
-	===Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides===	+	<StructureSection load='1t6j' size='340' side='right' caption='[[1t6j]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15350127}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6p\|1t6p]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 Rhodosporidium toruloides])</td></tr>
		+	<tr><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=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </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=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [http://www.ebi.ac.uk/pdbsum/1t6j 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/t6/1t6j_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 first three-dimensional structure of phenylalanine ammonia lyase (PAL) has been determined at 2.1 A resolution for PAL from Rhodosporidium toruloides. The enzyme is structurally similar to the mechanistically related histidine ammonia lyase (HAL), with PAL having an additional approximately 160 residues extending from the common fold. We propose that catalysis (including lowering the pK(a) of nonacidic C3 of l-phenylalanine for an E1cb mechanism) is potentially governed by dipole moments of seven alpha helices associated with the PAL active site (six positive poles and one negative pole). Cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. The helix dipoles appear fully compatible with a model of phenylalanine docked in the active site of PAL having the first covalent bond formed between the amino group of substrate and the methylidene group of MIO: 12 highly conserved residues (near the N termini of helices for enhancing function) are poised to serve roles in substrate recognition, MIO activation, product separation, proton donation, or polarizing electrons from the phenyl ring of substrate for activation of C3; and a highly conserved His residue (near the C terminus of the one helix that directs its negative pole toward the active site to increase the residue's basicity) is positioned to act as a general base, abstracting the pro-S hydrogen from C3 of substrate. A similar mechanism is proposed for HAL, which has a similar disposition of seven alpha helices and similar active-site residues. The helix dipoles appear incompatible with a proposed mechanism that invokes a carbocation intermediate.

-	~~==Function==~~	+	Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis.,Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T Biochemistry. 2004 Sep 14;43(36):11403-16. PMID:15350127<ref>PMID:15350127</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/PALY_RHOTO PALY_RHOTO]] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p~~-~~coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids~~.<ref>PMID:~~5102931~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1t6j]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:015350127</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]

OCA at 08:14, 23 April 2014

OCA — Wed, 23 Apr 2014 08:14:44 GMT

←Older revision		Revision as of 08:14, 23 April 2014
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-	[[Image:1t6j.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t6j", 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_1t6j\| PDB=1t6j \| SCENE= }}		{{STRUCTURE_1t6j\| PDB=1t6j \| SCENE= }}
-
	===Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides===		===Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides===
		+	{{ABSTRACT_PUBMED_15350127}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/PALY_RHOTO PALY_RHOTO]] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.<ref>PMID:5102931</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_15350127}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 15350127 is~~ the ~~PubMed ID number.~~	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_15350127}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:015350127</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015350127</ref><references group="xtra"/><references/>
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]

OCA: Protected "1t6j" [edit=sysop:move=sysop]

OCA — Wed, 16 Nov 2011 09:45:02 GMT

Protected "1t6j" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:45, 16 November 2011

OCA at 09:45, 16 November 2011

OCA — Wed, 16 Nov 2011 09:45:01 GMT

←Older revision		Revision as of 09:45, 16 November 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1t6j.png\|left\|200px]]		[[Image:1t6j.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1T6J~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA].	+	[[1t6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15350127~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015350127</ref><references group="xtra"/>
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]
Line 32:		Line 31:
	[[Category: Mio]]		[[Category: Mio]]
	[[Category: Triple helix coiled coil]]		[[Category: Triple helix coiled coil]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 22 09:04:49 2010''