1t6p - Revision history

OCA at 06:26, 23 August 2023

OCA — Wed, 23 Aug 2023 06:26:54 GMT

←Older revision		Revision as of 06:26, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1t6p' size='340' side='right'caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1t6p' size='340' side='right'caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T6P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
-	</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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.7Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1t6j\|1t6j]]</div>~~</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=MSE:SELENOMETHIONINE'>MSE</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [https://pdbe.org/1t6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [https://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p 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=4.3.1.23, 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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [~~http~~://pdbe.org/1t6p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p 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]]
Line 38:		Line 36:
	__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 11:43:47 GMT

←Older revision		Revision as of 11:43, 24 December 2020
Line 1:		Line 1:

	==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==		==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
-	<StructureSection load='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1t6p' size='340' side='right'caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T6P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
	</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>		</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">[[1t6j\|1t6j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t6j\|1t6j]]</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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p 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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p 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/t6/1t6p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6p_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 33:		Line 33:

	==See Also==		==See Also==
-	*[[Aminomutase\|Aminomutase]]	+	*[[Aminomutase 3D structures\|Aminomutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</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 09:20, 12 October 2017

OCA — Thu, 12 Oct 2017 09:20:24 GMT

←Older revision		Revision as of 09:20, 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='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 7:		Line 8:
	<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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p 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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 09:51, 8 February 2016

OCA — Mon, 08 Feb 2016 09:51:59 GMT

←Older revision		Revision as of 09:51, 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=1t6p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1t6p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1t6p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminomutase\|Aminomutase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:24, 10 September 2015

OCA — Thu, 10 Sep 2015 10:24:00 GMT

←Older revision		Revision as of 10:24, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
	</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>		</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">[[1t6j\|1t6j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6j\|1t6j]]</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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p 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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p 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 1t6p" 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 22:27, 24 December 2014

OCA — Wed, 24 Dec 2014 22:27:52 GMT

←Older revision		Revision as of 22:27, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6P FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
-	</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>	+	</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">[[1t6j\|1t6j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6j\|1t6j]]</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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p 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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p 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 33:		Line 35:
	[[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 18:39, 29 September 2014

OCA — Mon, 29 Sep 2014 18:39:21 GMT

←Older revision		Revision as of 18:39, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1t6p.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
		+	<StructureSection load='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t6p]] is a 8 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=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
		+	</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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t6j\|1t6j]]</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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p 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/t6/1t6p_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.

-	~~{{STRUCTURE_1t6p\| PDB=1t6p \| SCENE= }}~~	+	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>

-	~~===Crystal Structure~~ of ~~Phenylalanine Ammonia Lyase from Rhodosporidium toruloides===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15350127}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1t6p]] is a 8 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=1T6P OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015350127<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]

OCA: Protected "1t6p" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:21:45 GMT

Protected "1t6p" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:21, 5 January 2013

OCA at 11:21, 5 January 2013

OCA — Sat, 05 Jan 2013 11:21:42 GMT

←Older revision		Revision as of 11:21, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1t6p.png\|left\|200px]]		[[Image:1t6p.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t6p", 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_1t6p\| PDB=1t6p \| SCENE= }}		{{STRUCTURE_1t6p\| PDB=1t6p \| SCENE= }}

	===Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides===		===Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides===

-
-	<!--
-	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}}		{{ABSTRACT_PUBMED_15350127}}

	==About this Structure==		==About this Structure==
-	~~1T6P~~ is a 8 ~~chains~~ structure ~~of 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=1T6P OCA].	+	[[1t6p]] is a 8 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=1T6P OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15350127~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015350127</ref><references group="xtra"/>
-	[[Category: ~~Phenylalanine ammonia-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]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:07:09 2009''

OCA at 19:07, 16 February 2009

OCA — Mon, 16 Feb 2009 19:07:10 GMT

←Older revision		Revision as of 19:07, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1T6P is a ~~[[Single protein]]~~ structure of ~~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=1T6P OCA].	+	1T6P is a 8 chains structure of 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=1T6P OCA].

	==Reference==		==Reference==
-	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:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15350127 15350127]~~	+	<ref group="xtra">PMID:15350127</ref><references group="xtra"/>
	[[Category: Phenylalanine ammonia-lyase]]		[[Category: Phenylalanine ammonia-lyase]]
	[[Category: Rhodosporidium toruloides]]		[[Category: Rhodosporidium toruloides]]
-	[[Category: Single protein]]
	[[Category: Calabrese, J C.]]		[[Category: Calabrese, J C.]]
	[[Category: Jordan, D B.]]		[[Category: Jordan, D B.]]
Line 33:		Line 32:
	[[Category: Triple helix coiled coil]]		[[Category: Triple helix coiled coil]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 01~~:51:~~50 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:07:09 2009''