3fdd - Revision history

OCA at 00:31, 28 December 2023

2023-12-28T00:31:11Z

←Older revision		Revision as of 00:31, 28 December 2023
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	<StructureSection load='3fdd' size='340' side='right'caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='3fdd' size='340' side='right'caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"pseudomonas_dacunhae"_gray_and_thornton_1928 "pseudomonas~~ dacunhae~~" gray and thornton 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_dacunhae_ATCC_21192 Pseudomonas dacunhae ATCC 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FDD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.35Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>aspD, GI:28875527 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~207291~~ "~~Pseudomonas dacunhae~~" ~~Gray and Thornton 1928])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	~~<tr id~~='~~activity~~'><~~td class="sblockLbl"~~><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Aspartate_4~~-~~decarboxylase Aspartate 4~~-~~decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [https://pdbe.org/3fdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [https://www.ebi.ac.uk/pdbsum/3fdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdd ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [https://pdbe.org/3fdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [https://www.ebi.ac.uk/pdbsum/3fdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q845W8_COMTE Q845W8_COMTE]
	== 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: Pseudomonas dacunhae gray and thornton 1928]]
-	[[Category: Aspartate 4-decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Huang, C]]	+	[[Category: Huang C]]
-	[[Category: Khristoforov, R]]	+	[[Category: Khristoforov R]]
-	[[Category: Lima, S]]	+	[[Category: Lima S]]
-	[[Category: Momany, C]]	+	[[Category: Momany C]]
-	[[Category: Phillips~~, R S~~]]	+	[[Category: Phillips RS]]
-	[[Category: Sundararaju, B]]	+	[[Category: Sundararaju B]]
-	~~[[Category: Abdc]]~~	+
-	~~[[Category: Aspd]]~~	+
-	~~[[Category: Dodecamer]]~~	+
-	~~[[Category: L-aspartate 4-carboxy-lyase]]~~	+
-	~~[[Category: L-aspartate-beta-decarboxylase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Pyridoxal-5'-phosphate~~]]	+

OCA at 07:58, 2 March 2022

2022-03-02T07:58:20Z

←Older revision		Revision as of 07:58, 2 March 2022
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	==The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme==		==The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme==
-	<StructureSection load='3fdd' size='340' side='right' caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='3fdd' size='340' side='right'caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"pseudomonas_dacunhae"_gray_and_thornton_1928 "pseudomonas dacunhae" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_dacunhae"_gray_and_thornton_1928 "pseudomonas dacunhae" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FDD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 "Pseudomonas dacunhae" Gray and Thornton 1928])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 "Pseudomonas dacunhae" Gray and Thornton 1928])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </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=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [~~http~~://pdbe.org/3fdd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fdd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdd ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [https://pdbe.org/3fdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [https://www.ebi.ac.uk/pdbsum/3fdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Aspartate decarboxylase\|Aspartate decarboxylase]]	+	*[[Aspartate decarboxylase 3D structures\|Aspartate decarboxylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	[[Category: Pseudomonas dacunhae gray and thornton 1928]]		[[Category: Pseudomonas dacunhae gray and thornton 1928]]
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
		+	[[Category: Large Structures]]
	[[Category: Huang, C]]		[[Category: Huang, C]]
	[[Category: Khristoforov, R]]		[[Category: Khristoforov, R]]

OCA at 07:44, 5 December 2018

2018-12-05T07:44:50Z

←Older revision		Revision as of 07:44, 5 December 2018
Line 1:		Line 1:
		+
	==The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme==		==The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme==
	<StructureSection load='3fdd' size='340' side='right' caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='3fdd' size='340' side='right' caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 "Pseudomonas dacunhae" Gray and Thornton 1928])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 "Pseudomonas dacunhae" Gray and Thornton 1928])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </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=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [http://pdbe.org/3fdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [http://www.ebi.ac.uk/pdbsum/3fdd 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=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [http://pdbe.org/3fdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [http://www.ebi.ac.uk/pdbsum/3fdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fdd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/3fdd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/3fdd_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 01:16, 9 February 2016

2016-02-09T01:16:50Z

←Older revision		Revision as of 01:16, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3fdd' size='340' side='right' caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='3fdd' size='340' side='right' caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_dacunhae_atcc_21192 Pseudomonas~~ dacunhae ~~atcc 21192~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_dacunhae"_gray_and_thornton_1928 "pseudomonas dacunhae" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 Pseudomonas dacunhae ~~ATCC 21192~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 "Pseudomonas dacunhae" Gray and Thornton 1928])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </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=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [http://www.ebi.ac.uk/pdbsum/3fdd 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=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [http://pdbe.org/3fdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [http://www.ebi.ac.uk/pdbsum/3fdd PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3fdd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3fdd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aspartate decarboxylase\|Aspartate decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseudomonas dacunhae gray and thornton 1928]]
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
-	[[Category: Pseudomonas dacunhae atcc 21192]]
	[[Category: Huang, C]]		[[Category: Huang, C]]
	[[Category: Khristoforov, R]]		[[Category: Khristoforov, R]]

OCA at 08:34, 26 November 2014

2014-11-26T08:34:54Z

←Older revision		Revision as of 08:34, 26 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3fdd.~~png~~\|~~left~~\|200px]]	+	==The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme==
		+	<StructureSection load='3fdd' size='340' side='right' caption='[[3fdd]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3fdd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FDD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspD, GI:28875527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=207291 Pseudomonas dacunhae ATCC 21192])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_4-decarboxylase Aspartate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.12 4.1.1.12] </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=3fdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fdd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fdd RCSB], [http://www.ebi.ac.uk/pdbsum/3fdd 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/fd/3fdd_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 Pseudomonas dacunhael-aspartate-beta-decarboxylase (ABDC, aspartate 4-decarboxylase, aspartate 4-carboxylyase, E.C. 4.1.1.12) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the beta-decarboxylation of l-aspartate to produce l-alanine and CO(2). This catalytically versatile enzyme is known to form functional dodecamers at its optimal pH and is thought to work in conjunction with an l-Asp/l-Ala antiporter to establish a proton gradient across the membrane that can be used for ATP biosynthesis. We have solved the atomic structure of ABDC to 2.35 A resolution using single-wavelength anomalous dispersion phasing. The structure reveals that ABDC oligomerizes as a homododecamer in an unknown mode among PLP-dependent enzymes and has highest structural homology with members of the PLP-dependent aspartate aminotransferase subfamily. The structure shows that the ABDC active site is very similar to that of aspartate aminotransferase. However, an additional arginine side chain (Arg37) was observed flanking the re-side of the PLP ring in the ABDC active site. The mutagenesis results show that although Arg37 is not required for activity, it appears to be involved in the ABDC catalytic cycle.

-	~~{{STRUCTURE_3fdd\| PDB=3fdd \| SCENE= }}~~	+	The crystal structure of the Pseudomonas dacunhae aspartate-beta-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5'-phosphate-dependent enzyme.,Lima S, Sundararaju B, Huang C, Khristoforov R, Momany C, Phillips RS J Mol Biol. 2009 Apr 24;388(1):98-108. Epub 2009 Mar 2. PMID:19265705<ref>PMID:19265705</ref>

-	~~===The Crystal Structure~~ of the ~~Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19265705}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3fdd]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019265705<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
	[[Category: Pseudomonas dacunhae atcc 21192]]		[[Category: Pseudomonas dacunhae atcc 21192]]
-	[[Category: Huang, C.]]	+	[[Category: Huang, C]]
-	[[Category: Khristoforov, R.]]	+	[[Category: Khristoforov, R]]
-	[[Category: Lima, S.]]	+	[[Category: Lima, S]]
-	[[Category: Momany, C.]]	+	[[Category: Momany, C]]
-	[[Category: Phillips, R S.]]	+	[[Category: Phillips, R S]]
-	[[Category: Sundararaju, B.]]	+	[[Category: Sundararaju, B]]
	[[Category: Abdc]]		[[Category: Abdc]]
-	[[Category: Aspartate 4-decarboxylase]]
	[[Category: Aspd]]		[[Category: Aspd]]
	[[Category: Dodecamer]]		[[Category: Dodecamer]]

OCA: Protected "3fdd" [edit=sysop:move=sysop]

2013-02-13T10:52:53Z

Protected "3fdd" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:52, 13 February 2013

OCA at 10:52, 13 February 2013

2013-02-13T10:52:47Z

←Older revision		Revision as of 10:52, 13 February 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3fdd.png\|left\|200px]]		[[Image:3fdd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fdd", 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_3fdd\| PDB=3fdd \| SCENE= }}		{{STRUCTURE_3fdd\| PDB=3fdd \| SCENE= }}

	===The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme===		===The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19265705}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19265705 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19265705}}		{{ABSTRACT_PUBMED_19265705}}

	==About this Structure==		==About this Structure==
-	~~3FDD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].	+	[[3fdd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19265705~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019265705</ref><references group="xtra"/>
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
	[[Category: Pseudomonas dacunhae atcc 21192]]		[[Category: Pseudomonas dacunhae atcc 21192]]
Line 38:		Line 26:
	[[Category: L-aspartate 4-carboxy-lyase]]		[[Category: L-aspartate 4-carboxy-lyase]]
	[[Category: L-aspartate-beta-decarboxylase]]		[[Category: L-aspartate-beta-decarboxylase]]
		+	[[Category: Lyase]]
	[[Category: Plp]]		[[Category: Plp]]
	[[Category: Pyridoxal-5'-phosphate]]		[[Category: Pyridoxal-5'-phosphate]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 09:53:39 2009''

OCA at 06:53, 1 July 2009

2009-07-01T06:53:41Z

←Older revision		Revision as of 06:53, 1 July 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3FDD is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].	+	3FDD is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].

	==Reference==		==Reference==
-	The Crystal Structure of the Pseudomonas dacunhae Aspartate-beta-Decarboxylase Dodecamer Reveals an Unknown Oligomeric Assembly for a Pyridoxal-5'-Phosphate-Dependent Enzyme., Lima S, Sundararaju B, Huang C, Khristoforov R, Momany C, Phillips RS, J Mol Biol. 2009 Mar 2. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19265705 19265705]~~	+	<ref group="xtra">PMID:19265705</ref><references group="xtra"/>
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
	[[Category: Pseudomonas dacunhae atcc 21192]]		[[Category: Pseudomonas dacunhae atcc 21192]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Huang, C.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Khristoforov, R.]]
		+	[[Category: Lima, S.]]
		+	[[Category: Momany, C.]]
		+	[[Category: Phillips, R S.]]
		+	[[Category: Sundararaju, B.]]
	[[Category: Abdc]]		[[Category: Abdc]]
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
Line 37:		Line 41:
	[[Category: Pyridoxal-5'-phosphate]]		[[Category: Pyridoxal-5'-phosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 25 20~~:14:57 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 09:53:39 2009''

OCA at 18:14, 25 March 2009

2009-03-25T18:14:58Z

←Older revision		Revision as of 18:14, 25 March 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3fdd.~~jpg~~\|left\|200px]]	+	[[Image:3fdd.png\|left\|200px]]

	<!--		<!--
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3FDD is a ~~1 chain~~ structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].	+	3FDD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].

	==Reference==		==Reference==
-	~~<ref group="xtra">~~PMID:~~19265705<~~/~~ref><references group="xtra"~~/>	+	The Crystal Structure of the Pseudomonas dacunhae Aspartate-beta-Decarboxylase Dodecamer Reveals an Unknown Oligomeric Assembly for a Pyridoxal-5'-Phosphate-Dependent Enzyme., Lima S, Sundararaju B, Huang C, Khristoforov R, Momany C, Phillips RS, J Mol Biol. 2009 Mar 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19265705 19265705]
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
	[[Category: Pseudomonas dacunhae atcc 21192]]		[[Category: Pseudomonas dacunhae atcc 21192]]
-	[[Category: ~~Huang, C.~~]]	+	[[Category: Single protein]]
-	[[Category: ~~Khristoforov~~, ~~R.]]~~	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-	~~[[Category~~: ~~Lima, S.]]~~	+
-	~~[[Category: Momany, C.]]~~	+
-	~~[[Category: Phillips, R S.]]~~	+
-	~~[[Category: Sundararaju, B~~.]]	+
	[[Category: Abdc]]		[[Category: Abdc]]
	[[Category: Aspartate 4-decarboxylase]]		[[Category: Aspartate 4-decarboxylase]]
Line 41:		Line 37:
	[[Category: Pyridoxal-5'-phosphate]]		[[Category: Pyridoxal-5'-phosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 10:51:55 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 20:14:57 2009''

OCA at 08:51, 25 March 2009

2009-03-25T08:51:56Z

←Older revision		Revision as of 08:51, 25 March 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3fdd.jpg\|left\|200px]]

-	The ~~entry 3fdd~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3fdd", 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_3fdd\| PDB=3fdd \| SCENE= }}

-	~~Authors: Lima, S., Sundararaju, B., Huang, C., Khristoforov, R., Momany, C., Phillips, R.S.~~	+	===The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme===

-	Description: The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb~~ 25 09:23:43 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19265705}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19265705 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19265705}}
		+
		+	==About this Structure==
		+	3FDD is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_dacunhae_atcc_21192 Pseudomonas dacunhae atcc 21192]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FDD OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19265705</ref><references group="xtra"/>
		+	[[Category: Aspartate 4-decarboxylase]]
		+	[[Category: Pseudomonas dacunhae atcc 21192]]
		+	[[Category: Huang, C.]]
		+	[[Category: Khristoforov, R.]]
		+	[[Category: Lima, S.]]
		+	[[Category: Momany, C.]]
		+	[[Category: Phillips, R S.]]
		+	[[Category: Sundararaju, B.]]
		+	[[Category: Abdc]]
		+	[[Category: Aspartate 4-decarboxylase]]
		+	[[Category: Aspd]]
		+	[[Category: Dodecamer]]
		+	[[Category: L-aspartate 4-carboxy-lyase]]
		+	[[Category: L-aspartate-beta-decarboxylase]]
		+	[[Category: Plp]]
		+	[[Category: Pyridoxal-5'-phosphate]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 10:51:55 2009''