1d7v - Revision history

OCA at 05:55, 9 August 2023

OCA — Wed, 09 Aug 2023 05:55:56 GMT

←Older revision		Revision as of 05:55, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='1d7v' size='340' side='right'caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1d7v' size='340' side='right'caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"pseudomonas_cepacia"_burkholder_1950 "pseudomonas~~ cepacia~~" burkholder 1950~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</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]] 2.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [https://pdbe.org/1d7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [https://www.ebi.ac.uk/pdbsum/1d7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7v 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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [https://pdbe.org/1d7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [https://www.ebi.ac.uk/pdbsum/1d7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE]] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.	+	[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.
	== 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~~ cepacia ~~burkholder 1950~~]]	+	[[Category: Burkholderia cepacia]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jansonius~~, J N~~]]	+	[[Category: Jansonius JN]]
-	[[Category: Keller, J]]	+	[[Category: Keller J]]
-	[[Category: Malashkevich~~, V N~~]]	+	[[Category: Malashkevich VN]]
-	[[Category: Strop, P]]	+	[[Category: Strop P]]
-	[[Category: Toney~~, M D]]~~	+	[[Category: Toney MD]]
-	~~[[Category: Catalytic mechanism]]~~	+
-	~~[[Category: Decarboxylation inhibitor]]~~	+
-	~~[[Category: Enzyme complex]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:43, 14 July 2021

OCA — Wed, 14 Jul 2021 10:43:42 GMT

←Older revision		Revision as of 10:43, 14 July 2021
Line 3:		Line 3:
	<StructureSection load='1d7v' size='340' side='right'caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1d7v' size='340' side='right'caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1D7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [~~http~~://pdbe.org/1d7v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1d7v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7v 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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [https://pdbe.org/1d7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [https://www.ebi.ac.uk/pdbsum/1d7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE]] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.	+	[[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE]] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:53, 10 October 2019

OCA — Thu, 10 Oct 2019 06:53:32 GMT

←Older revision		Revision as of 06:53, 10 October 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA==		==CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA==
-	<StructureSection load='1d7v' size='340' side='right' caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1d7v' size='340' side='right'caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas cepacia burkholder 1950]]		[[Category: Pseudomonas cepacia burkholder 1950]]
		+	[[Category: Large Structures]]
	[[Category: Jansonius, J N]]		[[Category: Jansonius, J N]]
	[[Category: Keller, J]]		[[Category: Keller, J]]

OCA at 08:32, 6 December 2017

OCA — Wed, 06 Dec 2017 08:32:22 GMT

←Older revision		Revision as of 08:32, 6 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA==		==CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA==
	<StructureSection load='1d7v' size='340' side='right' caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1d7v' size='340' side='right' caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://pdbe.org/1d7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v 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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://pdbe.org/1d7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/d7/1d7v_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/1d7v_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 18:16, 8 February 2016

OCA — Mon, 08 Feb 2016 18:16:28 GMT

←Older revision		Revision as of 18:16, 8 February 2016
Line 18:		Line 18:
	<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=1d7v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:09, 10 September 2015

OCA — Thu, 10 Sep 2015 14:09:31 GMT

←Older revision		Revision as of 14:09, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1d7v' size='340' side='right' caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1d7v' size='340' side='right' caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_cepacia Burkholderia~~ cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v 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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://pdbe.org/1d7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1d7v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burkholderia~~ cepacia]]	+	[[Category: Pseudomonas cepacia burkholder 1950]]
	[[Category: Jansonius, J N]]		[[Category: Jansonius, J N]]
	[[Category: Keller, J]]		[[Category: Keller, J]]

OCA at 01:14, 25 December 2014

OCA — Thu, 25 Dec 2014 01:14:37 GMT

←Older revision		Revision as of 01:14, 25 December 2014
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	<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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v 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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE]] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:47, 22 December 2014

OCA — Mon, 22 Dec 2014 22:47:40 GMT

←Older revision		Revision as of 22:47, 22 December 2014
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	</StructureSection>		</StructureSection>
	[[Category: Burkholderia cepacia]]		[[Category: Burkholderia cepacia]]
-	[[Category: Jansonius, J N.]]	+	[[Category: Jansonius, J N]]
-	[[Category: Keller, J.]]	+	[[Category: Keller, J]]
-	[[Category: Malashkevich, V N.]]	+	[[Category: Malashkevich, V N]]
-	[[Category: Strop, P.]]	+	[[Category: Strop, P]]
-	[[Category: Toney, M D.]]	+	[[Category: Toney, M D]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
	[[Category: Decarboxylation inhibitor]]		[[Category: Decarboxylation inhibitor]]
	[[Category: Enzyme complex]]		[[Category: Enzyme complex]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 06:31, 10 October 2014

OCA — Fri, 10 Oct 2014 06:31:56 GMT

←Older revision		Revision as of 06:31, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v 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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:43, 4 September 2014

OCA — Thu, 04 Sep 2014 06:43:26 GMT

←Older revision		Revision as of 06:43, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1d7v.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA==
		+	<StructureSection load='1d7v' size='340' side='right' caption='[[1d7v]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1d7v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NMA:N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE'>NMA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d7u\|1d7u]], [[1d7r\|1d7r]], [[1d7s\|1d7s]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </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=1d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7v RCSB], [http://www.ebi.ac.uk/pdbsum/1d7v 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/d7/1d7v_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 crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observed in previous structures that differ in alkali metal ion content, and two active-site conformations have been shown to coexist in solution when a single type of metal ion is present. There is no indication of coexisting conformers in the structures reported here or in the previously reported structures, and the observed conformation is that expected based on the presence of potassium in the enzyme. Thus, although two active-site conformations coexist in solution, a single conformation, corresponding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the aldimine double bond to the pyridoxal phosphate cofactor to be fully out of the plane of the coenzyme ring, whereas the Calpha-CO2(-) bond lies close to it. This provides an explanation for the observed lack of decarboxylation reactivity with this amino acid. The carboxylate groups of both 1-aminocyclopropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally that alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction. The structures of d and l-cycloserine bound to the active-site show that the l-isomer is deprotonated at C(alpha), presumably by Lys272, while the d-isomer is not. This difference explains the approximately 3000-fold greater potency of the l versus the d-isomer as a competitive inhibitor of dialkylglycine decarboxylase.

-	~~{{STRUCTURE_1d7v\| PDB=1d7v \| SCENE= }}~~	+	Crystal structures of dialkylglycine decarboxylase inhibitor complexes.,Malashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD J Mol Biol. 1999 Nov 19;294(1):193-200. PMID:10556038<ref>PMID:10556038</ref>

-	~~===CRYSTAL STRUCTURE OF THE COMPLEX OF 2~~,~~2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10556038}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1d7v]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_cepacia Burkholderia cepacia]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1D7V OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010556038<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Burkholderia cepacia]]		[[Category: Burkholderia cepacia]]
	[[Category: Jansonius, J N.]]		[[Category: Jansonius, J N.]]