2dap - Revision history

OCA at 06:43, 9 August 2023

2023-08-09T06:43:19Z

←Older revision		Revision as of 06:43, 9 August 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DAP FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DAP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=API:~~2~~,6-DIAMINOPIMELIC+ACID'>API</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]] 2.2Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [https://pdbe.org/2dap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [https://www.ebi.ac.uk/pdbsum/2dap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dap 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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [https://pdbe.org/2dap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [https://www.ebi.ac.uk/pdbsum/2dap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dap ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DAPDH_CORGL DAPDH_CORGL]] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:8865347</ref> <ref>PMID:8865347</ref>	+	[https://www.uniprot.org/uniprot/DAPDH_CORGL DAPDH_CORGL] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:8865347</ref> <ref>PMID:8865347</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
-	[[Category: Diaminopimelate dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blanchard~~, J S~~]]	+	[[Category: Blanchard JS]]
-	[[Category: Cirilli, M]]	+	[[Category: Cirilli M]]
-	[[Category: Gao, Y]]	+	[[Category: Gao Y]]
-	[[Category: Reddy~~, S G~~]]	+	[[Category: Reddy SG]]
-	[[Category: Scapin, G]]	+	[[Category: Scapin G]]
-	[[Category: Vederas~~, J C]]~~	+	[[Category: Vederas JC]]
-	~~[[Category: D-amino acid dehydrogenase]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Diaminopimelate]]~~	+
-	~~[[Category: Lysine biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:29, 8 December 2021

2021-12-08T10:29:03Z

←Older revision		Revision as of 10:29, 8 December 2021
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	<StructureSection load='2dap' size='340' side='right'caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2dap' size='340' side='right'caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DAP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DAP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [~~http~~://pdbe.org/2dap PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dap PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dap 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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [https://pdbe.org/2dap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [https://www.ebi.ac.uk/pdbsum/2dap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dap ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAPDH_CORGL DAPDH_CORGL]] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:8865347</ref> <ref>PMID:8865347</ref>	+	[[https://www.uniprot.org/uniprot/DAPDH_CORGL DAPDH_CORGL]] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:8865347</ref> <ref>PMID:8865347</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:38, 4 March 2020

2020-03-04T07:38:47Z

←Older revision		Revision as of 07:38, 4 March 2020
Line 1:		Line 1:

	==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP==		==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP==
-	<StructureSection load='2dap' size='340' side='right' caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2dap' size='340' side='right'caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DAP FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DAP FirstGlance]. <br>
Line 35:		Line 35:
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Diaminopimelate dehydrogenase]]		[[Category: Diaminopimelate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Blanchard, J S]]		[[Category: Blanchard, J S]]
	[[Category: Cirilli, M]]		[[Category: Cirilli, M]]

OCA at 06:20, 30 May 2018

2018-05-30T06:20:33Z

←Older revision		Revision as of 06:20, 30 May 2018
Line 1:		Line 1:
		+
	==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP==		==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP==
	<StructureSection load='2dap' size='340' side='right' caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2dap' size='340' side='right' caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://pdbe.org/2dap PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap 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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://pdbe.org/2dap PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dap ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/2dap_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/2dap_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>
	</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=2dap ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:57, 11 September 2015

2015-09-11T22:57:42Z

←Older revision		Revision as of 22:57, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap 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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://pdbe.org/2dap PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~DDH_CORGL DDH_CORGL~~]] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:~~9521647~~</ref> <ref>PMID:8865347</ref>	+	[[http://www.uniprot.org/uniprot/DAPDH_CORGL DAPDH_CORGL]] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:8865347</ref> <ref>PMID:8865347</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 2dap" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:34, 25 December 2014

2014-12-25T20:34:10Z

←Older revision		Revision as of 20:34, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DAP FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DAP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap 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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDH_CORGL DDH_CORGL]] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:9521647</ref> <ref>PMID:8865347</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Diaminopimelate dehydrogenase]]		[[Category: Diaminopimelate dehydrogenase]]
-	[[Category: Blanchard, J S.]]	+	[[Category: Blanchard, J S]]
-	[[Category: Cirilli, M.]]	+	[[Category: Cirilli, M]]
-	[[Category: Gao, Y.]]	+	[[Category: Gao, Y]]
-	[[Category: Reddy, S G.]]	+	[[Category: Reddy, S G]]
-	[[Category: Scapin, G.]]	+	[[Category: Scapin, G]]
-	[[Category: Vederas, J C.]]	+	[[Category: Vederas, J C]]
	[[Category: D-amino acid dehydrogenase]]		[[Category: D-amino acid dehydrogenase]]
	[[Category: Dehydrogenase]]		[[Category: Dehydrogenase]]

OCA at 02:32, 30 September 2014

2014-09-30T02:32:33Z

←Older revision		Revision as of 02:32, 30 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2dap.~~png\|left~~\|200px]]	+	==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP==
		+	<StructureSection load='2dap' size='340' side='right' caption='[[2dap]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DAP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </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=2dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dap OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dap RCSB], [http://www.ebi.ac.uk/pdbsum/2dap 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/da/2dap_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 three-dimensional structures of Corynebacterium glutamicum diaminopimelate dehydrogenase as a binary complex with the substrate meso-diaminopimelate (meso-DAP) and a ternary complex with NADP+ and an isoxazoline inhibitor [Abbot, S.D., Lane-Bell, P., Kanwar, P.S.S., and Vederas, J. C. (1994) J. Am. Chem. Soc. 116, 6513-6520] have been solved and refined against X-ray diffraction data to 2.2 A. Diaminopimelate dehydrogenase is a homodimer of approximately 35,000 molecular weight subunits and is the only dehydrogenase present in the bacterial diaminopimelate/lysine biosynthetic pathway. Inhibitors of the enzymes of L-lysine biosynthesis have been proposed as potential antibiotics or herbicides, since mammals lack this metabolic pathway. Diaminopimelate dehydrogenase catalyzes the unique, reversible, pyridine dinucleotide-dependent oxidative deamination of the D-amino acid stereocenter of meso-diaminopimelate to generate L-2-amino-6-oxopimelate. The enzyme is absolutely specific for the meso stereoisomer of DAP and must distinguish between two opposite chiral amino acid centers on the same symmetric substrate. The determination of the three-dimensional structure of the enzyme--meso-diaminopimelate complex allows a description of the molecular basis of this stereospecific discrimination. The substrate is bound in an elongated cavity, in which the distribution of residues that act as hydrogen bond donors or acceptors defines a single orientation in which the substrate may bind in order to position the D-amino acid center of meso-DAP near the oxidized nucleotide. The previously described isoxazoline inhibitor binds at the same site as DAP but has its L-amino acid center positioned where the D-amino acid center of meso-DAP would normally be located, thereby generating a nonproductive inhibitor complex. The relative positions of the N-terminal dinucleotide and C-terminal substrate-binding domains in the diaminopimelate dehydrogenase--NADP+, diaminopimelate dehydrogenase--DAP, and diaminopimelate dehydrogenase--NADP(+)--inhibitor complexes confirm our previous observations that the enzyme undergoes significant conformational changes upon binding of both dinucleotide and substrate.

-	~~{{STRUCTURE_2dap\| PDB=2dap \| SCENE= }}~~	+	Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase.,Scapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS Biochemistry. 1998 Mar 10;37(10):3278-85. PMID:9521647<ref>PMID:9521647</ref>

-	~~===C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9521647}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dap]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009521647<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Diaminopimelate dehydrogenase]]		[[Category: Diaminopimelate dehydrogenase]]

OCA: Protected "2dap" [edit=sysop:move=sysop]

2013-01-06T11:44:54Z

Protected "2dap" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:44, 6 January 2013

OCA at 11:44, 6 January 2013

2013-01-06T11:44:50Z

←Older revision		Revision as of 11:44, 6 January 2013
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-	{{Seed}}
	[[Image:2dap.png\|left\|200px]]		[[Image:2dap.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dap", 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_2dap\| PDB=2dap \| SCENE= }}		{{STRUCTURE_2dap\| PDB=2dap \| SCENE= }}

	===C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP===		===C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9521647}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9521647 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9521647}}		{{ABSTRACT_PUBMED_9521647}}

	==About this Structure==		==About this Structure==
-	~~2DAP~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA].	+	[[2dap]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9521647~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009521647</ref><references group="xtra"/>
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Diaminopimelate dehydrogenase]]		[[Category: Diaminopimelate dehydrogenase]]
Line 37:		Line 25:
	[[Category: Lysine biosynthesis]]		[[Category: Lysine biosynthesis]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:24:27 2009''

OCA at 04:24, 18 February 2009

2009-02-18T04:24:29Z

←Older revision		Revision as of 04:24, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2DAP is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA].	+	2DAP is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DAP OCA].

	==Reference==		==Reference==
-	Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase., Scapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS, Biochemistry. 1998 Mar 10;37(10):3278-85. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9521647 9521647]~~	+	<ref group="xtra">PMID:9521647</ref><references group="xtra"/>
	[[Category: Corynebacterium glutamicum]]		[[Category: Corynebacterium glutamicum]]
	[[Category: Diaminopimelate dehydrogenase]]		[[Category: Diaminopimelate dehydrogenase]]
-	[[Category: Single protein]]
	[[Category: Blanchard, J S.]]		[[Category: Blanchard, J S.]]
	[[Category: Cirilli, M.]]		[[Category: Cirilli, M.]]
Line 39:		Line 38:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 13:~~06:~~58 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:24:27 2009''