3r5d - Revision history

OCA at 12:10, 14 March 2024

OCA — Thu, 14 Mar 2024 12:10:46 GMT

←Older revision		Revision as of 12:10, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3r5d' size='340' side='right'caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3r5d' size='340' side='right'caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[3r5a\|3r5a]]~~, [[~~3r5b~~\|~~3r5b]], [[3r5c\|3r5c~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dapD, PA3666 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~287~~ "~~Bacillus aeruginosus~~" ~~(Schroeter 1872) Trevisan 1885])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </~~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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [https://pdbe.org/3r5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [https://www.ebi.ac.uk/pdbsum/3r5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5d 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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [https://pdbe.org/3r5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [https://www.ebi.ac.uk/pdbsum/3r5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DAPD_PSEAE DAPD_PSEAE]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA. It can only accept L-2 aminopimelate as substrate.<ref>PMID:22359568</ref>	+	[https://www.uniprot.org/uniprot/DAPD_PSEAE DAPD_PSEAE] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA. It can only accept L-2 aminopimelate as substrate.<ref>PMID:22359568</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 A resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1DeltadapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.	+
-		+
-	Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.,Schnell R, Oehlmann W, Sandalova T, Braun Y, Huck C, Maringer M, Singh M, Schneider G PLoS One. 2012;7(2):e31133. doi: 10.1371/journal.pone.0031133. Epub 2012 Feb 16. PMID:22359568<ref>PMID:22359568</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3r5d" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sandalova, T~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Schneider, G~~]]	+	[[Category: Sandalova T]]
-	[[Category: ~~Schnell, R~~]]	+	[[Category: Schneider G]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Schnell R]]

OCA at 05:49, 15 June 2022

OCA — Wed, 15 Jun 2022 05:49:34 GMT

←Older revision		Revision as of 05:49, 15 June 2022
Line 1:		Line 1:

	==Pseudomonas aeruginosa DapD (PA3666) apoprotein==		==Pseudomonas aeruginosa DapD (PA3666) apoprotein==
-	<StructureSection load='3r5d' size='340' side='right' caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3r5d' size='340' side='right'caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3R5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [~~http~~://pdbe.org/3r5d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3r5d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5d 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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [https://pdbe.org/3r5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [https://www.ebi.ac.uk/pdbsum/3r5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAPD_PSEAE DAPD_PSEAE]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA. It can only accept L-2 aminopimelate as substrate.<ref>PMID:22359568</ref>	+	[[https://www.uniprot.org/uniprot/DAPD_PSEAE DAPD_PSEAE]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA. It can only accept L-2 aminopimelate as substrate.<ref>PMID:22359568</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]		[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Sandalova, T]]		[[Category: Sandalova, T]]
	[[Category: Schneider, G]]		[[Category: Schneider, G]]
	[[Category: Schnell, R]]		[[Category: Schnell, R]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:44, 8 March 2018

OCA — Thu, 08 Mar 2018 05:44:02 GMT

←Older revision		Revision as of 05:44, 8 March 2018
Line 8:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://pdbe.org/3r5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d 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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://pdbe.org/3r5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 16:47, 10 May 2016

OCA — Tue, 10 May 2016 16:47:52 GMT

←Older revision		Revision as of 16:47, 10 May 2016
Line 1:		Line 1:
		+
	==Pseudomonas aeruginosa DapD (PA3666) apoprotein==		==Pseudomonas aeruginosa DapD (PA3666) apoprotein==
	<StructureSection load='3r5d' size='340' side='right' caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3r5d' size='340' side='right' caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa Pseudomonas aeruginosa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 ~~Pseudomonas aeruginosa~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d 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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://pdbe.org/3r5d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAPD_PSEAE DAPD_PSEAE]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA. It can only accept L-2 aminopimelate as substrate.<ref>PMID:22359568</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The diaminopimelic acid pathway of lysine biosynthesis has been suggested to provide attractive targets for the development of novel antibacterial drugs. Here we report the characterization of two enzymes from this pathway in the human pathogen Pseudomonas aeruginosa, utilizing structural biology, biochemistry and genetics. We show that tetrahydrodipicolinate N-succinyltransferase (DapD) from P. aeruginosa is specific for the L-stereoisomer of the amino substrate L-2-aminopimelate, and its D-enantiomer acts as a weak inhibitor. The crystal structures of this enzyme with L-2-aminopimelate and D-2-aminopimelate, respectively, reveal that both compounds bind at the same site of the enzyme. Comparison of the binding interactions of these ligands in the enzyme active site suggests misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition. P. aeruginosa mutants where the dapA gene had been deleted were viable and able to grow in a mouse lung infection model, suggesting that DapA is not an optimal target for drug development against this organism. Structure-based sequence alignments, based on the DapA crystal structure determined to 1.6 A resolution revealed the presence of two homologues, PA0223 and PA4188, in P. aeruginosa that could substitute for DapA in the P. aeruginosa PAO1DeltadapA mutant. In vitro experiments using recombinant PA0223 protein could however not detect any DapA activity.
		+
		+	Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.,Schnell R, Oehlmann W, Sandalova T, Braun Y, Huck C, Maringer M, Singh M, Schneider G PLoS One. 2012;7(2):e31133. doi: 10.1371/journal.pone.0031133. Epub 2012 Feb 16. PMID:22359568<ref>PMID:22359568</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3r5d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]		[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
-	[[Category: Pseudomonas aeruginosa]]
	[[Category: Sandalova, T]]		[[Category: Sandalova, T]]
	[[Category: Schneider, G]]		[[Category: Schneider, G]]
	[[Category: Schnell, R]]		[[Category: Schnell, R]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:43, 4 January 2015

OCA — Sun, 04 Jan 2015 09:43:11 GMT

←Older revision		Revision as of 09:43, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5D FirstGlance]. <br>		<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d 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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d PDBsum]</span></td></tr>
-	<table>	+	</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]		[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: Sandalova, T.]]	+	[[Category: Sandalova, T]]
-	[[Category: Schneider, G.]]	+	[[Category: Schneider, G]]
-	[[Category: Schnell, R.]]	+	[[Category: Schnell, R]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:39, 5 June 2014

OCA — Thu, 05 Jun 2014 04:39:47 GMT

←Older revision		Revision as of 04:39, 5 June 2014
Line 1:		Line 1:
-	~~[[Image:3r5d.png\|left\|200px]]~~	+	==Pseudomonas aeruginosa DapD (PA3666) apoprotein==
-		+	<StructureSection load='3r5d' size='340' side='right' caption='[[3r5d]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~<!--~~	+	== Structural highlights ==
-	~~The line below this paragraph, containing "STRUCTURE_3r5d", creates the "Structure Box" on the page.~~	+	<table><tr><td colspan='2'>[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5D FirstGlance]. <br>
-	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r5a\|3r5a]], [[3r5b\|3r5b]], [[3r5c\|3r5c]]</td></tr>
-	~~or leave the SCENE parameter empty for the default display.~~	+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, PA3666 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>
-	~~-->~~	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </span></td></tr>
-	~~{{STRUCTURE_3r5d\| PDB=3r5d \| SCENE= }}~~	+	<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=3r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r5d RCSB], [http://www.ebi.ac.uk/pdbsum/3r5d PDBsum]</span></td></tr>
-		+	<table>
-	===Pseudomonas aeruginosa DapD (PA3666) apoprotein===	+	__TOC__
-		+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA].	+
	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]		[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]

OCA at 06:05, 1 February 2012

OCA — Wed, 01 Feb 2012 06:05:08 GMT

←Older revision		Revision as of 06:05, 1 February 2012
Line 1:		Line 1:
-	[[Image:3r5d.~~jpg~~\|left\|200px]]	+	[[Image:3r5d.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 9:
	{{STRUCTURE_3r5d\| PDB=3r5d \| SCENE= }}		{{STRUCTURE_3r5d\| PDB=3r5d \| SCENE= }}

-	===~~Pseudomona~~ aeruginosa DapD===	+	===Pseudomonas aeruginosa DapD (PA3666) apoprotein===

OCA at 06:42, 25 January 2012

OCA — Wed, 25 Jan 2012 06:42:56 GMT

←Older revision		Revision as of 06:42, 25 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3r5d.jpg\|left\|200px]]

-	The ~~entry 3r5d~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3r5d", 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_3r5d\| PDB=3r5d \| SCENE= }}

-	~~Authors: Sandalova, T., Schnell, R., Schneider, G.~~	+	===Pseudomona aeruginosa DapD===

-	~~Description~~: ~~Pseudomona~~ aeruginosa ~~DapD~~	+
		+	==About this Structure==
		+	[[3r5d]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5D OCA].
		+	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
		+	[[Category: Pseudomonas aeruginosa]]
		+	[[Category: Sandalova, T.]]
		+	[[Category: Schneider, G.]]
		+	[[Category: Schnell, R.]]
		+	[[Category: Transferase]]

OCA at 06:53, 27 April 2011

OCA — Wed, 27 Apr 2011 06:53:18 GMT

←Older revision		Revision as of 06:53, 27 April 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3r5d is ON HOLD	+	The entry 3r5d is ON HOLD until Paper Publication

	Authors: Sandalova, T., Schnell, R., Schneider, G.		Authors: Sandalova, T., Schnell, R., Schneider, G.

	Description: Pseudomona aeruginosa DapD		Description: Pseudomona aeruginosa DapD

OCA: Protected "3r5d" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2011 07:48:40 GMT

Protected "3r5d" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:48, 30 March 2011