5e3r - Revision history

OCA at 06:12, 5 July 2023

2023-07-05T06:12:09Z

←Older revision		Revision as of 06:12, 5 July 2023
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	<StructureSection load='5e3r' size='340' side='right'caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5e3r' size='340' side='right'caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e3r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Corgl Corgl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E3R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E3R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e3r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E3R FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NPI:(2S)~~-~~2-AMINOHEPTANEDIOIC+ACID'>NPI</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e3p\|5e3p]]~~, [[~~5e3q~~\|~~5e3q~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPI:(2S)-2-AMINOHEPTANEDIOIC+ACID'>NPI</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dapD, Cgl1106, cg1256 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=196627 CORGL])</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=5e3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e3r OCA], [https://pdbe.org/5e3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e3r RCSB], [https://www.ebi.ac.uk/pdbsum/5e3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e3r ProSAT]</span></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/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~~://proteopedia.org/fgij/fg.htm?mol=5e3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e3r OCA], [~~http~~://pdbe.org/5e3r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e3r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e3r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e3r ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DAPD_CORGL DAPD_CORGL]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA.	+	[https://www.uniprot.org/uniprot/DAPD_CORGL DAPD_CORGL] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]~~	+	[[Category: Corynebacterium glutamicum ATCC 13032]]
-	~~[[Category: Corgl~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, K J]]	+	[[Category: Kim K-J]]
-	[[Category: Sagong, H Y]]	+	[[Category: Sagong H-Y]]
-	~~[[Category: Corynebacterium glutamicum]]~~	+
-	~~[[Category: L-lysine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:44, 9 September 2020

2020-09-09T09:44:37Z

←Older revision		Revision as of 09:44, 9 September 2020
Line 1:		Line 1:

-	==Crystal ~~strcuture~~ of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum==	+	==Crystal structure of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum==
	<StructureSection load='5e3r' size='340' side='right'caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5e3r' size='340' side='right'caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 06:42, 22 April 2020

2020-04-22T06:42:52Z

←Older revision		Revision as of 06:42, 22 April 2020
Line 1:		Line 1:
		+
	==Crystal strcuture of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum==		==Crystal strcuture of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum==
-	<StructureSection load='5e3r' size='340' side='right' caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5e3r' size='340' side='right'caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e3r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E3R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E3R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e3r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Corgl Corgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E3R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E3R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPI:(2S)-2-AMINOHEPTANEDIOIC+ACID'>NPI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NPI:(2S)-2-AMINOHEPTANEDIOIC+ACID'>NPI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e3p\|5e3p]], [[5e3q\|5e3q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e3p\|5e3p]], [[5e3q\|5e3q]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapD, Cgl1106, cg1256 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</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=5e3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e3r OCA], [http://pdbe.org/5e3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e3r RCSB], [http://www.ebi.ac.uk/pdbsum/5e3r PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5e3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e3r OCA], [http://pdbe.org/5e3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e3r RCSB], [http://www.ebi.ac.uk/pdbsum/5e3r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e3r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		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: Corgl]]
		+	[[Category: Large Structures]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Sagong, H Y]]		[[Category: Sagong, H Y]]

OCA at 11:32, 30 December 2015

2015-12-30T11:32:35Z

←Older revision		Revision as of 11:32, 30 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal strcuture of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum==
		+	<StructureSection load='5e3r' size='340' side='right' caption='[[5e3r]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e3r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E3R FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NPI:(2S)-2-AMINOHEPTANEDIOIC+ACID'>NPI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5e3p\|5e3p]], [[5e3q\|5e3q]]</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=5e3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e3r OCA], [http://pdbe.org/5e3r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e3r RCSB], [http://www.ebi.ac.uk/pdbsum/5e3r PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAPD_CORGL DAPD_CORGL]] Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tetrahydrodipicolinate N-succinyltransferase (DapD) is an enzyme involved in the biosynthesis of l-lysine by converting tetrahydrodipicolinate into N-succinyl-l-2-amino-6-oxopimelate, using succinyl-CoA as a cofactor. We determined the crystal structure of DapD from Corynebacterium glutamicum (CgDapD). CgDapD functions as a trimer, and each monomer consists of three domains: an N-terminal helical domain (NTD), a left-handed beta-helix (LbetaH) domain, and a beta C-terminal domain (CTD). The mode of cofactor binding to CgDapD, elucidated by determining the structure in complex with succinyl-CoA, reveals that the position of the CTD changes slightly as the cofactor binds to the enzyme. The superposition of this structure with that of Mycobacterium tuberculosis shows differences in residues that make up cofactor-binding sites. Moreover, we determined the structure of CgDapD in complex with the substrate analogue 2-aminopimelate and revealed that the analogue was stabilized by conserved residues. The catalytic and substrate binding sites of CgDapD were confirmed by site-directed mutagenesis experiments.

-	~~The entry 5e3r is ON HOLD~~	+	Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum.,Sagong HY, Kim KJ J Agric Food Chem. 2015 Dec 16;63(49):10641-6. doi: 10.1021/acs.jafc.5b04785., Epub 2015 Dec 4. PMID:26602189<ref>PMID:26602189</ref>

-	~~Authors: Sagong~~, H.-Y.~~, Kim, K.-J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal strcuture of DapD in complex with 2~~-~~aminopimelate from Corynebacterium glutamicum~~	+	<div class="pdbe-citations 5e3r" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Kim, K.-J]]	+	<references/>
-	[[Category: Sagong, H.-Y]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
		+	[[Category: Kim, K J]]
		+	[[Category: Sagong, H Y]]
		+	[[Category: Corynebacterium glutamicum]]
		+	[[Category: L-lysine]]
		+	[[Category: Transferase]]

OCA: Protected "5e3r" [edit=sysop:move=sysop]

2015-10-16T02:57:07Z

Protected "5e3r" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:57, 16 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e3r is ON HOLD Authors: Sagong, H.-Y., Kim, K.-J. Description: Crystal strcuture of DapD in complex with 2-aminopimelate from Corynebacterium glut...

2015-10-16T02:57:05Z

New page: '''Unreleased structure''' The entry 5e3r is ON HOLD Authors: Sagong, H.-Y., Kim, K.-J. Description: Crystal strcuture of DapD in complex with 2-aminopimelate from Corynebacterium glut...

New page

'''Unreleased structure'''

The entry 5e3r is ON HOLD

Authors: Sagong, H.-Y., Kim, K.-J.

Description: Crystal strcuture of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Sagong, H.-Y]]