5m47 - Revision history

OCA at 18:24, 1 November 2023

OCA — Wed, 01 Nov 2023 18:24:56 GMT

←Older revision		Revision as of 18:24, 1 November 2023
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	<StructureSection load='5m47' size='340' side='right'caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='5m47' size='340' side='right'caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m47]] 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=5M47 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5M47 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m47]] 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=5M47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M47 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]] 2.59Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dapF, Cgl1943, cg2129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=196627 CORGL])</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_epimerase Diaminopimelate epimerase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7]~~ </~~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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [https://pdbe.org/5m47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [https://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [~~http~~://pdbe.org/5m47 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL]] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref>	+	[https://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Corgl]]~~	+	[[Category: Corynebacterium glutamicum ATCC 13032]]
-	~~[[Category: Diaminopimelate epimerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, K J]]	+	[[Category: Kim K-J]]
-	[[Category: Sagong, H Y]]	+	[[Category: Sagong H-Y]]
-	~~[[Category: Isomerase~~]]	+

OCA at 09:43, 18 November 2020

OCA — Wed, 18 Nov 2020 09:43:34 GMT

←Older revision		Revision as of 09:43, 18 November 2020
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-	==Crystal ~~strcuture~~ of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate==	+	==Crystal structure of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate==
	<StructureSection load='5m47' size='340' side='right'caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='5m47' size='340' side='right'caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m47]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M47 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M47 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m47]] 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=5M47 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M47 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='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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF, Cgl1943, cg2129 ([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/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [http://pdbe.org/5m47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [http://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [http://pdbe.org/5m47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [http://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Corgl]]
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 11:00, 12 August 2020

OCA — Wed, 12 Aug 2020 11:00:45 GMT

←Older revision		Revision as of 11:00, 12 August 2020
Line 1:		Line 1:

	==Crystal strcuture of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate==		==Crystal strcuture of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate==
-	<StructureSection load='5m47' size='340' side='right' caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>	+	<StructureSection load='5m47' size='340' side='right'caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m47]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M47 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M47 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m47]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M47 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M47 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_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [http://pdbe.org/5m47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [http://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [http://pdbe.org/5m47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [http://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
		+	[[Category: Large Structures]]
	[[Category: Kim, K J]]		[[Category: Kim, K J]]
	[[Category: Sagong, H Y]]		[[Category: Sagong, H Y]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 16:43, 20 October 2017

OCA — Fri, 20 Oct 2017 16:43:14 GMT

←Older revision		Revision as of 16:43, 20 October 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL]] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref>		[[http://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL]] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diaminopimelate epimerase (DapF) is one of the crucial enzymes involved in l-lysine biosynthesis, where it converts l,l-diaminopimelate (l,l-DAP) into d,l-DAP. DapF is also considered as an attractive target for the development of antibacterial drugs. Here, we report the crystal structure of DapF from Corynebacterium glutamicum (CgDapF). Structures of CgDapF obtained under both oxidized and reduced conditions reveal that the function of CgDapF is regulated by redox-switch modulation via reversible disulfide bond formation between two catalytic cysteine residues. Under oxidized condition, two catalytic cysteine residues form a disulfide bond; these same cysteine residues exist in reduced form under reduced condition. Disulfide bond formation also induces a subsequent structural change in the dynamic catalytic loop at the active site, which results in open/closed conformational change at the active site. We also determined the crystal structure of CgDapF in complex with its product d,l-DAP, and elucidated how the enzyme recognizes its substrate l,l-DAP as a substrate. Moreover, the structure in complex with the d,l-DAP product reveals that CgDapF undergoes a large open/closed domain movement upon substrate binding, resulting in a completely buried active site with the substrate bound.
		+
		+	Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.,Sagong HY, Kim KJ Sci Rep. 2017 Feb 8;7:42318. doi: 10.1038/srep42318. PMID:28176858<ref>PMID:28176858</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5m47" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:31, 2 November 2016

OCA — Wed, 02 Nov 2016 18:31:29 GMT

←Older revision		Revision as of 18:31, 2 November 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5m47 is ~~ON HOLD~~	+	==Crystal strcuture of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate==
-		+	<StructureSection load='5m47' size='340' side='right' caption='[[5m47]], [[Resolution\|resolution]] 2.59Å' scene=''>
-	~~Authors~~: ~~Sagong~~, H.-Y., ~~Kim~~, K.-J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5m47]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M47 FirstGlance]. <br>
-	~~Description~~: ~~Crystal strcuture~~ of ~~DapF from Corynebacterium glutamicum in complex with D~~,L-diaminopimelate	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </span></td></tr>
-	[[Category: Kim, K.-J]]	+	<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=5m47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m47 OCA], [http://pdbe.org/5m47 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m47 RCSB], [http://www.ebi.ac.uk/pdbsum/5m47 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m47 ProSAT]</span></td></tr>
-	[[Category: Sagong, H.-Y]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAPF_CORGL DAPF_CORGL]] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Involved in the succinylase branch of the diaminopimelate biosynthesis.<ref>PMID:12948639</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Diaminopimelate epimerase]]
		+	[[Category: Kim, K J]]
		+	[[Category: Sagong, H Y]]
		+	[[Category: Isomerase]]

OCA: Protected "5m47" [edit=sysop:move=sysop]

OCA — Wed, 26 Oct 2016 16:23:22 GMT

Protected "5m47" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:23, 26 October 2016

OCA: New page: '''Unreleased structure''' The entry 5m47 is ON HOLD Authors: Sagong, H.-Y., Kim, K.-J. Description: Crystal strcuture of DapF from Corynebacterium glutamicum in complex with D,L-diami...

OCA — Wed, 26 Oct 2016 16:23:21 GMT

New page: '''Unreleased structure''' The entry 5m47 is ON HOLD Authors: Sagong, H.-Y., Kim, K.-J. Description: Crystal strcuture of DapF from Corynebacterium glutamicum in complex with D,L-diami...

New page

'''Unreleased structure'''

The entry 5m47 is ON HOLD

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

Description: Crystal strcuture of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Sagong, H.-Y]]