2q9j - Revision history

OCA at 11:26, 30 August 2023

2023-08-30T11:26:07Z

←Older revision		Revision as of 11:26, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2q9j' size='340' side='right'caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2q9j' size='340' side='right'caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium~~ influenzae~~" lehmann and neumann 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">dapF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [https://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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [https://pdbe.org/2q9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [https://www.ebi.ac.uk/pdbsum/2q9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9j 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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [https://pdbe.org/2q9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [https://www.ebi.ac.uk/pdbsum/2q9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN]] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref>	+	[https://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ influenzae ~~lehmann and neumann 1896]]~~	+	[[Category: Haemophilus influenzae]]
-	~~[[Category: Diaminopimelate epimerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blanchard~~, J S~~]]	+	[[Category: Blanchard JS]]
-	[[Category: Cherney, M]]	+	[[Category: Cherney M]]
-	[[Category: Diaper~~, C M~~]]	+	[[Category: Diaper CM]]
-	[[Category: Pillai, B]]	+	[[Category: Pillai B]]
-	[[Category: Sutherland, A]]	+	[[Category: Sutherland A]]
-	[[Category: Vederas~~, J C]]~~	+	[[Category: Vederas JC]]
-	~~[[Category: C217s mutant]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Open conformation of the apo-enzyme]]~~	+
-	~~[[Category: Two domain~~]]	+

OCA at 08:13, 25 June 2021

2021-06-25T08:13:05Z

OCA at 18:59, 24 January 2018

2018-01-24T18:59:21Z

←Older revision		Revision as of 18:59, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of the C217S mutant of diaminopimelate epimerase==		==Crystal structure of the C217S mutant of diaminopimelate epimerase==
	<StructureSection load='2q9j' size='340' side='right' caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2q9j' size='340' side='right' caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://pdbe.org/2q9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j 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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://pdbe.org/2q9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q9/2q9j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q9/2q9j_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 15:10, 8 February 2016

2016-02-08T15:10:44Z

←Older revision		Revision as of 15:10, 8 February 2016
Line 20:		Line 20:
	<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=2q9j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:48, 10 September 2015

2015-09-10T12:48:23Z

←Older revision		Revision as of 12:48, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2q9j' size='340' side='right' caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2q9j' size='340' side='right' caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Haemophilus_influenzae Haemophilus~~ influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 ~~Haemophilus~~ influenzae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j 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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://pdbe.org/2q9j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	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 2q9j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium influenzae lehmann and neumann 1896]]
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
-	[[Category: Haemophilus influenzae]]
	[[Category: Blanchard, J S]]		[[Category: Blanchard, J S]]
	[[Category: Cherney, M]]		[[Category: Cherney, M]]

OCA at 00:14, 25 December 2014

2014-12-25T00:14:53Z

←Older revision		Revision as of 00:14, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j 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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN]] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: Blanchard, J S]]		[[Category: Blanchard, J S]]
-	[[Category: Cherney, M.]]	+	[[Category: Cherney, M]]
-	[[Category: Diaper, C M.]]	+	[[Category: Diaper, C M]]
	[[Category: Pillai, B]]		[[Category: Pillai, B]]
-	[[Category: Sutherland, A.]]	+	[[Category: Sutherland, A]]
-	[[Category: Vederas, J C.]]	+	[[Category: Vederas, J C]]
	[[Category: C217s mutant]]		[[Category: C217s mutant]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Open conformation of the apo-enzyme]]		[[Category: Open conformation of the apo-enzyme]]
	[[Category: Two domain]]		[[Category: Two domain]]

OCA at 20:10, 30 September 2014

2014-09-30T20:10:54Z

←Older revision		Revision as of 20:10, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2q9j.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the C217S mutant of diaminopimelate epimerase==
		+	<StructureSection load='2q9j' size='340' side='right' caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [http://www.ebi.ac.uk/pdbsum/2q9j 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/q9/2q9j_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 ==
		+	Diaminopimelate (DAP) epimerase catalyzes the stereoinversion of ll-DAP to meso-DAP, a precursor of l-lysine and an essential component of the bacterial peptidoglycan. This function is vital to bacteria and the enzyme therefore represents an attractive target for the design of novel anti-bacterials. DAP epimerase belongs to the group of PLP-independent amino acid racemases that function through a rather unusual mechanism involving two cysteines acting in concert as a base (thiolate) and an acid (thiol). We have solved the crystal structures of the apo-forms of DAP epimerase mutants (C73S and C217S) from Haemophilus influenzae at 2.3A and 2.2A resolution, respectively. These structures provide a snapshot of the enzyme in the first step of the catalytic cycle. Comparisons with the structures of the inhibitor-bound form reveal that the enzyme adopts an 'open conformation' in the absence of substrates or inhibitors with the two active site cysteines existing as a thiol-thiolate pair. Substrate binding to the C-terminal domain triggers the closure of the N-terminal domain coupled with tight encapsulation of the ligand, stabilization of the conformation of an active site loop containing Cys73 and expulsion of water molecules with concomitant desolvation of the thiolate base. This structural rearrangement is critical for catalysis.

-	~~{{STRUCTURE_2q9j\| PDB=2q9j \| SCENE= }}~~	+	Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.,Pillai B, Cherney M, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MN Biochem Biophys Res Commun. 2007 Nov 23;363(3):547-53. Epub 2007 Sep 17. PMID:17889830<ref>PMID:17889830</ref>

-	~~===Crystal structure~~ of the ~~C217S mutant of diaminopimelate epimerase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17889830}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2q9j]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Haemophilus_influenzae Haemophilus influenzae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017889830<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]

OCA: Protected "2q9j" [edit=sysop:move=sysop]

2013-01-07T20:17:52Z

Protected "2q9j" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:17, 7 January 2013

OCA at 20:17, 7 January 2013

2013-01-07T20:17:49Z

←Older revision		Revision as of 20:17, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2q9j.png\|left\|200px]]		[[Image:2q9j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2q9j", 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_2q9j\| PDB=2q9j \| SCENE= }}		{{STRUCTURE_2q9j\| PDB=2q9j \| SCENE= }}

	===Crystal structure of the C217S mutant of diaminopimelate epimerase===		===Crystal structure of the C217S mutant of diaminopimelate epimerase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17889830}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17889830 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17889830}}		{{ABSTRACT_PUBMED_17889830}}

	==About this Structure==		==About this Structure==
-	~~2Q9J~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA].	+	[[2q9j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17889830~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017889830</ref><references group="xtra"/>
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
Line 36:		Line 24:
	[[Category: Open conformation of the apo-enzyme]]		[[Category: Open conformation of the apo-enzyme]]
	[[Category: Two domain]]		[[Category: Two domain]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:54:35 2009''

OCA at 21:54, 16 February 2009

2009-02-16T21:54:36Z

←Older revision		Revision as of 21:54, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Q9J is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA].	+	2Q9J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA].

	==Reference==		==Reference==
-	Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase., Pillai B, Cherney M, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MN, Biochem Biophys Res Commun. 2007 Nov 23;363(3):547-53. Epub 2007 Sep 17. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17889830 17889830]~~	+	<ref group="xtra">PMID:17889830</ref><references group="xtra"/>
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
-	[[Category: Single protein]]
	[[Category: Blanchard, J S]]		[[Category: Blanchard, J S]]
	[[Category: Cherney, M.]]		[[Category: Cherney, M.]]
Line 38:		Line 37:
	[[Category: Two domain]]		[[Category: Two domain]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 04~~:15:~~15 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 23:54:35 2009''

←Older revision		Revision as of 08:13, 25 June 2021
Line 1:		Line 1:

	==Crystal structure of the C217S mutant of diaminopimelate epimerase==		==Crystal structure of the C217S mutant of diaminopimelate epimerase==
-	<StructureSection load='2q9j' size='340' side='right' caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2q9j' size='340' side='right'caption='[[2q9j]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q9j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q9J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gqz\|1gqz]], [[1bwz\|1bwz]], [[2gke\|2gke]], [[2gkj\|2gkj]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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'>[https://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [https://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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [~~http~~://pdbe.org/2q9j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2q9j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9j 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=2q9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q9j OCA], [https://pdbe.org/2q9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q9j RCSB], [https://www.ebi.ac.uk/pdbsum/2q9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q9j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN]] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref>	+	[[https://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN]] 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. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 38:
	[[Category: Bacterium influenzae lehmann and neumann 1896]]		[[Category: Bacterium influenzae lehmann and neumann 1896]]
	[[Category: Diaminopimelate epimerase]]		[[Category: Diaminopimelate epimerase]]
		+	[[Category: Large Structures]]
	[[Category: Blanchard, J S]]		[[Category: Blanchard, J S]]
	[[Category: Cherney, M]]		[[Category: Cherney, M]]