2pur - Revision history

OCA at 11:09, 30 August 2023

OCA — Wed, 30 Aug 2023 11:09:20 GMT

←Older revision		Revision as of 11:09, 30 August 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pur]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pur]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUR 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>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.7Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene><~~/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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">dapA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [https://pdbe.org/2pur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [https://www.ebi.ac.uk/pdbsum/2pur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pur 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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [https://pdbe.org/2pur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [https://www.ebi.ac.uk/pdbsum/2pur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pur ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>	+	[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dobson~~, R C.J~~]]	+	[[Category: Dobson RCJ]]
-	[[Category: Gerrard~~, J A~~]]	+	[[Category: Gerrard JA]]
-	[[Category: Jameson~~, G B]]~~	+	[[Category: Jameson GB]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 15:33, 17 June 2021

OCA — Thu, 17 Jun 2021 15:33:18 GMT

←Older revision		Revision as of 15:33, 17 June 2021
Line 1:		Line 1:

	==Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.==		==Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.==
-	<StructureSection load='2pur' size='340' side='right' caption='[[2pur]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='2pur' size='340' side='right'caption='[[2pur]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pur]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pur]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUR 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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [~~http~~://pdbe.org/2pur PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pur PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pur 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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [https://pdbe.org/2pur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [https://www.ebi.ac.uk/pdbsum/2pur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pur ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>	+	[[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2pur" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2pur" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]		[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Dobson, R C.J]]		[[Category: Dobson, R C.J]]
	[[Category: Gerrard, J A]]		[[Category: Gerrard, J A]]

OCA at 18:58, 24 January 2018

OCA — Wed, 24 Jan 2018 18:58:50 GMT

←Older revision		Revision as of 18:58, 24 January 2018
Line 1:		Line 1:
		+
	==Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.==		==Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.==
	<StructureSection load='2pur' size='340' side='right' caption='[[2pur]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2pur' size='340' side='right' caption='[[2pur]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://pdbe.org/2pur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur 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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://pdbe.org/2pur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pur ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pur_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pur_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pur ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2pur" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2pur" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:17, 11 September 2015

OCA — Fri, 11 Sep 2015 08:17:23 GMT

←Older revision		Revision as of 08:17, 11 September 2015
Line 6:		Line 6:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Dihydrodipicolinate_synthase Dihydrodipicolinate~~ synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.52 4.2.1.52] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur 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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://pdbe.org/2pur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2pur" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrodipicolinate~~ synthase]]	+	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Dobson, R C.J]]		[[Category: Dobson, R C.J]]

OCA at 13:44, 25 December 2014

OCA — Thu, 25 Dec 2014 13:44:58 GMT

←Older revision		Revision as of 13:44, 25 December 2014
Line 9:		Line 9:
	<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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur 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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 39:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Dobson, R C.J]]		[[Category: Dobson, R C.J]]
-	[[Category: Gerrard, J A.]]	+	[[Category: Gerrard, J A]]
-	[[Category: Jameson, G B.]]	+	[[Category: Jameson, G B]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 06:26, 10 October 2014

OCA — Fri, 10 Oct 2014 06:26:14 GMT

←Older revision		Revision as of 06:26, 10 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2pur.~~png~~\|~~left~~\|200px]]	+	==Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.==
		+	<StructureSection load='2pur' size='340' side='right' caption='[[2pur]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pur]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PUR 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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KGC:N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE'>KGC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrodipicolinate_synthase Dihydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.52 4.2.1.52] </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=2pur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pur OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pur RCSB], [http://www.ebi.ac.uk/pdbsum/2pur 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/pu/2pur_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 ==
		+	In plants and bacteria, the branch point of (S)-lysine biosynthesis is the condensation of (S)-aspartate-beta-semialdehyde and pyruvate, a reaction catalysed by dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52). In this study, we probe the function of threonine 44 in Escherichia coli DHDPS, with respect to its role in the proton relay. Removal of the hydroxyl moiety of threonine 44, by mutation to valine, significantly attenuates activity (0.1% of wild-type) because the proton relay is broken. It was thus predicted that mutation of threonine 44 to serine would re-establish the proton relay and thus enzymatic activity. Following site-directed mutagenesis and purification to yield the DHDPS-Thr44Ser mutant enzyme, kinetic and structural studies were undertaken. The crystal structure of DHDPS-Thr44Ser showed that the active site was intact and that Ser44 and Tyr107 have some conformational flexibility, which is consistent with the observed loss of activity compared to the wild-type enzyme. Electron density was observed at the active site of DHDPS-Thr44Ser, which was identified as a trapped pyruvate analogue, alpha-ketoglutarate. The activity was indeed found to be increased relative to DHDPS-Thr44Val, but was still reduced to only approximately 8% of that of the wild-type enzyme. Interestingly, there was a shift in the kinetic mechanism, from the substituted-enzyme mechanism, observed in the wild-type, to the ternary-complex mechanism, consistent with the trapped substrate analogue. Increased flexibility in the active site appears to facilitate the binding/reaction of substrate analogues, suggesting that wild-type DHDPS has evolved a relatively rigid active site in order to maintain substrate specificity for pyruvate.

-	~~{{STRUCTURE_2pur\| PDB=2pur \| SCENE= }}~~	+	Specificity versus catalytic potency: The role of threonine 44 in Escherichia coli dihydrodipicolinate synthase mediated catalysis.,Dobson RC, Perugini MA, Jameson GB, Gerrard JA Biochimie. 2009 Aug;91(8):1036-44. Epub 2009 Jun 6. PMID:19505526<ref>PMID:19505526</ref>

-	~~===Structure~~ of ~~dihydrodipicolinate synthase mutant Thr44Ser at 1~~.~~7 A~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19505526}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2pur]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].~~	+

	==See Also==		==See Also==
-	*[[Dihydrodipicolinate ~~Synthase~~\|Dihydrodipicolinate ~~Synthase~~]]	+	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019505526<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

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

OCA — Sat, 20 Oct 2012 17:24:23 GMT

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

←Older revision

Revision as of 17:24, 20 October 2012

OCA at 17:24, 20 October 2012

OCA — Sat, 20 Oct 2012 17:24:21 GMT

←Older revision		Revision as of 17:24, 20 October 2012
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-	{{Seed}}
	[[Image:2pur.png\|left\|200px]]		[[Image:2pur.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2pur\| PDB=2pur \| SCENE= }}		{{STRUCTURE_2pur\| PDB=2pur \| SCENE= }}

	===Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.===		===Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19505526}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19505526 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19505526}}		{{ABSTRACT_PUBMED_19505526}}

	==About this Structure==		==About this Structure==
-	~~2PUR~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].	+	[[2pur]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].
		+
		+	==See Also==
		+	*[[Dihydrodipicolinate Synthase\|Dihydrodipicolinate Synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19505526~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019505526</ref><references group="xtra"/>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
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	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 29 12:25:04 2009''

OCA at 09:25, 29 July 2009

OCA — Wed, 29 Jul 2009 09:25:05 GMT

←Older revision		Revision as of 09:25, 29 July 2009
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	===Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.===		===Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19505526}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19505526 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19505526}}

	==About this Structure==		==About this Structure==
	2PUR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].		2PUR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19505526</ref><references group="xtra"/>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
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	[[Category: Tim barrel]]		[[Category: Tim barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 17~~:47:07 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 29 12:25:04 2009''

OCA at 15:47, 17 February 2009

OCA — Tue, 17 Feb 2009 15:47:09 GMT

←Older revision		Revision as of 15:47, 17 February 2009
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		+	[[Image:2pur.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2pur\| PDB=2pur \| SCENE= }}		{{STRUCTURE_2pur\| PDB=2pur \| SCENE= }}

-	~~'''~~Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.~~'''~~	+	===Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A.===


	==About this Structure==		==About this Structure==
-	2PUR is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].	+	2PUR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PUR OCA].
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Dobson, R C.J]]		[[Category: Dobson, R C.J]]
	[[Category: Gerrard, J A.]]		[[Category: Gerrard, J A.]]
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	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed May 28 09~~:13:~~34 2008~~''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:47:07 2009''