1yxc - Revision history

OCA at 08:13, 25 October 2023

2023-10-25T08:13:03Z

←Older revision		Revision as of 08:13, 25 October 2023
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	<StructureSection load='1yxc' size='340' side='right'caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1yxc' size='340' side='right'caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yxc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YXC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YXC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yxc]] 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=1YXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YXC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [https://pdbe.org/1yxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [https://www.ebi.ac.uk/pdbsum/1yxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yxc 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/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~~://proteopedia.org/fgij/fg.htm?mol=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [~~http~~://pdbe.org/1yxc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yxc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yxc 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]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 4-hydroxy-tetrahydrodipicolinate synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dobson~~, R C.J~~]]	+	[[Category: Dobson RCJ]]
-	[[Category: Gerrard~~, J A~~]]	+	[[Category: Gerrard JA]]
-	[[Category: Griffin~~, M D.W~~]]	+	[[Category: Griffin MDW]]
-	[[Category: Jameson~~, G B]]~~	+	[[Category: Jameson GB]]
-	~~[[Category: Dihydrodipicolinate synthase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 08:54, 20 January 2021

2021-01-20T08:54:44Z

←Older revision		Revision as of 08:54, 20 January 2021
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	==Structure of E. coli dihydrodipicolinate synthase to 1.9 A==		==Structure of E. coli dihydrodipicolinate synthase to 1.9 A==
-	<StructureSection load='1yxc' size='340' side='right' caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1yxc' size='340' side='right'caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yxc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YXC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yxc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YXC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</div></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 "Bacillus coli" Migula 1895])</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 "Bacillus coli" Migula 1895])</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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://pdbe.org/1yxc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yxc 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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://pdbe.org/1yxc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yxc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/1yxc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/1yxc_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>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1yxc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1yxc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]		[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Dobson, R C.J]]		[[Category: Dobson, R C.J]]
	[[Category: Gerrard, J A]]		[[Category: Gerrard, J A]]

OCA at 08:25, 12 October 2017

2017-10-12T08:25:53Z

←Older revision		Revision as of 08:25, 12 October 2017
Line 1:		Line 1:
		+
	==Structure of E. coli dihydrodipicolinate synthase to 1.9 A==		==Structure of E. coli dihydrodipicolinate synthase to 1.9 A==
	<StructureSection load='1yxc' size='340' side='right' caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1yxc' size='340' side='right' caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<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 "Bacillus coli" Migula 1895])</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 "Bacillus coli" Migula 1895])</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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://pdbe.org/1yxc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc 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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://pdbe.org/1yxc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yxc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1yxc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1yxc" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:25, 7 February 2016

2016-02-07T18:25:43Z

←Older revision		Revision as of 18:25, 7 February 2016
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	<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=1yxc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:01, 10 September 2015

2015-09-10T04:01:39Z

←Older revision		Revision as of 04:01, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1yxc' size='340' side='right' caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1yxc' size='340' side='right' caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yxc]] 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=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YXC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yxc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YXC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</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 "Bacillus coli" Migula 1895])</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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc 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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://pdbe.org/1yxc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1yxc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrodipicolinate synthase~~]]	+	[[Category: Bacillus coli migula 1895]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
	[[Category: Dobson, R C.J]]		[[Category: Dobson, R C.J]]
	[[Category: Gerrard, J A]]		[[Category: Gerrard, J A]]
	[[Category: Griffin, M D.W]]		[[Category: Griffin, M D.W]]
	[[Category: Jameson, G B]]		[[Category: Jameson, G B]]
		+	[[Category: Dihydrodipicolinate synthase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 17:24, 24 December 2014

2014-12-24T17:24:53Z

←Older revision		Revision as of 17:24, 24 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yxc]] 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=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YXC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yxc]] 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=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YXC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</td></tr>
-	<tr><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><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/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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc 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=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc 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 36:		Line 38:
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[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: Griffin, M D.W.]]	+	[[Category: Griffin, M D.W]]
-	[[Category: Jameson, G B~~.]]~~	+	[[Category: Jameson, G B]]
-	~~[[Category: Dihydrodipicolinate synthase~~]]	+
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 08:26, 3 October 2014

2014-10-03T08:26:32Z

←Older revision		Revision as of 08:26, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1yxc.~~png~~\|~~left~~\|200px]]	+	==Structure of E. coli dihydrodipicolinate synthase to 1.9 A==
		+	<StructureSection load='1yxc' size='340' side='right' caption='[[1yxc]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yxc]] 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=1YXC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YXC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dhp\|1dhp]], [[1s5t\|1s5t]], [[1s5v\|1s5v]], [[1s5w\|1s5w]], [[1yxd\|1yxd]]</td></tr>
		+	<tr><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><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yxc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yxc RCSB], [http://www.ebi.ac.uk/pdbsum/1yxc 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/yx/1yxc_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 ==
		+	Dihydrodipicolinate synthase (DHDPS) mediates the key first reaction common to the biosynthesis of (S)-lysine and meso-diaminopimelate. The activity of DHDPS is allosterically regulated by the feedback inhibitor (S)-lysine. The crystal structure of DHDPS from Escherichia coli has previously been published, but to only a resolution of 2.5 A, and the structure of the lysine-bound adduct was known to only 2.94 A resolution. Here, the crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from E. coli are presented to 1.9 and 2.0 A, respectively, resolutions that allow, in particular, more accurate definition of the protein structure. The general architecture of the active site is found to be consistent with previously determined structures, but with some important differences. Arg138, which is situated at the entrance of the active site and is thought to be involved in substrate binding, has an altered conformation and is connected via a water molecule to Tyr133 of the active-site catalytic triad. This suggests a hitherto unknown function for Arg138 in the DHDPS mechanism. Additionally, a re-evaluation of the dimer-dimer interface reveals a more extensive network of interactions than first thought. Of particular interest is the higher resolution structure of DHDPS with (S)-lysine bound at the allosteric site, which is remote to the active site, although connected to it by a chain of conserved water molecules. (S)-Lysine has a slightly altered conformation from that originally determined and does not appear to alter the DHDPS structure as others have reported.

-	~~{{STRUCTURE_1yxc\| PDB=1yxc \| SCENE= }}~~	+	The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.,Dobson RC, Griffin MD, Jameson GB, Gerrard JA Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1116-24. Epub 2005, Jul 20. PMID:16041077<ref>PMID:16041077</ref>

-	~~===Structure~~ of E. ~~coli dihydrodipicolinate synthase to 1~~.~~9 A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16041077}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yxc]] 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=1YXC OCA].~~	+

	==See Also==		==See Also==
-	*[[Dihydrodipicolinate ~~Synthase~~\|Dihydrodipicolinate ~~Synthase~~]]	+	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016041077<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "1yxc" [edit=sysop:move=sysop]

2012-10-20T07:30:59Z

Protected "1yxc" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:30, 20 October 2012

OCA at 07:30, 20 October 2012

2012-10-20T07:30:57Z

←Older revision		Revision as of 07:30, 20 October 2012
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-	{{Seed}}
	[[Image:1yxc.png\|left\|200px]]		[[Image:1yxc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yxc", 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_1yxc\| PDB=1yxc \| SCENE= }}		{{STRUCTURE_1yxc\| PDB=1yxc \| SCENE= }}

	===Structure of E. coli dihydrodipicolinate synthase to 1.9 A===		===Structure of E. coli dihydrodipicolinate synthase to 1.9 A===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16041077}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16041077 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16041077}}		{{ABSTRACT_PUBMED_16041077}}

	==About this Structure==		==About this Structure==
-	~~1YXC~~ 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=1YXC OCA].	+	[[1yxc]] 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=1YXC OCA].
		+
		+	==See Also==
		+	*[[Dihydrodipicolinate Synthase\|Dihydrodipicolinate Synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16041077~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016041077</ref><references group="xtra"/>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 31:		Line 22:
	[[Category: Jameson, G B.]]		[[Category: Jameson, G B.]]
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
-		+	[[Category: Lyase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 15:44:28 2009''~~	+

OCA at 13:44, 16 February 2009

2009-02-16T13:44:34Z

←Older revision		Revision as of 13:44, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1YXC 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=1YXC OCA].	+	1YXC 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=1YXC OCA].

	==Reference==		==Reference==
-	The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance., Dobson RC, Griffin MD, Jameson GB, Gerrard JA, Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1116-24. Epub 2005, Jul 20. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16041077 16041077]~~	+	<ref group="xtra">PMID:16041077</ref><references group="xtra"/>
	[[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.]]
Line 33:		Line 32:
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 18~~:43:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:44:28 2009''