2a6l - Revision history

OCA at 09:11, 14 February 2024

OCA — Wed, 14 Feb 2024 09:11:26 GMT

←Older revision		Revision as of 09:11, 14 February 2024
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	<StructureSection load='2a6l' size='340' side='right'caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2a6l' size='340' side='right'caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a6l]] is a 2 chain structure with sequence from [https://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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.05Å</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~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [https://pdbe.org/2a6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [https://www.ebi.ac.uk/pdbsum/2a6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6l 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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [https://pdbe.org/2a6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [https://www.ebi.ac.uk/pdbsum/2a6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6l 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]]
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	</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=2a6l 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=2a6l ConSurf].
	<div style="clear:both"></div>		<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 [(S)-ASA] and pyruvate, a reaction catalyzed by dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52). It has been proposed that Arg138, a residue situated at the entrance to the active site of DHDPS, is responsible for binding the carboxyl of (S)-ASA and may additionally be involved in the mechanism of (S)-lysine inhibition. This study tests these assertions by mutation of Arg138 to both histidine and alanine. Following purification, DHDPS-R138H and DHDPS-R138A each showed severely compromised activity (approximately 0.1% that of the wild type), and the apparent Michaelis-Menten constant for (S)-ASA in each mutant, calculated using a pseudo-single substrate analysis, was significantly higher than that of the wild type. This provides good evidence that Arg138 is indeed essential for catalysis and plays a key role in substrate binding. To test whether structural changes could account for the change in kinetic behavior, the solution structure was probed via far-UV circular dichroism, confirming that the mutations at position 138 did not modify secondary structure. The crystal structures of both mutant enzymes were determined, confirming the presence of the mutations and suggesting that Arg138 plays an important role in catalysis: the stabilization of the catalytic triad residues, a motif we have previously demonstrated to be essential for activity. In addition, the role of Arg138 in (S)-lysine inhibition was examined. Both mutant enzymes showed the same IC(50) values as the wild type but different partial inhibition patterns, from which it is concluded that arginine 138 is not essential for (S)-lysine inhibition.
-
-	Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase.,Dobson RC, Devenish SR, Turner LA, Clifford VR, Pearce FG, Jameson GB, Gerrard JA Biochemistry. 2005 Oct 4;44(39):13007-13. PMID:16185069<ref>PMID:16185069</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2a6l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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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: Clifford~~, V R~~]]	+	[[Category: Clifford VR]]
-	[[Category: Devenish~~, S R~~]]	+	[[Category: Devenish SR]]
-	[[Category: Dobson~~, R C~~]]	+	[[Category: Dobson RC]]
-	[[Category: Gerrard~~, J A~~]]	+	[[Category: Gerrard JA]]
-	[[Category: Jameson~~, G B~~]]	+	[[Category: Jameson GB]]
-	[[Category: Pearce~~, F G~~]]	+	[[Category: Pearce FG]]
-	[[Category: Turner~~, L A]]~~	+	[[Category: Turner LA]]
-	~~[[Category: Beta-alpha-barrel]]~~	+
-	~~[[Category: Dihydrodipicolinate synthase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 08:26, 27 January 2021

OCA — Wed, 27 Jan 2021 08:26:22 GMT

←Older revision		Revision as of 08:26, 27 January 2021
Line 1:		Line 1:

	==Dihydrodipicolinate synthase (E. coli)- mutant R138H==		==Dihydrodipicolinate synthase (E. coli)- mutant R138H==
-	<StructureSection load='2a6l' size='340' side='right' caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='2a6l' size='340' side='right'caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2A6L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a6l]] is a 2 chain structure with sequence from [https://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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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='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 "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'>[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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [~~http~~://pdbe.org/2a6l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2a6l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6l 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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [https://pdbe.org/2a6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [https://www.ebi.ac.uk/pdbsum/2a6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6l 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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2a6l" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2a6l" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]		[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Clifford, V R]]		[[Category: Clifford, V R]]
	[[Category: Devenish, S R]]		[[Category: Devenish, S R]]

OCA at 06:36, 31 January 2018

OCA — Wed, 31 Jan 2018 06:36:27 GMT

←Older revision		Revision as of 06:36, 31 January 2018
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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/a6/2a6l_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/2a6l_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 16:29, 12 October 2017

OCA — Thu, 12 Oct 2017 16:29:52 GMT

←Older revision		Revision as of 16:29, 12 October 2017
Line 1:		Line 1:
		+
	==Dihydrodipicolinate synthase (E. coli)- mutant R138H==		==Dihydrodipicolinate synthase (E. coli)- mutant R138H==
	<StructureSection load='2a6l' size='340' side='right' caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2a6l' size='340' side='right' caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' 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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://pdbe.org/2a6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l 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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://pdbe.org/2a6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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=2a6l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2a6l" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2a6l" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:22, 11 September 2015

OCA — Fri, 11 Sep 2015 16:22:30 GMT

←Older revision		Revision as of 16:22, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2a6l' size='340' side='right' caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='2a6l' size='340' side='right' caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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 ~~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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l 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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://pdbe.org/2a6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l 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 2a6l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dihydrodipicolinate synthase~~]]	+	[[Category: Bacillus coli migula 1895]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
	[[Category: Clifford, V R]]		[[Category: Clifford, V R]]
	[[Category: Devenish, S R]]		[[Category: Devenish, S R]]
Line 45:		Line 46:
	[[Category: Turner, L A]]		[[Category: Turner, L A]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
		+	[[Category: Dihydrodipicolinate synthase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 18:56, 25 December 2014

OCA — Thu, 25 Dec 2014 18:56:52 GMT

←Older revision		Revision as of 18:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6L FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6L FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=K:POTASSIUM+ION'>K</scene></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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l 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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l 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 35:		Line 37:
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Clifford, V R.]]	+	[[Category: Clifford, V R]]
-	[[Category: Devenish, S R.]]	+	[[Category: Devenish, S R]]
-	[[Category: Dobson, R C.]]	+	[[Category: Dobson, R C]]
-	[[Category: Gerrard, J A.]]	+	[[Category: Gerrard, J A]]
-	[[Category: Jameson, G B.]]	+	[[Category: Jameson, G B]]
-	[[Category: Pearce, F G.]]	+	[[Category: Pearce, F G]]
-	[[Category: Turner, L A.]]	+	[[Category: Turner, L A]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
-	[[Category: Dihydrodipicolinate synthase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 11:51, 3 October 2014

OCA — Fri, 03 Oct 2014 11:51:18 GMT

←Older revision		Revision as of 11:51, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2a6l.~~png~~\|~~left~~\|200px]]	+	==Dihydrodipicolinate synthase (E. coli)- mutant R138H==
		+	<StructureSection load='2a6l' size='340' side='right' caption='[[2a6l]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2a6l]] 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=2A6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6L FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene><br>
		+	<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=2a6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a6l RCSB], [http://www.ebi.ac.uk/pdbsum/2a6l 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/a6/2a6l_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 [(S)-ASA] and pyruvate, a reaction catalyzed by dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52). It has been proposed that Arg138, a residue situated at the entrance to the active site of DHDPS, is responsible for binding the carboxyl of (S)-ASA and may additionally be involved in the mechanism of (S)-lysine inhibition. This study tests these assertions by mutation of Arg138 to both histidine and alanine. Following purification, DHDPS-R138H and DHDPS-R138A each showed severely compromised activity (approximately 0.1% that of the wild type), and the apparent Michaelis-Menten constant for (S)-ASA in each mutant, calculated using a pseudo-single substrate analysis, was significantly higher than that of the wild type. This provides good evidence that Arg138 is indeed essential for catalysis and plays a key role in substrate binding. To test whether structural changes could account for the change in kinetic behavior, the solution structure was probed via far-UV circular dichroism, confirming that the mutations at position 138 did not modify secondary structure. The crystal structures of both mutant enzymes were determined, confirming the presence of the mutations and suggesting that Arg138 plays an important role in catalysis: the stabilization of the catalytic triad residues, a motif we have previously demonstrated to be essential for activity. In addition, the role of Arg138 in (S)-lysine inhibition was examined. Both mutant enzymes showed the same IC(50) values as the wild type but different partial inhibition patterns, from which it is concluded that arginine 138 is not essential for (S)-lysine inhibition.

-	~~{{STRUCTURE_2a6l\| PDB=2a6l \| SCENE= }}~~	+	Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase.,Dobson RC, Devenish SR, Turner LA, Clifford VR, Pearce FG, Jameson GB, Gerrard JA Biochemistry. 2005 Oct 4;44(39):13007-13. PMID:16185069<ref>PMID:16185069</ref>

-	~~===Dihydrodipicolinate synthase (E. coli)- mutant R138H===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16185069}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2a6l]] 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=2A6L OCA].~~	+

	==See Also==		==See Also==
-	*[[Dihydrodipicolinate ~~Synthase~~\|Dihydrodipicolinate ~~Synthase~~]]	+	*[[Dihydrodipicolinate synthase\|Dihydrodipicolinate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016185069<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "2a6l" [edit=sysop:move=sysop]

OCA — Sat, 20 Oct 2012 20:15:19 GMT

Protected "2a6l" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:15, 20 October 2012

OCA at 20:15, 20 October 2012

OCA — Sat, 20 Oct 2012 20:15:15 GMT

←Older revision		Revision as of 20:15, 20 October 2012
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-	{{Seed}}
	[[Image:2a6l.png\|left\|200px]]		[[Image:2a6l.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2a6l", 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_2a6l\| PDB=2a6l \| SCENE= }}		{{STRUCTURE_2a6l\| PDB=2a6l \| SCENE= }}

	===Dihydrodipicolinate synthase (E. coli)- mutant R138H===		===Dihydrodipicolinate synthase (E. coli)- mutant R138H===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16185069}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16185069 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16185069}}		{{ABSTRACT_PUBMED_16185069}}

	==About this Structure==		==About this Structure==
-	~~2A6L~~ 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=2A6L OCA].	+	[[2a6l]] 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=2A6L OCA].
		+
		+	==See Also==
		+	*[[Dihydrodipicolinate Synthase\|Dihydrodipicolinate Synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16185069~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016185069</ref><references group="xtra"/>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 35:		Line 26:
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
-		+	[[Category: Lyase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 03:39:59 2009''~~	+

OCA at 01:40, 18 February 2009

OCA — Wed, 18 Feb 2009 01:40:00 GMT

←Older revision		Revision as of 01:40, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2A6L 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=2A6L OCA].	+	2A6L 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=2A6L OCA].

	==Reference==		==Reference==
-	Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase., Dobson RC, Devenish SR, Turner LA, Clifford VR, Pearce FG, Jameson GB, Gerrard JA, Biochemistry. 2005 Oct 4;44(39):13007-13. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16185069 16185069]~~	+	<ref group="xtra">PMID:16185069</ref><references group="xtra"/>
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Clifford, V R.]]		[[Category: Clifford, V R.]]
	[[Category: Devenish, S R.]]		[[Category: Devenish, S R.]]
Line 37:		Line 36:
	[[Category: Dihydrodipicolinate synthase]]		[[Category: Dihydrodipicolinate synthase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 09~~:54:~~14 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:39:59 2009''