1mka - Revision history

OCA at 08:37, 10 April 2024

OCA — Wed, 10 Apr 2024 08:37:36 GMT

←Older revision		Revision as of 08:37, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1mka' size='340' side='right'caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1mka' size='340' side='right'caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1MKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MKA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DAC:~~2~~-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>FABA ([http://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=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/3-hydroxyacyl-[acyl-carrier-protein]_dehydratase 3-hydroxyacyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.59 4.2.1.59] </~~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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [https://pdbe.org/1mka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [https://www.ebi.ac.uk/pdbsum/1mka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mka 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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [~~http~~://pdbe.org/1mka PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1mka PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1mka ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FABA_ECOLI FABA_ECOLI]] Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)-decenoyl-ACP. Can catalyze the dehydratase reaction for beta-hydroxyacyl-ACPs with saturated chain lengths up to 16:0, being most active on intermediate chain length. Is inactive in the dehydration of long chain unsaturated beta-hydroxyacyl-ACP.<ref>PMID:8910376</ref>	+	[https://www.uniprot.org/uniprot/FABA_ECOLI FABA_ECOLI] Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)-decenoyl-ACP. Can catalyze the dehydratase reaction for beta-hydroxyacyl-ACPs with saturated chain lengths up to 16:0, being most active on intermediate chain length. Is inactive in the dehydration of long chain unsaturated beta-hydroxyacyl-ACP.<ref>PMID:8910376</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1mka 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=1mka ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND. Escherichia coli beta-hydroxydecanoyl thiol ester dehydrase (dehydrase) is essential to the biosynthesis of unsaturated fatty acids, by shunting a 10-carbon intermediate from the saturated fatty acid pathway into the unsaturated fatty acid pathway. Dehydrase catalyzes reactions of dehydration and of double-bond isomerization on 10-carbon thiol esters of acyl carrier protein (ACP). The aim of this work is to elucidate mechanisms for the two enzymatic reactions, which occur in an unusual bifunctional active site, and to understand the specificity of the enzyme for substrates with 10-carbon fatty acyl chains. RESULTS. Crystal structures at 2.0 A resolution for free dehydrase and for the enzyme modified by its classic, mechanism-based inactivator, 3-decynoyl-N-acetylcysteamine, have been determined. Dehydrase is a symmetric dimer with an unusual alpha+beta 'hot dog' fold. Each of the two independent active sites is located between the two subunits of the enzyme, and is a tunnel-shaped pocket completely isolated from the general solvent. Side chains of histidine from one subunit and aspartic acid from the other are the only potentially reactive protein groups in the active site. CONCLUSION. A two-base mechanism by which the histidine and aspartic acid together catalyze dehydration and isomerization reactions is consistent with the active-site structure. The unique topology of the protein fold and the identification of the active-site components reveal features of predictive value for another enzyme, FabZ, which may be the non-specific dehydratase involved in elongation of fatty acyl chains. A positively charged area surrounding the entrance to the active site, which could interact with the negatively charged ACP, was also found.
-
-	Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site.,Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL Structure. 1996 Mar 15;4(3):253-64. PMID:8805534<ref>PMID:8805534</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1mka" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Leesong, M]]	+	[[Category: Leesong M]]
-	~~[[Category: Fatty acid biosynthesis~~]]	+

OCA at 08:38, 2 December 2020

OCA — Wed, 02 Dec 2020 08:38:13 GMT

←Older revision		Revision as of 08:38, 2 December 2020
Line 1:		Line 1:

	==E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE==		==E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE==
-	<StructureSection load='1mka' size='340' side='right' caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1mka' size='340' side='right'caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1MKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1MKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABA ([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">FABA ([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/3-hydroxyacyl-[acyl-carrier-protein]_dehydratase 3-hydroxyacyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.59 4.2.1.59] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxyacyl-[acyl-carrier-protein]_dehydratase 3-hydroxyacyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.59 4.2.1.59] </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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://pdbe.org/1mka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mka 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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://pdbe.org/1mka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1mka" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1mka" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-hydroxyacyl-acyl carrier protein dehydratase 3D structures\|Beta-hydroxyacyl-acyl carrier protein dehydratase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Leesong, M]]		[[Category: Leesong, M]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]

OCA at 08:14, 31 January 2018

OCA — Wed, 31 Jan 2018 08:14:10 GMT

←Older revision		Revision as of 08:14, 31 January 2018
Line 1:		Line 1:
		+
	==E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE==		==E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE==
	<StructureSection load='1mka' size='340' side='right' caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1mka' size='340' side='right' caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABA ([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">FABA ([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/3-hydroxyacyl-[acyl-carrier-protein]_dehydratase 3-hydroxyacyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.59 4.2.1.59] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxyacyl-[acyl-carrier-protein]_dehydratase 3-hydroxyacyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.59 4.2.1.59] </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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://pdbe.org/1mka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka 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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://pdbe.org/1mka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mk/1mka_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mk/1mka_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1mka" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1mka" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-hydroxyacyl-acyl carrier protein dehydratase\|Beta-hydroxyacyl-acyl carrier protein dehydratase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:46, 8 February 2016

OCA — Mon, 08 Feb 2016 15:46:59 GMT

←Older revision		Revision as of 15:46, 8 February 2016
Line 18:		Line 18:
	<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=1mka ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:05, 10 September 2015

OCA — Thu, 10 Sep 2015 13:05:53 GMT

←Older revision		Revision as of 13:05, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1mka' size='340' side='right' caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1mka' size='340' side='right' caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MKA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABA ([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">FABA ([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/3-~~hydroxydecanoyl~~-[acyl-carrier-protein]_dehydratase 3-~~hydroxydecanoyl~~-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.60 4.2.1.60] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxyacyl-[acyl-carrier-protein]_dehydratase 3-hydroxyacyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.59 4.2.1.59] </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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka 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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://pdbe.org/1mka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1mka" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Leesong, M]]		[[Category: Leesong, M]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]

OCA at 00:25, 25 December 2014

OCA — Thu, 25 Dec 2014 00:25:55 GMT

←Older revision		Revision as of 00:25, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MKA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MKA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABA ([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">FABA ([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/3-hydroxydecanoyl-[acyl-carrier-protein]_dehydratase 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.60 4.2.1.60] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxydecanoyl-[acyl-carrier-protein]_dehydratase 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.60 4.2.1.60] </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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka 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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FABA_ECOLI FABA_ECOLI]] Necessary for the introduction of cis unsaturation into fatty acids. Catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to E-(2)-decenoyl-ACP and then its isomerization to Z-(3)-decenoyl-ACP. Can catalyze the dehydratase reaction for beta-hydroxyacyl-ACPs with saturated chain lengths up to 16:0, being most active on intermediate chain length. Is inactive in the dehydration of long chain unsaturated beta-hydroxyacyl-ACP.<ref>PMID:8910376</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Leesong, M.]]	+	[[Category: Leesong, M]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]

OCA at 15:18, 28 September 2014

OCA — Sun, 28 Sep 2014 15:18:21 GMT

←Older revision		Revision as of 15:18, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1mka.~~png~~\|~~left~~\|200px]]	+	==E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE==
		+	<StructureSection load='1mka' size='340' side='right' caption='[[1mka]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1mka]] 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=1MKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MKA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAC:2-DECENOYL+N-ACETYL+CYSTEAMINE'>DAC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FABA ([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/3-hydroxydecanoyl-[acyl-carrier-protein]_dehydratase 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.60 4.2.1.60] </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=1mka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1mka RCSB], [http://www.ebi.ac.uk/pdbsum/1mka 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/mk/1mka_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 ==
		+	BACKGROUND. Escherichia coli beta-hydroxydecanoyl thiol ester dehydrase (dehydrase) is essential to the biosynthesis of unsaturated fatty acids, by shunting a 10-carbon intermediate from the saturated fatty acid pathway into the unsaturated fatty acid pathway. Dehydrase catalyzes reactions of dehydration and of double-bond isomerization on 10-carbon thiol esters of acyl carrier protein (ACP). The aim of this work is to elucidate mechanisms for the two enzymatic reactions, which occur in an unusual bifunctional active site, and to understand the specificity of the enzyme for substrates with 10-carbon fatty acyl chains. RESULTS. Crystal structures at 2.0 A resolution for free dehydrase and for the enzyme modified by its classic, mechanism-based inactivator, 3-decynoyl-N-acetylcysteamine, have been determined. Dehydrase is a symmetric dimer with an unusual alpha+beta 'hot dog' fold. Each of the two independent active sites is located between the two subunits of the enzyme, and is a tunnel-shaped pocket completely isolated from the general solvent. Side chains of histidine from one subunit and aspartic acid from the other are the only potentially reactive protein groups in the active site. CONCLUSION. A two-base mechanism by which the histidine and aspartic acid together catalyze dehydration and isomerization reactions is consistent with the active-site structure. The unique topology of the protein fold and the identification of the active-site components reveal features of predictive value for another enzyme, FabZ, which may be the non-specific dehydratase involved in elongation of fatty acyl chains. A positively charged area surrounding the entrance to the active site, which could interact with the negatively charged ACP, was also found.

-	~~{{STRUCTURE_1mka\| PDB=1mka \| SCENE= }}~~	+	Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site.,Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL Structure. 1996 Mar 15;4(3):253-64. PMID:8805534<ref>PMID:8805534</ref>

-	~~===E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR~~, ~~3-DECYNOYL-N-ACETYL CYSTEAMINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_8805534}}~~	+	==See Also==
-		+	*[[Beta-hydroxyacyl-acyl carrier protein dehydratase\|Beta-hydroxyacyl-acyl carrier protein dehydratase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1mka~~]] 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=1MKA OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:008805534<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Leesong, M.]]		[[Category: Leesong, M.]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]

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

OCA — Wed, 05 Dec 2012 21:27:46 GMT

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

←Older revision

Revision as of 21:27, 5 December 2012

OCA at 21:27, 5 December 2012

OCA — Wed, 05 Dec 2012 21:27:43 GMT

←Older revision		Revision as of 21:27, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1mka.png\|left\|200px]]		[[Image:1mka.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1mka", 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_1mka\| PDB=1mka \| SCENE= }}		{{STRUCTURE_1mka\| PDB=1mka \| SCENE= }}

	===E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE===		===E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8805534}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8805534 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8805534}}		{{ABSTRACT_PUBMED_8805534}}

	==About this Structure==		==About this Structure==
-	~~1MKA~~ 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=1MKA OCA].	+	[[1mka]] 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=1MKA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8805534~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008805534</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Leesong, M.]]		[[Category: Leesong, M.]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:08:27 2009''

OCA at 22:08, 16 February 2009

OCA — Mon, 16 Feb 2009 22:08:28 GMT

←Older revision		Revision as of 22:08, 16 February 2009
Line 20:		Line 20:

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

	==Reference==		==Reference==
-	Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site., Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL, Structure. 1996 Mar 15;4(3):253-64. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8805534 8805534]~~	+	<ref group="xtra">PMID:8805534</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Leesong, M.]]		[[Category: Leesong, M.]]
	[[Category: Fatty acid biosynthesis]]		[[Category: Fatty acid biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3~~ 00:10:~~13 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:08:27 2009''