1kez - Revision history

OCA at 07:46, 7 February 2024

OCA — Wed, 07 Feb 2024 07:46:17 GMT

←Older revision		Revision as of 07:46, 7 February 2024
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	<StructureSection load='1kez' size='340' side='right'caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1kez' size='340' side='right'caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
-	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>~~[https://en.wikipedia.org/wiki/6~~-~~deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.~~3.1.94 2.3.1.94] </span>~~</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]] 2.8Å</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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [https://pdbe.org/1kez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [https://www.ebi.ac.uk/pdbsum/1kez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kez 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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [https://pdbe.org/1kez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [https://www.ebi.ac.uk/pdbsum/1kez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kez ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ERYA3_SACER ERYA3_SACER]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 19:
	</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=1kez 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=1kez ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	As the first structural elucidation of a modular polyketide synthase (PKS) domain, the crystal structure of the macrocycle-forming thioesterase (TE) domain from the 6-deoxyerythronolide B synthase (DEBS) was solved by a combination of multiple isomorphous replacement and multiwavelength anomalous dispersion and refined to an R factor of 24.1% to 2.8-A resolution. Its overall tertiary architecture belongs to the alpha/beta-hydrolase family, with two unusual features unprecedented in this family: a hydrophobic leucine-rich dimer interface and a substrate channel that passes through the entire protein. The active site triad, comprised of Asp-169, His-259, and Ser-142, is located in the middle of the substrate channel, suggesting the passage of the substrate through the protein. Modeling indicates that the active site can accommodate and orient the 6-deoxyerythronolide B precursor uniquely, while at the same time shielding the active site from external water and catalyzing cyclization by macrolactone formation. The geometry and organization of functional groups explain the observed substrate specificity of this TE and offer strategies for engineering macrocycle biosynthesis. Docking of a homology model of the upstream acyl carrier protein (ACP6) against the TE suggests that the 2-fold axis of the TE dimer may also be the axis of symmetry that determines the arrangement of domains in the entire DEBS. Sequence conservation suggests that all TEs from modular polyketide synthases have a similar fold, dimer 2-fold axis, and substrate channel geometry.
-
-	Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel.,Tsai SC, Miercke LJ, Krucinski J, Gokhale R, Chen JC, Foster PG, Cane DE, Khosla C, Stroud RM Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14808-13. PMID:11752428<ref>PMID:11752428</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kez" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[6-deoxyerythronolide B synthase 3D structures\|6-deoxyerythronolide B synthase 3D structures]]		*[[6-deoxyerythronolide B synthase 3D structures\|6-deoxyerythronolide B synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 6-deoxyerythronolide-B synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cane~~, D E~~]]	+	[[Category: Saccharopolyspora erythraea]]
-	[[Category: Chen~~, J C.~~H]]	+	[[Category: Cane DE]]
-	[[Category: Foster~~, P G~~]]	+	[[Category: Chen JC-H]]
-	[[Category: Gokhale, R]]	+	[[Category: Foster PG]]
-	[[Category: Khosla, C]]	+	[[Category: Gokhale R]]
-	[[Category: Krucinski, J]]	+	[[Category: Khosla C]]
-	[[Category: Miercke~~, L J.W~~]]	+	[[Category: Krucinski J]]
-	[[Category: Stroud~~, R M~~]]	+	[[Category: Miercke LJW]]
-	[[Category: Tsai, S C]]	+	[[Category: Stroud RM]]
-	~~[[Category: 6-deb]]~~	+	[[Category: Tsai S-C]]
-	~~[[Category: 6-deoxyerythronolide synthase]]~~	+
-	~~[[Category: Alpha]]~~	+
-	~~[[Category: Beta-hydrolase]]~~	+
-	~~[[Category: Deb]]~~	+
-	~~[[Category: Macrocycle]]~~	+
-	~~[[Category: Modular polyketide synthase]]~~	+
-	~~[[Category: Polyketide synthase]]~~	+
-	~~[[Category: Te]]~~	+
-	~~[[Category: Thioesterase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:50, 28 April 2021

OCA — Wed, 28 Apr 2021 05:50:46 GMT

←Older revision		Revision as of 05:50, 28 April 2021
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	<StructureSection load='1kez' size='340' side='right'caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1kez' size='340' side='right'caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [~~http~~://pdbe.org/1kez PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kez PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kez 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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [https://pdbe.org/1kez PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [https://www.ebi.ac.uk/pdbsum/1kez PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kez ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 06:48, 24 July 2019

OCA — Wed, 24 Jul 2019 06:48:25 GMT

←Older revision		Revision as of 06:48, 24 July 2019
Line 1:		Line 1:

	==Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)==		==Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)==
-	<StructureSection load='1kez' size='340' side='right' caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1kez' size='340' side='right'caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
Line 26:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1kez" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kez" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[6-deoxyerythronolide B synthase 3D structures\|6-deoxyerythronolide B synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: 6-deoxyerythronolide-B synthase]]		[[Category: 6-deoxyerythronolide-B synthase]]
		+	[[Category: Large Structures]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]
	[[Category: Chen, J C.H]]		[[Category: Chen, J C.H]]

OCA at 21:28, 24 January 2018

OCA — Wed, 24 Jan 2018 21:28:42 GMT

←Older revision		Revision as of 21:28, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)==		==Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)==
	<StructureSection load='1kez' size='340' side='right' caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1kez' size='340' side='right' caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://pdbe.org/1kez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez 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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://pdbe.org/1kez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kez ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ke/1kez_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ke/1kez_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 13:02, 7 February 2016

OCA — Sun, 07 Feb 2016 13:02:28 GMT

←Older revision		Revision as of 13:02, 7 February 2016
Line 14:		Line 14:
	<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=1kez ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:42, 10 September 2015

OCA — Thu, 10 Sep 2015 01:42:40 GMT

←Older revision		Revision as of 01:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kez' size='340' side='right' caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1kez' size='340' side='right' caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharopolyspora_erythraea Saccharopolyspora erythraea~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_erythreus"_(sic)_waksman_1923 "actinomyces erythreus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez 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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://pdbe.org/1kez PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1kez" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: 6-deoxyerythronolide-B synthase]]		[[Category: 6-deoxyerythronolide-B synthase]]
-	[[Category: Saccharopolyspora erythraea]]
	[[Category: Cane, D E]]		[[Category: Cane, D E]]
	[[Category: Chen, J C.H]]		[[Category: Chen, J C.H]]

OCA at 16:39, 5 January 2015

OCA — Mon, 05 Jan 2015 16:39:49 GMT

←Older revision		Revision as of 16:39, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez 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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	[[Category: 6-deoxyerythronolide-B synthase]]		[[Category: 6-deoxyerythronolide-B synthase]]
	[[Category: Saccharopolyspora erythraea]]		[[Category: Saccharopolyspora erythraea]]
-	[[Category: Cane, D E.]]	+	[[Category: Cane, D E]]
-	[[Category: Chen, J C.H.]]	+	[[Category: Chen, J C.H]]
-	[[Category: Foster, P G.]]	+	[[Category: Foster, P G]]
-	[[Category: Gokhale, R.]]	+	[[Category: Gokhale, R]]
-	[[Category: Khosla, C.]]	+	[[Category: Khosla, C]]
-	[[Category: Krucinski, J.]]	+	[[Category: Krucinski, J]]
-	[[Category: Miercke, L J.W.]]	+	[[Category: Miercke, L J.W]]
-	[[Category: Stroud, R M.]]	+	[[Category: Stroud, R M]]
-	[[Category: Tsai, S C.]]	+	[[Category: Tsai, S C]]
	[[Category: 6-deb]]		[[Category: 6-deb]]
	[[Category: 6-deoxyerythronolide synthase]]		[[Category: 6-deoxyerythronolide synthase]]

OCA at 12:38, 28 September 2014

OCA — Sun, 28 Sep 2014 12:38:32 GMT

←Older revision		Revision as of 12:38, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1kez.~~png\|left~~\|200px]]	+	==Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)==
		+	<StructureSection load='1kez' size='340' side='right' caption='[[1kez]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KEZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=1kez FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kez OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kez RCSB], [http://www.ebi.ac.uk/pdbsum/1kez 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/ke/1kez_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 ==
		+	As the first structural elucidation of a modular polyketide synthase (PKS) domain, the crystal structure of the macrocycle-forming thioesterase (TE) domain from the 6-deoxyerythronolide B synthase (DEBS) was solved by a combination of multiple isomorphous replacement and multiwavelength anomalous dispersion and refined to an R factor of 24.1% to 2.8-A resolution. Its overall tertiary architecture belongs to the alpha/beta-hydrolase family, with two unusual features unprecedented in this family: a hydrophobic leucine-rich dimer interface and a substrate channel that passes through the entire protein. The active site triad, comprised of Asp-169, His-259, and Ser-142, is located in the middle of the substrate channel, suggesting the passage of the substrate through the protein. Modeling indicates that the active site can accommodate and orient the 6-deoxyerythronolide B precursor uniquely, while at the same time shielding the active site from external water and catalyzing cyclization by macrolactone formation. The geometry and organization of functional groups explain the observed substrate specificity of this TE and offer strategies for engineering macrocycle biosynthesis. Docking of a homology model of the upstream acyl carrier protein (ACP6) against the TE suggests that the 2-fold axis of the TE dimer may also be the axis of symmetry that determines the arrangement of domains in the entire DEBS. Sequence conservation suggests that all TEs from modular polyketide synthases have a similar fold, dimer 2-fold axis, and substrate channel geometry.

-	~~{{STRUCTURE_1kez\| PDB=1kez \| SCENE= }}~~	+	Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel.,Tsai SC, Miercke LJ, Krucinski J, Gokhale R, Chen JC, Foster PG, Cane DE, Khosla C, Stroud RM Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14808-13. PMID:11752428<ref>PMID:11752428</ref>

-	~~===Crystal Structure~~ of the ~~Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11752428}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1kez]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011752428<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 6-deoxyerythronolide-B synthase]]		[[Category: 6-deoxyerythronolide-B synthase]]
	[[Category: Saccharopolyspora erythraea]]		[[Category: Saccharopolyspora erythraea]]

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

OCA — Wed, 05 Dec 2012 20:57:19 GMT

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

←Older revision

Revision as of 20:57, 5 December 2012

OCA at 20:57, 5 December 2012

OCA — Wed, 05 Dec 2012 20:57:16 GMT

←Older revision		Revision as of 20:57, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1kez.png\|left\|200px]]		[[Image:1kez.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kez", 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_1kez\| PDB=1kez \| SCENE= }}		{{STRUCTURE_1kez\| PDB=1kez \| SCENE= }}

	===Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)===		===Crystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11752428}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11752428 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11752428}}		{{ABSTRACT_PUBMED_11752428}}

	==About this Structure==		==About this Structure==
-	~~1KEZ~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA].	+	[[1kez]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharopolyspora_erythraea Saccharopolyspora erythraea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11752428~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011752428</ref><references group="xtra"/>
-	[[Category: ~~Erythronolide~~ synthase]]	+	[[Category: 6-deoxyerythronolide-B synthase]]
	[[Category: Saccharopolyspora erythraea]]		[[Category: Saccharopolyspora erythraea]]
	[[Category: Cane, D E.]]		[[Category: Cane, D E.]]
Line 45:		Line 33:
	[[Category: Te]]		[[Category: Te]]
	[[Category: Thioesterase]]		[[Category: Thioesterase]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 13:58:00 2009''~~	+