2k2q - Revision history

OCA at 06:43, 1 May 2024

2024-05-01T06:43:51Z

←Older revision		Revision as of 06:43, 1 May 2024
Line 1:		Line 1:

	==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==		==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==
-	<StructureSection load='2k2q' size='340' side='right'caption='[[2k2q~~]], [[NMR_Ensembles_of_Models \| 18 NMR models~~]]' scene=''>	+	<StructureSection load='2k2q' size='340' side='right'caption='[[2k2q]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2ron\|2ron]], [[2gdx\|2gdx]]</div></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [https://pdbe.org/2k2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [https://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q 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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [https://pdbe.org/2k2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [https://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA]] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product~~. [[https://www.uniprot.org/uniprot/SRFAD_BACSU SRFAD_BACSU]] Probable thioesterase involved in the biosynthesis of surfactin~~.	+	[https://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		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=2k2q 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=2k2q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) found in bacteria, fungi and plants use two different types of thioesterases for the production of highly active biological compounds. Type I thioesterases (TEI) catalyse the release step from the assembly line of the final product where it is transported from one reaction centre to the next as a thioester linked to a 4'-phosphopantetheine (4'-PP) cofactor that is covalently attached to thiolation (T) domains. The second enzyme involved in the synthesis of these secondary metabolites, the type II thioesterase (TEII), is a crucial repair enzyme for the regeneration of functional 4'-PP cofactors of holo-T domains of NRPS and PKS systems. Mispriming of 4'-PP cofactors by acetyl- and short-chain acyl-residues interrupts the biosynthetic system. This repair reaction is very important, because roughly 80% of CoA, the precursor of the 4'-PP cofactor, is acetylated in bacteria. Here we report the three-dimensional structure of a type II thioesterase from Bacillus subtilis free and in complex with a T domain. Comparison with structures of TEI enzymes shows the basis for substrate selectivity and the different modes of interaction of TEII and TEI enzymes with T domains. Furthermore, we show that the TEII enzyme exists in several conformations of which only one is selected on interaction with its native substrate, a modified holo-T domain.
-
-	Structural basis for the selectivity of the external thioesterase of the surfactin synthetase.,Koglin A, Lohr F, Bernhard F, Rogov VV, Frueh DP, Strieter ER, Mofid MR, Guntert P, Wagner G, Walsh CT, Marahiel MA, Dotsch V Nature. 2008 Aug 14;454(7206):907-11. PMID:18704089<ref>PMID:18704089</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2k2q" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
Line 36:		Line 24:
	[[Category: Brevibacillus parabrevis]]		[[Category: Brevibacillus parabrevis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernhard, F]]	+	[[Category: Bernhard F]]
-	[[Category: Dotsch, V]]	+	[[Category: Dotsch V]]
-	[[Category: Frueh~~, D P~~]]	+	[[Category: Frueh DP]]
-	[[Category: Guntert, P]]	+	[[Category: Guntert P]]
-	[[Category: Koglin, A]]	+	[[Category: Koglin A]]
-	[[Category: Lohr, F]]	+	[[Category: Lohr F]]
-	[[Category: Marahiel~~, M A~~]]	+	[[Category: Marahiel MA]]
-	[[Category: Mofid~~, M R~~]]	+	[[Category: Mofid MR]]
-	[[Category: Rogov~~, V V~~]]	+	[[Category: Rogov VV]]
-	[[Category: Strieter~~, E R~~]]	+	[[Category: Strieter ER]]
-	[[Category: Wagner, G]]	+	[[Category: Wagner G]]
-	[[Category: Walsh~~, C T]]~~	+	[[Category: Walsh CT]]
-	~~[[Category: A/b-hydrolase]]~~	+
-	~~[[Category: Antibiotic biosynthesis]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Ligase-hydrolase complex]]~~	+
-	~~[[Category: Multifunctional enzyme]]~~	+
-	~~[[Category: Non-ribosomal peptide synthetase]]~~	+
-	~~[[Category: Nrp]]~~	+
-	~~[[Category: Phosphopantetheine]]~~	+
-	~~[[Category: Sporulation]]~~	+
-	~~[[Category: Stress response]]~~	+
-	~~[[Category: Thioesterase]]~~	+
-	~~[[Category: Type ii thioesterase~~]]	+

OCA at 08:06, 7 April 2021

2021-04-07T08:06:52Z

←Older revision		Revision as of 08:06, 7 April 2021
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==		==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==
-	<StructureSection load='2k2q' size='340' side='right' caption='[[2k2q]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>	+	<StructureSection load='2k2q' size='340' side='right'caption='[[2k2q]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [~~http~~://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ron\|2ron]], [[2gdx\|2gdx]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [~~http~~://pdbe.org/2k2q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q 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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [https://pdbe.org/2k2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [https://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA]] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product. [[~~http~~://www.uniprot.org/uniprot/SRFAD_BACSU SRFAD_BACSU]] Probable thioesterase involved in the biosynthesis of surfactin.	+	[[https://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA]] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product. [[https://www.uniprot.org/uniprot/SRFAD_BACSU SRFAD_BACSU]] Probable thioesterase involved in the biosynthesis of surfactin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 35:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Brevibacillus parabrevis]]		[[Category: Brevibacillus parabrevis]]
		+	[[Category: Large Structures]]
	[[Category: Bernhard, F]]		[[Category: Bernhard, F]]
	[[Category: Dotsch, V]]		[[Category: Dotsch, V]]

OCA at 18:55, 24 January 2018

2018-01-24T18:55:07Z

←Older revision		Revision as of 18:55, 24 January 2018
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://pdbe.org/2k2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q ProSAT]</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://pdbe.org/2k2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q ProSAT]</span></td></tr>
	</table>		</table>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k2/2k2q_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k2/2k2q_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 44:		Line 44:
	[[Category: Marahiel, M A]]		[[Category: Marahiel, M A]]
	[[Category: Mofid, M R]]		[[Category: Mofid, M R]]
		+	[[Category: Rogov, V V]]
	[[Category: Strieter, E R]]		[[Category: Strieter, E R]]
-	[[Category: V V., Rogov]]
	[[Category: Wagner, G]]		[[Category: Wagner, G]]
	[[Category: Walsh, C T]]		[[Category: Walsh, C T]]

OCA at 09:39, 19 October 2016

2016-10-19T09:39:17Z

←Older revision		Revision as of 09:39, 19 October 2016
Line 1:		Line 1:
		+	{{Large structure}}
	==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==		==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==
	<StructureSection load='2k2q' size='340' side='right' caption='[[2k2q]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>		<StructureSection load='2k2q' size='340' side='right' caption='[[2k2q]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~54914~~ Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1423~~ Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://pdbe.org/2k2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q 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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://pdbe.org/2k2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2q ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
Line 18:		Line 19:
	<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=2k2q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 43:		Line 44:
	[[Category: Marahiel, M A]]		[[Category: Marahiel, M A]]
	[[Category: Mofid, M R]]		[[Category: Mofid, M R]]
-	[[Category: Rogov, V R]]
	[[Category: Strieter, E R]]		[[Category: Strieter, E R]]
		+	[[Category: V V., Rogov]]
	[[Category: Wagner, G]]		[[Category: Wagner, G]]
	[[Category: Walsh, C T]]		[[Category: Walsh, C T]]

OCA at 14:23, 11 September 2015

2015-09-11T14:23:28Z

←Older revision		Revision as of 14:23, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q 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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://pdbe.org/2k2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q PDBsum]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA]] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product. [[http://www.uniprot.org/uniprot/SRFAD_BACSU SRFAD_BACSU]] Probable thioesterase involved in the biosynthesis of surfactin.		[[http://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA]] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product. [[http://www.uniprot.org/uniprot/SRFAD_BACSU SRFAD_BACSU]] Probable thioesterase involved in the biosynthesis of surfactin.
Line 27:		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 2k2q" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:39, 25 December 2014

2014-12-25T17:39:53Z

←Older revision		Revision as of 17:39, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q 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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYCC_BREPA TYCC_BREPA]] Incorporates six amino acids (for tyrocidine A, Asn, Gln, Tyr, Val, Orn, and Leu) in their L-configuration into the peptide product. [[http://www.uniprot.org/uniprot/SRFAD_BACSU SRFAD_BACSU]] Probable thioesterase involved in the biosynthesis of surfactin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Brevibacillus parabrevis]]		[[Category: Brevibacillus parabrevis]]
-	[[Category: Bernhard, F.]]	+	[[Category: Bernhard, F]]
-	[[Category: Dotsch, V.]]	+	[[Category: Dotsch, V]]
-	[[Category: Frueh, D P.]]	+	[[Category: Frueh, D P]]
-	[[Category: Guntert, P.]]	+	[[Category: Guntert, P]]
-	[[Category: Koglin, A.]]	+	[[Category: Koglin, A]]
-	[[Category: Lohr, F.]]	+	[[Category: Lohr, F]]
-	[[Category: Marahiel, M A.]]	+	[[Category: Marahiel, M A]]
-	[[Category: Mofid, M R.]]	+	[[Category: Mofid, M R]]
-	[[Category: Rogov, V R.]]	+	[[Category: Rogov, V R]]
-	[[Category: Strieter, E R.]]	+	[[Category: Strieter, E R]]
-	[[Category: Wagner, G.]]	+	[[Category: Wagner, G]]
-	[[Category: Walsh, C T.]]	+	[[Category: Walsh, C T]]
	[[Category: A/b-hydrolase]]		[[Category: A/b-hydrolase]]
	[[Category: Antibiotic biosynthesis]]		[[Category: Antibiotic biosynthesis]]

OCA at 08:32, 30 September 2014

2014-09-30T08:32:51Z

←Older revision		Revision as of 08:32, 30 September 2014
Line 1:		Line 1:
-	~~{{Large structure}}~~	+	==complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain==
-	~~{{STRUCTURE_2k2q\| PDB=2k2q \| SCENE= }}~~	+	<StructureSection load='2k2q' size='340' side='right' caption='[[2k2q]], [[NMR_Ensembles_of_Models \| 18 NMR models]]' scene=''>
-	===complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain===	+	== Structural highlights ==
-	~~{{ABSTRACT_PUBMED_18704089}}~~	+	<table><tr><td colspan='2'>[[2k2q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [http://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K2Q FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ron\|2ron]], [[2gdx\|2gdx]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 Brevibacillus parabrevis]), srfAD, srfA4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=2k2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k2q RCSB], [http://www.ebi.ac.uk/pdbsum/2k2q 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/k2/2k2q_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 ==
		+	Non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) found in bacteria, fungi and plants use two different types of thioesterases for the production of highly active biological compounds. Type I thioesterases (TEI) catalyse the release step from the assembly line of the final product where it is transported from one reaction centre to the next as a thioester linked to a 4'-phosphopantetheine (4'-PP) cofactor that is covalently attached to thiolation (T) domains. The second enzyme involved in the synthesis of these secondary metabolites, the type II thioesterase (TEII), is a crucial repair enzyme for the regeneration of functional 4'-PP cofactors of holo-T domains of NRPS and PKS systems. Mispriming of 4'-PP cofactors by acetyl- and short-chain acyl-residues interrupts the biosynthetic system. This repair reaction is very important, because roughly 80% of CoA, the precursor of the 4'-PP cofactor, is acetylated in bacteria. Here we report the three-dimensional structure of a type II thioesterase from Bacillus subtilis free and in complex with a T domain. Comparison with structures of TEI enzymes shows the basis for substrate selectivity and the different modes of interaction of TEII and TEI enzymes with T domains. Furthermore, we show that the TEII enzyme exists in several conformations of which only one is selected on interaction with its native substrate, a modified holo-T domain.

-	~~==About this Structure==~~	+	Structural basis for the selectivity of the external thioesterase of the surfactin synthetase.,Koglin A, Lohr F, Bernhard F, Rogov VV, Frueh DP, Strieter ER, Mofid MR, Guntert P, Wagner G, Walsh CT, Marahiel MA, Dotsch V Nature. 2008 Aug 14;454(7206):907-11. PMID:18704089<ref>PMID:18704089</ref>
-	~~[[2k2q]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis] and [http~~:~~//en~~.~~wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full experimental information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2K2Q OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra">PMID:018704089<~~/~~ref~~><~~references group="xtra"~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Brevibacillus parabrevis]]		[[Category: Brevibacillus parabrevis]]

OCA at 07:49, 11 March 2013

2013-03-11T07:49:04Z

←Older revision		Revision as of 07:49, 11 March 2013
Line 1:		Line 1:
-	~~[[Image:2k2q.png\|left\|200px]]~~	+	{{Large structure}}
-		+
-	~~<!--~~	+
-	~~The line below this paragraph, containing "STRUCTURE_2k2q", 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_2k2q\| PDB=2k2q \| SCENE= }}		{{STRUCTURE_2k2q\| PDB=2k2q \| SCENE= }}
-
	===complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain===		===complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18704089}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18704089 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18704089}}		{{ABSTRACT_PUBMED_18704089}}

OCA: Protected "2k2q" [edit=sysop:move=sysop]

2012-06-10T15:49:43Z

Protected "2k2q" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:49, 10 June 2012