1thq - Revision history

OCA at 08:39, 14 February 2024

OCA — Wed, 14 Feb 2024 08:39:47 GMT

←Older revision		Revision as of 08:39, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1thq' size='340' side='right'caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1thq' size='340' side='right'caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1THQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1THQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mm4\|1mm4]], [[1mm5\|1mm5]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRCA, B0622 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [https://pdbe.org/1thq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [https://www.ebi.ac.uk/pdbsum/1thq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1thq 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=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [~~http~~://pdbe.org/1thq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1thq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1thq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PAGP_ECOLI PAGP_ECOLI]] PagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic antimicrobial peptides (CAMPs). It catalyzes the transfer of a palmitate chain (16:0) from the sn-1 position of a glycerophospholipid to the free hydroxyl group of the (R)-3-hydroxymyristate chain at position 2 of lipid A (endotoxin). Modifications of lipid A with a palmitate chain allow to evade host immune defenses by resisting antimicrobial peptides and attenuating the inflammatory response to infection triggered by lipopolysaccharide through the Toll-like receptor 4 (TLR4) signal transduction pathway. Phosphatidylglycerol (PtdGro), phosphatidylethanolamine (PtdEtn), phosphatidylserine (PtdSer) and phosphatidic acid (Ptd-OH) are all effective acyl donors.<ref>PMID:11013210</ref>	+	[https://www.uniprot.org/uniprot/PAGP_ECOLI PAGP_ECOLI] PagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic antimicrobial peptides (CAMPs). It catalyzes the transfer of a palmitate chain (16:0) from the sn-1 position of a glycerophospholipid to the free hydroxyl group of the (R)-3-hydroxymyristate chain at position 2 of lipid A (endotoxin). Modifications of lipid A with a palmitate chain allow to evade host immune defenses by resisting antimicrobial peptides and attenuating the inflammatory response to infection triggered by lipopolysaccharide through the Toll-like receptor 4 (TLR4) signal transduction pathway. Phosphatidylglycerol (PtdGro), phosphatidylethanolamine (PtdEtn), phosphatidylserine (PtdSer) and phosphatidic acid (Ptd-OH) are all effective acyl donors.<ref>PMID:11013210</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=1thq 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=1thq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The ability of enzymes to distinguish between fatty acyl groups can involve molecular measuring devices termed hydrocarbon rulers, but the molecular basis for acyl-chain recognition in any membrane-bound enzyme remains to be defined. PagP is an outer membrane acyltransferase that helps pathogenic bacteria to evade the host immune response by transferring a palmitate chain from a phospholipid to lipid A (endotoxin). PagP can distinguish lipid acyl chains that differ by a single methylene unit, indicating that the enzyme possesses a remarkably precise hydrocarbon ruler. We present the 1.9 A crystal structure of PagP, an eight-stranded beta-barrel with an unexpected interior hydrophobic pocket that is occupied by a single detergent molecule. The buried detergent is oriented normal to the presumed plane of the membrane, whereas the PagP beta-barrel axis is tilted by approximately 25 degrees. Acyl group specificity is modulated by mutation of Gly88 lining the bottom of the hydrophobic pocket, thus confirming the hydrocarbon ruler mechanism for palmitate recognition. A striking structural similarity between PagP and the lipocalins suggests an evolutionary link between these proteins.
-
-	A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin.,Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, Prive GG EMBO J. 2004 Aug 4;23(15):2931-41. Epub 2004 Jul 22. PMID:15272304<ref>PMID:15272304</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1thq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ahn~~, V E~~]]	+	[[Category: Ahn VE]]
-	[[Category: Bishop~~, R E~~]]	+	[[Category: Bishop RE]]
-	[[Category: Chen, L]]	+	[[Category: Chen L]]
-	[[Category: Engel~~, C K~~]]	+	[[Category: Engel CK]]
-	[[Category: Hwang~~, P M~~]]	+	[[Category: Hwang PM]]
-	[[Category: Kay~~, L E~~]]	+	[[Category: Kay LE]]
-	[[Category: Lo~~, E I~~]]	+	[[Category: Lo EI]]
-	[[Category: Prive~~, G G]]~~	+	[[Category: Prive GG]]
-	~~[[Category: Beta-barrel]]~~	+
-	~~[[Category: Outer membrane enzyme]]~~	+
-	~~[[Category: Pagp]]~~	+
-	~~[[Category: Palmitoyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:52, 24 December 2020

OCA — Thu, 24 Dec 2020 11:52:00 GMT

←Older revision		Revision as of 11:52, 24 December 2020
Line 1:		Line 1:

	==Crystal Structure of Outer Membrane Enzyme PagP==		==Crystal Structure of Outer Membrane Enzyme PagP==
-	<StructureSection load='1thq' size='340' side='right' caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1thq' size='340' side='right'caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1THQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1THQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mm4\|1mm4]], [[1mm5\|1mm5]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRCA, B0622 ([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">CRCA, B0622 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://pdbe.org/1thq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1thq 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=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://pdbe.org/1thq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1thq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Ahn, V E]]		[[Category: Ahn, V E]]
	[[Category: Bishop, R E]]		[[Category: Bishop, R E]]

OCA at 08:43, 21 March 2018

OCA — Wed, 21 Mar 2018 08:43:46 GMT

←Older revision		Revision as of 08:43, 21 March 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Outer Membrane Enzyme PagP==		==Crystal Structure of Outer Membrane Enzyme PagP==
	<StructureSection load='1thq' size='340' side='right' caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1thq' size='340' side='right' caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRCA, B0622 ([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">CRCA, B0622 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://pdbe.org/1thq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq 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=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://pdbe.org/1thq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1thq 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/th/1thq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/th/1thq_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 23:35, 8 February 2016

OCA — Mon, 08 Feb 2016 23:35:57 GMT

←Older revision		Revision as of 23:35, 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=1thq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:27, 10 September 2015

OCA — Thu, 10 Sep 2015 16:27:29 GMT

←Older revision		Revision as of 16:27, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1thq' size='340' side='right' caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1thq' size='340' side='right' caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1THQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1THQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRCA, B0622 ([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">CRCA, B0622 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq 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=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://pdbe.org/1thq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~CRCA_ECOLI CRCA_ECOLI~~]] PagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic antimicrobial peptides (CAMPs). It catalyzes the transfer of a palmitate chain (16:0) from the sn-1 position of a glycerophospholipid to the free hydroxyl group of the (R)-3-hydroxymyristate chain at position 2 of lipid A (endotoxin). Modifications of lipid A with a palmitate chain allow to evade host immune defenses by resisting antimicrobial peptides and attenuating the inflammatory response to infection triggered by lipopolysaccharide through the Toll-like receptor 4 (TLR4) signal transduction pathway. Phosphatidylglycerol (PtdGro), phosphatidylethanolamine (PtdEtn), phosphatidylserine (PtdSer) and phosphatidic acid (Ptd-OH) are all effective acyl donors.<ref>PMID:11013210</ref>	+	[[http://www.uniprot.org/uniprot/PAGP_ECOLI PAGP_ECOLI]] PagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic antimicrobial peptides (CAMPs). It catalyzes the transfer of a palmitate chain (16:0) from the sn-1 position of a glycerophospholipid to the free hydroxyl group of the (R)-3-hydroxymyristate chain at position 2 of lipid A (endotoxin). Modifications of lipid A with a palmitate chain allow to evade host immune defenses by resisting antimicrobial peptides and attenuating the inflammatory response to infection triggered by lipopolysaccharide through the Toll-like receptor 4 (TLR4) signal transduction pathway. Phosphatidylglycerol (PtdGro), phosphatidylethanolamine (PtdEtn), phosphatidylserine (PtdSer) and phosphatidic acid (Ptd-OH) are all effective acyl donors.<ref>PMID:11013210</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 1thq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ahn, V E]]		[[Category: Ahn, V E]]
	[[Category: Bishop, R E]]		[[Category: Bishop, R E]]

OCA at 02:55, 25 December 2014

OCA — Thu, 25 Dec 2014 02:55:27 GMT

←Older revision		Revision as of 02:55, 25 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1THQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1THQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRCA, B0622 ([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">CRCA, B0622 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq 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=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CRCA_ECOLI CRCA_ECOLI]] PagP is required both for biosynthesis of hepta-acylated lipid A species containing palmitate and for resistance to cationic antimicrobial peptides (CAMPs). It catalyzes the transfer of a palmitate chain (16:0) from the sn-1 position of a glycerophospholipid to the free hydroxyl group of the (R)-3-hydroxymyristate chain at position 2 of lipid A (endotoxin). Modifications of lipid A with a palmitate chain allow to evade host immune defenses by resisting antimicrobial peptides and attenuating the inflammatory response to infection triggered by lipopolysaccharide through the Toll-like receptor 4 (TLR4) signal transduction pathway. Phosphatidylglycerol (PtdGro), phosphatidylethanolamine (PtdEtn), phosphatidylserine (PtdSer) and phosphatidic acid (Ptd-OH) are all effective acyl donors.<ref>PMID:11013210</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Ahn, V E.]]	+	[[Category: Ahn, V E]]
-	[[Category: Bishop, R E.]]	+	[[Category: Bishop, R E]]
-	[[Category: Chen, L.]]	+	[[Category: Chen, L]]
-	[[Category: Engel, C K.]]	+	[[Category: Engel, C K]]
-	[[Category: Hwang, P M.]]	+	[[Category: Hwang, P M]]
-	[[Category: Kay, L E.]]	+	[[Category: Kay, L E]]
-	[[Category: Lo, E I.]]	+	[[Category: Lo, E I]]
-	[[Category: Prive, G G.]]	+	[[Category: Prive, G G]]
	[[Category: Beta-barrel]]		[[Category: Beta-barrel]]
	[[Category: Outer membrane enzyme]]		[[Category: Outer membrane enzyme]]

OCA at 18:35, 29 September 2014

OCA — Mon, 29 Sep 2014 18:35:21 GMT

←Older revision		Revision as of 18:35, 29 September 2014
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-	[[~~Image:~~1thq.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Outer Membrane Enzyme PagP==
		+	<StructureSection load='1thq' size='340' side='right' caption='[[1thq]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1thq]] is a 1 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=1THQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1THQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mm4\|1mm4]], [[1mm5\|1mm5]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRCA, B0622 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1thq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1thq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1thq RCSB], [http://www.ebi.ac.uk/pdbsum/1thq 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/th/1thq_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 ==
		+	The ability of enzymes to distinguish between fatty acyl groups can involve molecular measuring devices termed hydrocarbon rulers, but the molecular basis for acyl-chain recognition in any membrane-bound enzyme remains to be defined. PagP is an outer membrane acyltransferase that helps pathogenic bacteria to evade the host immune response by transferring a palmitate chain from a phospholipid to lipid A (endotoxin). PagP can distinguish lipid acyl chains that differ by a single methylene unit, indicating that the enzyme possesses a remarkably precise hydrocarbon ruler. We present the 1.9 A crystal structure of PagP, an eight-stranded beta-barrel with an unexpected interior hydrophobic pocket that is occupied by a single detergent molecule. The buried detergent is oriented normal to the presumed plane of the membrane, whereas the PagP beta-barrel axis is tilted by approximately 25 degrees. Acyl group specificity is modulated by mutation of Gly88 lining the bottom of the hydrophobic pocket, thus confirming the hydrocarbon ruler mechanism for palmitate recognition. A striking structural similarity between PagP and the lipocalins suggests an evolutionary link between these proteins.

-	~~{{STRUCTURE_1thq\| PDB=1thq \| SCENE= }}~~	+	A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin.,Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, Prive GG EMBO J. 2004 Aug 4;23(15):2931-41. Epub 2004 Jul 22. PMID:15272304<ref>PMID:15272304</ref>

-	~~===Crystal Structure~~ of ~~Outer Membrane Enzyme PagP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15272304}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1thq]] is a 1 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=1THQ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015272304<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ahn, V E.]]		[[Category: Ahn, V E.]]

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

OCA — Sat, 05 Jan 2013 11:16:07 GMT

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

←Older revision

Revision as of 11:16, 5 January 2013

OCA at 11:16, 5 January 2013

OCA — Sat, 05 Jan 2013 11:16:04 GMT

←Older revision		Revision as of 11:16, 5 January 2013
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-	{{Seed}}
	[[Image:1thq.png\|left\|200px]]		[[Image:1thq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1thq", 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_1thq\| PDB=1thq \| SCENE= }}		{{STRUCTURE_1thq\| PDB=1thq \| SCENE= }}

	===Crystal Structure of Outer Membrane Enzyme PagP===		===Crystal Structure of Outer Membrane Enzyme PagP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15272304}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15272304 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15272304}}		{{ABSTRACT_PUBMED_15272304}}

	==About this Structure==		==About this Structure==
-	~~1THQ~~ is a 1 chain 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=1THQ OCA].	+	[[1thq]] is a 1 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=1THQ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15272304~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015272304</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ahn, V E.]]		[[Category: Ahn, V E.]]
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	[[Category: Pagp]]		[[Category: Pagp]]
	[[Category: Palmitoyltransferase]]		[[Category: Palmitoyltransferase]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 04:26:58 2009''~~	+

OCA at 02:27, 17 February 2009

OCA — Tue, 17 Feb 2009 02:27:00 GMT

←Older revision		Revision as of 02:27, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1THQ 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=1THQ OCA].	+	1THQ is a 1 chain 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=1THQ OCA].

	==Reference==		==Reference==
-	A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin., Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, Prive GG, EMBO J. 2004 Aug 4;23(15):2931-41. Epub 2004 Jul 22. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15272304 15272304]~~	+	<ref group="xtra">PMID:15272304</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Ahn, V E.]]		[[Category: Ahn, V E.]]
	[[Category: Bishop, R E.]]		[[Category: Bishop, R E.]]
Line 39:		Line 38:
	[[Category: Palmitoyltransferase]]		[[Category: Palmitoyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 07~~:53:~~03 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:26:58 2009''