3i3a - Revision history

OCA at 10:03, 21 February 2024

OCA — Wed, 21 Feb 2024 10:03:06 GMT

←Older revision		Revision as of 10:03, 21 February 2024
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	<StructureSection load='3i3a' size='340' side='right'caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='3i3a' size='340' side='right'caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I3A FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=S2N:S~~-~~[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3~~,~~3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.12Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3hsq\|3hsq]], [[3i3x\|3i3x]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S2N:S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>LA3949, LA_3949, lpxA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~173~~ "~~Leptospira icteroides~~" ~~Noguchi 1919])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acyl~~-[~~acyl~~-~~carrier~~-~~protein]~~--~~UDP~~-~~N-acetylglucosamine_O-acyltransferase Acyl~~-[~~acyl~~-~~carrier-protein~~]--~~UDP~~-N-~~acetylglucosamine O-acyltransferase~~]~~, with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.~~3~~.1.129 2.3.1.129]~~ </~~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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [https://pdbe.org/3i3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [https://www.ebi.ac.uk/pdbsum/3i3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i3a 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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [https://pdbe.org/3i3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [https://www.ebi.ac.uk/pdbsum/3i3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i3a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q8EZA6_LEPIN Q8EZA6_LEPIN]] Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[SAAS:SAAS00064151]	+	[https://www.uniprot.org/uniprot/Q8EZA6_LEPIN Q8EZA6_LEPIN] Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[SAAS:SAAS00064151]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i3a 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=3i3a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The first step of lipid A biosynthesis is catalyzed by LpxA in Escherichia coli (EcLpxA), an acyltransferase selective for UDP-GlcNAc and R-3-hydroxymyristoyl-acyl carrier protein (ACP). Leptospira interrogans LpxA (LiLpxA) is extremely selective for R-3-hydroxylauroyl-ACP and an analogue of UDP-GlcNAc, designated UDP-GlcNAc3N, in which NH(2) replaces the GlcNAc 3-OH group. EcLpxA does not discriminate between UDP-GlcNAc and UDP-GlcNAc3N; however, E. coli does not make UDP-GlcNAc3N. With LiLpxA, R-3-hydroxylauroyl-methylphosphopantetheine efficiently substitutes for R-3-hydroxylauroyl-ACP. We now present crystal structures of free LiLpxA and its complexes with its product UDP-3-N-(R-3-hydroxylauroyl)-GlcNAc3N and with its substrate R-3-hydroxylauroyl-methylphosphopantetheine. The positions of the acyl chains of the R-3-hydroxylauroyl-methylphosphopantetheine and the UDP-3-N-(R-3-hydroxylauroyl)-GlcNAc3N are almost identical and are similar to that of the acyl chain in the EcLpxA/UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc complex. The selectivity of LiLpxA for UDP-GlcNAc3N may be explained by the orientation of the backbone carbonyl group of Q68, which differs by approximately 82 degrees from the corresponding Q73 carbonyl group in EcLpxA. This arrangement provides an extra hydrogen-bond acceptor for the 3-NH(2) group of UDP-GlcNAc3N in LiLpxA. The R-3-hydroxylauroyl selectivity of LiLpxA is explained by the position of the K171 side chain, which limits the length of the acyl-chain-binding groove. Our results support the role of LiLpxA H120 (which corresponds to EcLpxA H125) as the catalytic base and provide the first structural information about the orientation of the phosphopantetheine moiety during LpxA catalysis.
-
-	Structural basis for the sugar nucleotide and acyl-chain selectivity of Leptospira interrogans LpxA.,Robins LI, Williams AH, Raetz CR Biochemistry. 2009 Jul 7;48(26):6191-201. PMID:19456129<ref>PMID:19456129</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3i3a" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[UDP-N-acetylglucosamine acyltransferase\|UDP-N-acetylglucosamine acyltransferase]]		*[[UDP-N-acetylglucosamine acyltransferase\|UDP-N-acetylglucosamine acyltransferase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Leptospira icteroides noguchi 1919]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Williams, A H]]~~	+	[[Category: Leptospira interrogans]]
-	~~[[Category: Acyltransferase]]~~	+	[[Category: Williams AH]]
-	~~[[Category: Leptospira interrogan]]~~	+
-	[[Category: Leptospira interrogans ~~complex~~]]	+
-	[[Category: ~~Lipid a biosynthesis]]~~	+
-	~~[[Category: Lipid synthesis]]~~	+
-	~~[[Category: Lpxa]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:21, 6 April 2022

OCA — Wed, 06 Apr 2022 11:21:17 GMT

←Older revision		Revision as of 11:21, 6 April 2022
Line 1:		Line 1:

	==Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA==		==Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA==
-	<StructureSection load='3i3a' size='340' side='right' caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>	+	<StructureSection load='3i3a' size='340' side='right'caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I3A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2N:S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S2N:S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hsq\|3hsq]], [[3i3x\|3i3x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hsq\|3hsq]], [[3i3x\|3i3x]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA3949, LA_3949, lpxA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 "Leptospira icteroides" Noguchi 1919])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA3949, LA_3949, lpxA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 "Leptospira icteroides" Noguchi 1919])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine_O-acyltransferase Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.129 2.3.1.129] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine_O-acyltransferase Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.129 2.3.1.129] </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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [~~http~~://pdbe.org/3i3a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i3a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i3a 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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [https://pdbe.org/3i3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [https://www.ebi.ac.uk/pdbsum/3i3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i3a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/Q8EZA6_LEPIN Q8EZA6_LEPIN]] Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[SAAS:SAAS00064151]	+	[[https://www.uniprot.org/uniprot/Q8EZA6_LEPIN Q8EZA6_LEPIN]] Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[SAAS:SAAS00064151]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Leptospira icteroides noguchi 1919]]		[[Category: Leptospira icteroides noguchi 1919]]
		+	[[Category: Large Structures]]
	[[Category: Williams, A H]]		[[Category: Williams, A H]]
	[[Category: Acyltransferase]]		[[Category: Acyltransferase]]

OCA at 09:24, 19 December 2018

OCA — Wed, 19 Dec 2018 09:24:35 GMT

←Older revision		Revision as of 09:24, 19 December 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/3i3a_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/3i3a_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3i3a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3i3a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[UDP-N-acetylglucosamine acyltransferase\|UDP-N-acetylglucosamine acyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:49, 5 August 2016

OCA — Fri, 05 Aug 2016 15:49:40 GMT

←Older revision		Revision as of 15:49, 5 August 2016
Line 1:		Line 1:
		+
	==Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA==		==Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA==
	<StructureSection load='3i3a' size='340' side='right' caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='3i3a' size='340' side='right' caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Leptospira_interrogans Leptospira interrogans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I3A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"leptospira_icteroides"_noguchi_1919 "leptospira icteroides" noguchi 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I3A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2N:S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2N:S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hsq\|3hsq]], [[3i3x\|3i3x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hsq\|3hsq]], [[3i3x\|3i3x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA3949, LA_3949, lpxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira ~~interrogans~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA3949, LA_3949, lpxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 "Leptospira icteroides" Noguchi 1919])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine_O-acyltransferase Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.129 2.3.1.129] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine_O-acyltransferase Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.129 2.3.1.129] </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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [http://www.ebi.ac.uk/pdbsum/3i3a 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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [http://pdbe.org/3i3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [http://www.ebi.ac.uk/pdbsum/3i3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i3a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3i3a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3i3a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Leptospira ~~interrogans~~]]	+	[[Category: Leptospira icteroides noguchi 1919]]
	[[Category: Williams, A H]]		[[Category: Williams, A H]]
	[[Category: Acyltransferase]]		[[Category: Acyltransferase]]

OCA at 20:02, 25 December 2014

OCA — Thu, 25 Dec 2014 20:02:12 GMT

←Older revision		Revision as of 20:02, 25 December 2014
Line 9:		Line 9:
	<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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [http://www.ebi.ac.uk/pdbsum/3i3a 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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [http://www.ebi.ac.uk/pdbsum/3i3a PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q8EZA6_LEPIN Q8EZA6_LEPIN]] Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[SAAS:SAAS00064151]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:14, 18 December 2014

OCA — Thu, 18 Dec 2014 06:14:38 GMT

←Older revision		Revision as of 06:14, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3i3a\| PDB=3i3a \| SCENE= }}~~	+	==Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA==
-	===Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA===	+	<StructureSection load='3i3a' size='340' side='right' caption='[[3i3a]], [[Resolution\|resolution]] 2.12Å' scene=''>
-	{{~~ABSTRACT_PUBMED_19456129~~}}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i3a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I3A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2N:S-[2-({N-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(METHOXY)PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANYL}AMINO)ETHYL]+(3R)-3-HYDROXYDODECANETHIOATE'>S2N</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hsq\|3hsq]], [[3i3x\|3i3x]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LA3949, LA_3949, lpxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=173 Leptospira interrogans])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine_O-acyltransferase Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.129 2.3.1.129] </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=3i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i3a RCSB], [http://www.ebi.ac.uk/pdbsum/3i3a 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/i3/3i3a_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 first step of lipid A biosynthesis is catalyzed by LpxA in Escherichia coli (EcLpxA), an acyltransferase selective for UDP-GlcNAc and R-3-hydroxymyristoyl-acyl carrier protein (ACP). Leptospira interrogans LpxA (LiLpxA) is extremely selective for R-3-hydroxylauroyl-ACP and an analogue of UDP-GlcNAc, designated UDP-GlcNAc3N, in which NH(2) replaces the GlcNAc 3-OH group. EcLpxA does not discriminate between UDP-GlcNAc and UDP-GlcNAc3N; however, E. coli does not make UDP-GlcNAc3N. With LiLpxA, R-3-hydroxylauroyl-methylphosphopantetheine efficiently substitutes for R-3-hydroxylauroyl-ACP. We now present crystal structures of free LiLpxA and its complexes with its product UDP-3-N-(R-3-hydroxylauroyl)-GlcNAc3N and with its substrate R-3-hydroxylauroyl-methylphosphopantetheine. The positions of the acyl chains of the R-3-hydroxylauroyl-methylphosphopantetheine and the UDP-3-N-(R-3-hydroxylauroyl)-GlcNAc3N are almost identical and are similar to that of the acyl chain in the EcLpxA/UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc complex. The selectivity of LiLpxA for UDP-GlcNAc3N may be explained by the orientation of the backbone carbonyl group of Q68, which differs by approximately 82 degrees from the corresponding Q73 carbonyl group in EcLpxA. This arrangement provides an extra hydrogen-bond acceptor for the 3-NH(2) group of UDP-GlcNAc3N in LiLpxA. The R-3-hydroxylauroyl selectivity of LiLpxA is explained by the position of the K171 side chain, which limits the length of the acyl-chain-binding groove. Our results support the role of LiLpxA H120 (which corresponds to EcLpxA H125) as the catalytic base and provide the first structural information about the orientation of the phosphopantetheine moiety during LpxA catalysis.

-	~~==About this Structure==~~	+	Structural basis for the sugar nucleotide and acyl-chain selectivity of Leptospira interrogans LpxA.,Robins LI, Williams AH, Raetz CR Biochemistry. 2009 Jul 7;48(26):6191-201. PMID:19456129<ref>PMID:19456129</ref>
-	~~[[3i3a]] is a 3~~ chain ~~structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans~~ Leptospira interrogans]. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann.ac.il~~/~~oca-bin/ocashort?id=3I3A OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra">PMID:019456129<~~/~~ref~~><~~references group="xtra"~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Leptospira interrogans]]		[[Category: Leptospira interrogans]]
-	[[Category: Williams, A H.]]	+	[[Category: Williams, A H]]
	[[Category: Acyltransferase]]		[[Category: Acyltransferase]]
	[[Category: Leptospira interrogan]]		[[Category: Leptospira interrogan]]

OCA: Protected "3i3a" [edit=sysop:move=sysop]

OCA — Wed, 13 Mar 2013 10:50:21 GMT

Protected "3i3a" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:50, 13 March 2013

OCA at 10:50, 13 March 2013

OCA — Wed, 13 Mar 2013 10:50:18 GMT

←Older revision		Revision as of 10:50, 13 March 2013
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-	{{Seed}}
-	[[Image:3i3a.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i3a", 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_3i3a\| PDB=3i3a \| SCENE= }}		{{STRUCTURE_3i3a\| PDB=3i3a \| SCENE= }}
-
	===Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA===		===Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19456129}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19456129 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19456129}}		{{ABSTRACT_PUBMED_19456129}}

	==About this Structure==		==About this Structure==
-	~~3I3A~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA].	+	[[3i3a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19456129~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019456129</ref><references group="xtra"/>
	[[Category: Leptospira interrogans]]		[[Category: Leptospira interrogans]]
	[[Category: Williams, A H.]]		[[Category: Williams, A H.]]
Line 33:		Line 17:
	[[Category: Lpxa]]		[[Category: Lpxa]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 15:58:03 2009''

OCA at 12:58, 3 September 2009

OCA — Thu, 03 Sep 2009 12:58:05 GMT

←Older revision		Revision as of 12:58, 3 September 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3i3a.jpg\|left\|200px]]

-	The ~~entry 3i3a~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3i3a", 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_3i3a\| PDB=3i3a \| SCENE= }}

-	~~Authors: Williams, A.H.~~	+	===Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA===

-	Description: Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug~~ ~~5 09~~:47:07 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19456129}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19456129 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19456129}}
		+
		+	==About this Structure==
		+	3I3A is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Leptospira_interrogans Leptospira interrogans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3A OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19456129</ref><references group="xtra"/>
		+	[[Category: Leptospira interrogans]]
		+	[[Category: Williams, A H.]]
		+	[[Category: Acyltransferase]]
		+	[[Category: Leptospira interrogan]]
		+	[[Category: Leptospira interrogans complex]]
		+	[[Category: Lipid a biosynthesis]]
		+	[[Category: Lipid synthesis]]
		+	[[Category: Lpxa]]
		+	[[Category: Transferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 15:58:03 2009''

OCA at 06:47, 5 August 2009

OCA — Wed, 05 Aug 2009 06:47:07 GMT

←Older revision		Revision as of 06:47, 5 August 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3i3a is ON HOLD	+	The entry 3i3a is ON HOLD until Paper Publication

	Authors: Williams, A.H.		Authors: Williams, A.H.
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	Description: Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA		Description: Structural Basis for the Sugar Nucleotide and Acyl Chain Selectivity of Leptospira interrogans LpxA

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 15 08~~:29:29 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 5 09:47:07 2009''