5xsz - Revision history

OCA at 08:13, 22 November 2023

OCA — Wed, 22 Nov 2023 08:13:04 GMT

←Older revision		Revision as of 08:13, 22 November 2023
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	<StructureSection load='5xsz' size='340' side='right'caption='[[5xsz]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='5xsz' size='340' side='right'caption='[[5xsz]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xsz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XSZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xsz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XSZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=OLC:(2R)~~-2,3~~-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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]] 3.2Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.~~2~~.1.17~~ 3~~.2.1.17]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></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=5xsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsz OCA], [~~http~~://pdbe.org/5xsz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xsz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xsz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsz 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=5xsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsz OCA], [https://pdbe.org/5xsz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xsz RCSB], [https://www.ebi.ac.uk/pdbsum/5xsz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q08BG4_DANRE Q08BG4_DANRE] [https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	==See Also==		==See Also==
	*[[Lysophosphatidic acid receptor\|Lysophosphatidic acid receptor]]		*[[Lysophosphatidic acid receptor\|Lysophosphatidic acid receptor]]
		+	*[[Sandbox Reserved 1789\|Sandbox Reserved 1789]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Danio rerio]]
		+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Ishitani R]]
-	[[Category: Ishitani, R]]	+	[[Category: Nishizawa T]]
-	[[Category: Nishizawa, T]]	+	[[Category: Nureki O]]
-	[[Category: Nureki, O]]	+	[[Category: Taniguchi R]]
-	[[Category: Taniguchi, R]]	+
-	~~[[Category: Alpha helical]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 06:58, 14 October 2020

OCA — Wed, 14 Oct 2020 06:58:25 GMT

←Older revision		Revision as of 06:58, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of zebrafish lysophosphatidic acid receptor LPA6==		==Crystal structure of zebrafish lysophosphatidic acid receptor LPA6==
-	<StructureSection load='5xsz' size='340' side='right' caption='[[5xsz]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='5xsz' size='340' side='right'caption='[[5xsz]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xsz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XSZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xsz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XSZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5xsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsz OCA], [http://pdbe.org/5xsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsz RCSB], [http://www.ebi.ac.uk/pdbsum/5xsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsz 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=5xsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsz OCA], [http://pdbe.org/5xsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsz RCSB], [http://www.ebi.ac.uk/pdbsum/5xsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5xsz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xsz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysophosphatidic acid receptor\|Lysophosphatidic acid receptor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA: Protected "5xsz" [edit=sysop:move=sysop]

OCA — Wed, 30 Aug 2017 04:02:00 GMT

Protected "5xsz" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:02, 30 August 2017

OCA: New page: ==Crystal structure of zebrafish lysophosphatidic acid receptor LPA6==
OCA — Wed, 30 Aug 2017 04:01:58 GMT

New page: ==Crystal structure of zebrafish lysophosphatidic acid receptor LPA6== <StructureSection load='5xsz' size='340' side='right' caption='5xsz, resolution 3.20Å' scen...

New page

==Crystal structure of zebrafish lysophosphatidic acid receptor LPA6==
<StructureSection load='5xsz' size='340' side='right' caption='[[5xsz]], [[Resolution|resolution]] 3.20Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5xsz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XSZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XSZ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5xsz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xsz OCA], [http://pdbe.org/5xsz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xsz RCSB], [http://www.ebi.ac.uk/pdbsum/5xsz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xsz ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lysophosphatidic acid (LPA) is a bioactive lipid composed of a phosphate group, a glycerol backbone, and a single acyl chain that varies in length and saturation. LPA activates six class A G-protein-coupled receptors to provoke various cellular reactions. Because LPA signalling has been implicated in cancer and fibrosis, the LPA receptors are regarded as promising drug targets. The six LPA receptors are subdivided into the endothelial differentiation gene (EDG) family (LPA1-LPA3) and the phylogenetically distant non-EDG family (LPA4-LPA6). The structure of LPA1 has enhanced our understanding of the EDG family of LPA receptors. By contrast, the functional and pharmacological characteristics of the non-EDG family of LPA receptors have remained unknown, owing to the lack of structural information. Although the non-EDG LPA receptors share sequence similarity with the P2Y family of nucleotide receptors, the LPA recognition mechanism cannot be deduced from the P2Y1 and P2Y12 structures because of the large differences in the chemical structures of their ligands. Here we determine the 3.2 A crystal structure of LPA6, the gene deletion of which is responsible for congenital hair loss, to clarify the ligand recognition mechanism of the non-EDG family of LPA receptors. Notably, the ligand-binding pocket of LPA6 is laterally open towards the membrane, and the acyl chain of the lipid used for the crystallization is bound within this pocket, indicating the binding mode of the LPA acyl chain. Docking and mutagenesis analyses also indicated that the conserved positively charged residues within the central cavity recognize the phosphate head group of LPA by inducing an inward shift of transmembrane helices 6 and 7, suggesting that the receptor activation is triggered by this conformational rearrangement.

Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6.,Taniguchi R, Inoue A, Sayama M, Uwamizu A, Yamashita K, Hirata K, Yoshida M, Tanaka Y, Kato HE, Nakada-Nakura Y, Otani Y, Nishizawa T, Doi T, Ohwada T, Ishitani R, Aoki J, Nureki O Nature. 2017 Aug 17;548(7667):356-360. doi: 10.1038/nature23448. Epub 2017 Aug 9. PMID:28792932<ref>PMID:28792932</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xsz" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Lysozyme]]
[[Category: Ishitani, R]]
[[Category: Nishizawa, T]]
[[Category: Nureki, O]]
[[Category: Taniguchi, R]]
[[Category: Alpha helical]]
[[Category: Membrane protein]]