5kdw - Revision history

OCA at 09:58, 27 September 2023

OCA — Wed, 27 Sep 2023 09:58:54 GMT

←Older revision		Revision as of 09:58, 27 September 2023
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	<StructureSection load='5kdw' size='340' side='right'caption='[[5kdw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5kdw' size='340' side='right'caption='[[5kdw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kdw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kdw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KDW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.85Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5kd2\|5kd2]]~~, ~~[[5kd5\|5kd5]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdx\|5kdx]]</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PA0572 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</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=5kdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdw OCA], [https://pdbe.org/5kdw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kdw RCSB], [https://www.ebi.ac.uk/pdbsum/5kdw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdw 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=5kdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdw OCA], [~~http~~://pdbe.org/5kdw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kdw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kdw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/IMPA_PSEAE IMPA_PSEAE]] Protease that degrades several proteins of the host immune system. Cleaves P-selectin glycoprotein ligand-1 (PSGL-1), leading to its functional inhibition; PSGL-1 is a leukocyte cell-surface receptor essential for leukocyte recruitment to the site of infection. Next to PSGL-1, targets host CD43 and CD44 that are also involved in leukocyte homing. Thus, prevents neutrophil extravasation and thereby protects P.aeruginosa from neutrophil attack. Is also able to inhibit the decay accelerating factor (CD55), but not the cell-surface receptors CD46 and CD31.<ref>PMID:22309196</ref>	+	[https://www.uniprot.org/uniprot/IMPA_PSEAE IMPA_PSEAE] Protease that degrades several proteins of the host immune system. Cleaves P-selectin glycoprotein ligand-1 (PSGL-1), leading to its functional inhibition; PSGL-1 is a leukocyte cell-surface receptor essential for leukocyte recruitment to the site of infection. Next to PSGL-1, targets host CD43 and CD44 that are also involved in leukocyte homing. Thus, prevents neutrophil extravasation and thereby protects P.aeruginosa from neutrophil attack. Is also able to inhibit the decay accelerating factor (CD55), but not the cell-surface receptors CD46 and CD31.<ref>PMID:22309196</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Boraston AB]]
-	[[Category: Noach, I]]	+	[[Category: Noach I]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: O-glycopeptidase]]~~	+
-	~~[[Category: Pf13402/m60-like~~]]	+

OCA at 15:23, 8 July 2020

OCA — Wed, 08 Jul 2020 15:23:38 GMT

←Older revision		Revision as of 15:23, 8 July 2020
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	==IMPa metallopeptidase from Pseudomonas aeruginosa==		==IMPa metallopeptidase from Pseudomonas aeruginosa==
-	<StructureSection load='5kdw' size='340' side='right' caption='[[5kdw]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5kdw' size='340' side='right'caption='[[5kdw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kdw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kdw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KDW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kd2\|5kd2]], [[5kd5\|5kd5]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdx\|5kdx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kd2\|5kd2]], [[5kd5\|5kd5]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdx\|5kdx]]</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=5kdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdw OCA], [http://pdbe.org/5kdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdw RCSB], [http://www.ebi.ac.uk/pdbsum/5kdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdw ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA0572 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=5kdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdw OCA], [http://pdbe.org/5kdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdw RCSB], [http://www.ebi.ac.uk/pdbsum/5kdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Boraston, A B]]		[[Category: Boraston, A B]]
	[[Category: Noach, I]]		[[Category: Noach, I]]

OCA at 11:03, 1 February 2017

OCA — Wed, 01 Feb 2017 11:03:51 GMT

←Older revision		Revision as of 11:03, 1 February 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/IMPA_PSEAE IMPA_PSEAE]] Protease that degrades several proteins of the host immune system. Cleaves P-selectin glycoprotein ligand-1 (PSGL-1), leading to its functional inhibition; PSGL-1 is a leukocyte cell-surface receptor essential for leukocyte recruitment to the site of infection. Next to PSGL-1, targets host CD43 and CD44 that are also involved in leukocyte homing. Thus, prevents neutrophil extravasation and thereby protects P.aeruginosa from neutrophil attack. Is also able to inhibit the decay accelerating factor (CD55), but not the cell-surface receptors CD46 and CD31.<ref>PMID:22309196</ref>		[[http://www.uniprot.org/uniprot/IMPA_PSEAE IMPA_PSEAE]] Protease that degrades several proteins of the host immune system. Cleaves P-selectin glycoprotein ligand-1 (PSGL-1), leading to its functional inhibition; PSGL-1 is a leukocyte cell-surface receptor essential for leukocyte recruitment to the site of infection. Next to PSGL-1, targets host CD43 and CD44 that are also involved in leukocyte homing. Thus, prevents neutrophil extravasation and thereby protects P.aeruginosa from neutrophil attack. Is also able to inhibit the decay accelerating factor (CD55), but not the cell-surface receptors CD46 and CD31.<ref>PMID:22309196</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.
		+
		+	Recognition of protein-linked glycans as a determinant of peptidase activity.,Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB Proc Natl Acad Sci U S A. 2017 Jan 17. pii: 201615141. doi:, 10.1073/pnas.1615141114. PMID:28096352<ref>PMID:28096352</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kdw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:30, 18 January 2017

OCA — Wed, 18 Jan 2017 16:30:18 GMT

←Older revision		Revision as of 16:30, 18 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kdw is ~~ON HOLD~~ ~~until Paper Publication~~	+	==IMPa metallopeptidase from Pseudomonas aeruginosa==
-		+	<StructureSection load='5kdw' size='340' side='right' caption='[[5kdw]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kdw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KDW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KDW FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kd2\|5kd2]], [[5kd5\|5kd5]], [[5kd8\|5kd8]], [[5kdj\|5kdj]], [[5kdn\|5kdn]], [[5kds\|5kds]], [[5kdu\|5kdu]], [[5kdv\|5kdv]], [[5kdx\|5kdx]]</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=5kdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdw OCA], [http://pdbe.org/5kdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdw RCSB], [http://www.ebi.ac.uk/pdbsum/5kdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IMPA_PSEAE IMPA_PSEAE]] Protease that degrades several proteins of the host immune system. Cleaves P-selectin glycoprotein ligand-1 (PSGL-1), leading to its functional inhibition; PSGL-1 is a leukocyte cell-surface receptor essential for leukocyte recruitment to the site of infection. Next to PSGL-1, targets host CD43 and CD44 that are also involved in leukocyte homing. Thus, prevents neutrophil extravasation and thereby protects P.aeruginosa from neutrophil attack. Is also able to inhibit the decay accelerating factor (CD55), but not the cell-surface receptors CD46 and CD31.<ref>PMID:22309196</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Boraston, A B]]
		+	[[Category: Noach, I]]
		+	[[Category: Hydrolase]]
		+	[[Category: O-glycopeptidase]]
		+	[[Category: Pf13402/m60-like]]

OCA at 00:17, 13 July 2016

OCA — Wed, 13 Jul 2016 00:17:13 GMT

←Older revision		Revision as of 00:17, 13 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kdw is ON HOLD	+	The entry 5kdw is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Mon, 20 Jun 2016 13:48:28 GMT

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

←Older revision

Revision as of 13:48, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kdw is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Mon, 20 Jun 2016 13:48:27 GMT

New page: '''Unreleased structure''' The entry 5kdw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kdw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]