5wdk - Revision history

OCA at 14:11, 4 October 2023

OCA — Wed, 04 Oct 2023 14:11:12 GMT

←Older revision		Revision as of 14:11, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5wdk' size='340' side='right'caption='[[5wdk]], [[Resolution\|resolution]] 2.36Å' scene=''>		<StructureSection load='5wdk' size='340' side='right'caption='[[5wdk]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wdk]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pard8 Pard8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WDK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wdk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Parabacteroides_distasonis_ATCC_8503 Parabacteroides distasonis ATCC 8503]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WDK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=T1O:5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide'>T1O</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]] 2.36Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BDI_2249 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=435591 PARD8])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=T1O:5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide'>T1O</scene></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=5wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wdk OCA], [~~http~~://pdbe.org/5wdk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wdk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wdk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wdk 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=5wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wdk OCA], [https://pdbe.org/5wdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wdk RCSB], [https://www.ebi.ac.uk/pdbsum/5wdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wdk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A6LE66_PARD8 A6LE66_PARD8]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pard8~~]]	+	[[Category: Parabacteroides distasonis ATCC 8503]]
-	[[Category: Chatterjee, S]]	+	[[Category: Chatterjee S]]
-	[[Category: Jiang, Z]]	+	[[Category: Jiang Z]]
-	[[Category: ODonoghue~~, A J~~]]	+	[[Category: ODonoghue AJ]]
-	[[Category: Solania, A]]	+	[[Category: Solania A]]
-	[[Category: Wolan~~, D W~~]]	+	[[Category: Wolan DW]]
-	[[Category: Xu~~, J H]]~~	+	[[Category: Xu JH]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protease~~]]	+

OCA at 08:31, 24 July 2019

OCA — Wed, 24 Jul 2019 08:31:14 GMT

←Older revision		Revision as of 08:31, 24 July 2019
Line 1:		Line 1:

	==A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis==		==A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis==
-	<StructureSection load='5wdk' size='340' side='right' caption='[[5wdk]], [[Resolution\|resolution]] 2.36Å' scene=''>	+	<StructureSection load='5wdk' size='340' side='right'caption='[[5wdk]], [[Resolution\|resolution]] 2.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wdk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wdk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pard8 Pard8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WDK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=T1O:5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide'>T1O</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=T1O:5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide'>T1O</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BDI_2249 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=435591 PARD8])</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=5wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wdk OCA], [http://pdbe.org/5wdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wdk RCSB], [http://www.ebi.ac.uk/pdbsum/5wdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wdk ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wdk OCA], [http://pdbe.org/5wdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wdk RCSB], [http://www.ebi.ac.uk/pdbsum/5wdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wdk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteases within the C1B hydrolase family are encoded by many organisms. We subjected a putative C1B-like cysteine protease secreted by the human gut commensal Parabacteroides distasonis to mass spectrometry-based substrate profiling to find preferred peptide substrates. The P. distasonis protease, which we termed Pd_dinase, has a sequential diaminopeptidase activity with strong specificity for N-terminal glycine residues. Using the substrate sequence information, we verified the importance of the P2 glycine residue with a panel of fluorogenic substrates and calculated kcat and KM for the dipeptide glycine-arginine-AMC. A potent and irreversible dipeptide inhibitor with a C-terminal acyloxymethyl ketone warhead, glycine-arginine- AOMK, was then synthesized and demonstrated that the Pd_dinase active site requires a free N-terminal amine for potent and rapid inhibition. We next determined the homohexameric Pd_dinase structure in complex with glycine-arginine- AOMK and uncovered unexpected active site features that govern the strict substrate preferences and differentiate this protease from members of the C1B and broader papain-like C1 protease families. We finally showed that Pd_dinase hydrolyzes several human antimicrobial peptides and therefore posit that this P. distasonis enzyme may be secreted into the extracellular milieu to assist in gut colonization by inactivation of host antimicrobial peptides.
		+
		+	A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.,Xu JH, Jiang Z, Solania A, Chatterjee S, Suzuki B, Lietz CB, Hook VYH, O'Donoghue AJ, Wolan DW ACS Chem Biol. 2018 Sep 21;13(9):2513-2521. doi: 10.1021/acschembio.8b00420. Epub, 2018 Aug 23. PMID:30085657<ref>PMID:30085657</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5wdk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pard8]]
	[[Category: Chatterjee, S]]		[[Category: Chatterjee, S]]
	[[Category: Jiang, Z]]		[[Category: Jiang, Z]]

OCA at 05:35, 11 July 2018

OCA — Wed, 11 Jul 2018 05:35:55 GMT

←Older revision		Revision as of 05:35, 11 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wdk ~~is ON HOLD until Paper Publication~~	+	==A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis==
-		+	<StructureSection load='5wdk' size='340' side='right' caption='[[5wdk]], [[Resolution\|resolution]] 2.36Å' scene=''>
-	~~Authors~~: ~~Wolan, D~~.W.~~, Xu, J~~.H., ~~Solania~~, A., ~~Chatterjee~~, S., ~~Jiang~~, Z., ~~ODonoghue, A~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5wdk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WDK FirstGlance]. <br>
-	~~Description~~: ~~A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P~~. ~~distasonis~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=T1O:5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide'>T1O</scene></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	<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=5wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wdk OCA], [http://pdbe.org/5wdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wdk RCSB], [http://www.ebi.ac.uk/pdbsum/5wdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wdk ProSAT]</span></td></tr>
-	[[Category: ~~Odonoghue~~, ~~A.J~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chatterjee, S]]
	[[Category: Jiang, Z]]		[[Category: Jiang, Z]]
-	[[Category: ~~Wolan, D.W]]~~	+	[[Category: ODonoghue, A J]]
-	~~[[Category: Chatterjee, S]]~~	+
-	~~[[Category: Xu~~, J.H]]	+
	[[Category: Solania, A]]		[[Category: Solania, A]]
		+	[[Category: Wolan, D W]]
		+	[[Category: Xu, J H]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protease]]

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

OCA — Wed, 27 Sep 2017 14:42:49 GMT

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

←Older revision

Revision as of 14:42, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wdk is ON HOLD until Paper Publication Authors: Wolan, D.W., Xu, J.H., Solania, A., Chatterjee, S., Jiang, Z., ODonoghue, A.J. Description: A proc...

OCA — Wed, 27 Sep 2017 14:42:48 GMT

New page: '''Unreleased structure''' The entry 5wdk is ON HOLD until Paper Publication Authors: Wolan, D.W., Xu, J.H., Solania, A., Chatterjee, S., Jiang, Z., ODonoghue, A.J. Description: A proc...

New page

'''Unreleased structure'''

The entry 5wdk is ON HOLD until Paper Publication

Authors: Wolan, D.W., Xu, J.H., Solania, A., Chatterjee, S., Jiang, Z., ODonoghue, A.J.

Description: A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis
[[Category: Unreleased Structures]]
[[Category: Odonoghue, A.J]]
[[Category: Jiang, Z]]
[[Category: Wolan, D.W]]
[[Category: Chatterjee, S]]
[[Category: Xu, J.H]]
[[Category: Solania, A]]