5jxk - Revision history

OCA at 19:14, 20 September 2023

OCA — Wed, 20 Sep 2023 19:14:11 GMT

←Older revision		Revision as of 19:14, 20 September 2023
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	<StructureSection load='5jxk' size='340' side='right'caption='[[5jxk]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='5jxk' size='340' side='right'caption='[[5jxk]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jxk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JXK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jxk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_endodontalis_ATCC_35406 Porphyromonas endodontalis ATCC 35406]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JXK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.85Å</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=5jxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxk OCA], [~~http~~://pdbe.org/5jxk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jxk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jxk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxk ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=5jxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxk OCA], [https://pdbe.org/5jxk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jxk RCSB], [https://www.ebi.ac.uk/pdbsum/5jxk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPP11_POREA DPP11_POREA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bezerra~~, G A~~]]	+	[[Category: Porphyromonas endodontalis ATCC 35406]]
-	[[Category: Cornaciu, I]]	+	[[Category: Bezerra GA]]
-	[[Category: Djinovic-Carugo, K]]	+	[[Category: Cornaciu I]]
-	[[Category: Hoffmann, G]]	+	[[Category: Djinovic-Carugo K]]
-	[[Category: Marquez~~, J A]]~~	+	[[Category: Hoffmann G]]
-	~~[[Category: Bacterial enzyme]]~~	+	[[Category: Marquez JA]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidase~~]]	+

OCA at 11:44, 17 June 2020

OCA — Wed, 17 Jun 2020 11:44:23 GMT

←Older revision		Revision as of 11:44, 17 June 2020
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	==Crystal structure of Porphyromonas endodontalis DPP11==		==Crystal structure of Porphyromonas endodontalis DPP11==
-	<StructureSection load='5jxk' size='340' side='right' caption='[[5jxk]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='5jxk' size='340' side='right'caption='[[5jxk]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jxk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JXK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jxk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JXK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5jxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxk OCA], [http://pdbe.org/5jxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxk RCSB], [http://www.ebi.ac.uk/pdbsum/5jxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxk 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=5jxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxk OCA], [http://pdbe.org/5jxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxk RCSB], [http://www.ebi.ac.uk/pdbsum/5jxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxk 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 5jxk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jxk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dipeptidyl peptidase 3D structures\|Dipeptidyl peptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bezerra, G A]]		[[Category: Bezerra, G A]]
	[[Category: Cornaciu, I]]		[[Category: Cornaciu, I]]

OCA at 10:33, 3 August 2017

OCA — Thu, 03 Aug 2017 10:33:21 GMT

←Older revision		Revision as of 10:33, 3 August 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5jxk is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Porphyromonas endodontalis DPP11==
		+	<StructureSection load='5jxk' size='340' side='right' caption='[[5jxk]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jxk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JXK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5jxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxk OCA], [http://pdbe.org/5jxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxk RCSB], [http://www.ebi.ac.uk/pdbsum/5jxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.

-	~~Authors~~:	+	Bacterial protease uses distinct thermodynamic signatures for substrate recognition.,Bezerra GA, Ohara-Nemoto Y, Cornaciu I, Fedosyuk S, Hoffmann G, Round A, Marquez JA, Nemoto TK, Djinovic-Carugo K Sci Rep. 2017 Jun 6;7(1):2848. doi: 10.1038/s41598-017-03220-y. PMID:28588213<ref>PMID:28588213</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jxk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bezerra, G A]]
		+	[[Category: Cornaciu, I]]
		+	[[Category: Djinovic-Carugo, K]]
		+	[[Category: Hoffmann, G]]
		+	[[Category: Marquez, J A]]
		+	[[Category: Bacterial enzyme]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidase]]

OCA at 12:12, 4 January 2017

OCA — Wed, 04 Jan 2017 12:12:56 GMT

←Older revision		Revision as of 12:12, 4 January 2017
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	The entry 5jxk is ON HOLD until Paper Publication		The entry 5jxk is ON HOLD until Paper Publication

-	Authors: ~~Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A.~~	+	Authors:

-	Description: ~~Crystal structure of Porphyromonas endodontalis DPP11~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Djinovic-Carugo, K]]
-	[[Category: Marquez, J.A]]
-	[[Category: Cornaciu, I]]
-	[[Category: Bezerra, G.A]]
-	[[Category: Hoffmann, G]]

OCA at 13:39, 9 September 2016

OCA — Fri, 09 Sep 2016 13:39:05 GMT

←Older revision		Revision as of 13:39, 9 September 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A.		Authors: Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A.

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

OCA — Wed, 01 Jun 2016 14:00:30 GMT

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

←Older revision

Revision as of 14:00, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jxk is ON HOLD Authors: Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A. Description: Crystal structure of Porphyromo...

OCA — Wed, 01 Jun 2016 14:00:29 GMT

New page: '''Unreleased structure''' The entry 5jxk is ON HOLD Authors: Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A. Description: Crystal structure of Porphyromo...

New page

'''Unreleased structure'''

The entry 5jxk is ON HOLD

Authors: Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A.

Description: Crystal structure of Porphyromonas endodontalis DPP11
[[Category: Unreleased Structures]]
[[Category: Djinovic-Carugo, K]]
[[Category: Marquez, J.A]]
[[Category: Cornaciu, I]]
[[Category: Bezerra, G.A]]
[[Category: Hoffmann, G]]