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


The entry 5jxp is ON HOLD
==Crystal structure of Porphyromonas endodontalis DPP11 in alternate conformation==
<StructureSection load='5jxp' size='340' side='right'caption='[[5jxp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5jxp]] is a 1 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=5JXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JXP FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=5jxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxp OCA], [https://pdbe.org/5jxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jxp RCSB], [https://www.ebi.ac.uk/pdbsum/5jxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPP11_POREA DPP11_POREA]
<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: Bezerra, G.A., Cornaciu, I., Hoffmann, G., Djinovic-Carugo, K., Marquez, J.A.
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: Crystal structure of Porphyromonas endodontalis DPP11 in alternate conformation
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Djinovic-Carugo, K]]
<div class="pdbe-citations 5jxp" style="background-color:#fffaf0;"></div>
[[Category: Marquez, J.A]]
 
[[Category: Cornaciu, I]]
==See Also==
[[Category: Bezerra, G.A]]
*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
[[Category: Hoffmann, G]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Porphyromonas endodontalis ATCC 35406]]
[[Category: Bezerra GA]]
[[Category: Cornaciu I]]
[[Category: Djinovic-Carugo K]]
[[Category: Hoffmann G]]
[[Category: Marquez JA]]
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