5jwi: Difference between revisions
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New page: '''Unreleased structure''' The entry 5jwi is ON HOLD until Paper Publication Authors: Bezerra, G.A., Fedosyuk, S., Ohara-Nemoto, Y., Nemoto, T.K., Djinovic-Carugo, K. Description: Crys... |
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==Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Glu== | |||
<StructureSection load='5jwi' size='340' side='right'caption='[[5jwi]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5jwi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_endodontalis Porphyromonas endodontalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JWI 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]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</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=5jwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jwi OCA], [https://pdbe.org/5jwi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jwi RCSB], [https://www.ebi.ac.uk/pdbsum/5jwi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jwi 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5jwi" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]] | ||
[[Category: Ohara-Nemoto | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Porphyromonas endodontalis]] | |||
[[Category: Bezerra GA]] | |||
[[Category: Djinovic-Carugo K]] | |||
[[Category: Fedosyuk S]] | |||
[[Category: Nemoto TK]] | |||
[[Category: Ohara-Nemoto Y]] | |||
Latest revision as of 19:12, 20 September 2023
Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Glu
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