View source for 5jxf


==Crystal structure of Flavobacterium psychrophilum DPP11 in complex with dipeptide Arg-Asp==
<StructureSection load='5jxf' size='340' side='right'caption='[[5jxf]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5jxf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_psychrophilum Flavobacterium psychrophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JXF 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]] 2.1&#8491;</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=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5jxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxf OCA], [https://pdbe.org/5jxf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jxf RCSB], [https://www.ebi.ac.uk/pdbsum/5jxf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPP11_FLAPJ DPP11_FLAPJ] Catalyzes the removal of dipeptides from the N-terminus of oligopeptides. Shows a strict specificity for acidic residues (Asp or Glu) in the P1 position, and has probably a hydrophobic residue preference at the P2 position. Preferentially cleaves the synthetic substrate Leu-Asp-methylcoumaryl-7-amide (Leu-Asp-MCA) as compared to Leu-Glu-MCA.<ref>PMID:23246913</ref> 
<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5jxf" style="background-color:#fffaf0;"></div>

==See Also==
*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Flavobacterium psychrophilum]]
[[Category: Large Structures]]
[[Category: Bezerra GA]]
[[Category: Djinovic-Carugo K]]
[[Category: Fedosyuk S]]
[[Category: Nemoto TK]]
[[Category: Ohara-Nemoto Y]]