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5jxf
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of Flavobacterium psychrophilum DPP11 in complex with dipeptide Arg-Asp== | |
| + | <StructureSection load='5jxf' size='340' side='right' caption='[[5jxf]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5jxf]] is a 4 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JXF FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jxf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jxf OCA], [http://pdbe.org/5jxf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jxf RCSB], [http://www.ebi.ac.uk/pdbsum/5jxf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jxf ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[http://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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 5jxf" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bezerra, G A]] | ||
| + | [[Category: Djinovic-Carugo, K]] | ||
| + | [[Category: Fedosyuk, S]] | ||
| + | [[Category: Nemoto, T K]] | ||
| + | [[Category: Ohara-Nemoto, Y]] | ||
| + | [[Category: Bacterial enzyme]] | ||
| + | [[Category: Dipeptide]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Peptidase]] | ||
Revision as of 09:41, 3 August 2017
Crystal structure of Flavobacterium psychrophilum DPP11 in complex with dipeptide Arg-Asp
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