4y06

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'''Unreleased structure'''
 
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The entry 4y06 is ON HOLD
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==Crystal structure of the DAP BII (G675R) dipeptide complex==
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<StructureSection load='4y06' size='340' side='right'caption='[[4y06]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4y06]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoxanthomonas_mexicana Pseudoxanthomonas mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y06 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.18&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4y06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y06 OCA], [https://pdbe.org/4y06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y06 RCSB], [https://www.ebi.ac.uk/pdbsum/4y06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y06 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DAPB2_PSEMX DAPB2_PSEMX] Exopeptidase that catalyzes the removal of dipeptide units (NH2-P2-P1-) from the free amino termini of oligopeptides and small proteins (PubMed:24598890, PubMed:24827749, PubMed:8892831). Peptide digestion is sequential and substrate recognition is non-specific, with the exception that Pro is not suitable as a P1 residue (PubMed:24827749). Removes many residues of bioactive oligopeptides such as angiotensin I and neuromedin N and cleaves also oxidized insulin B chain. Able to hydrolyze an X-Pro bond, an imido bond. No endopeptidase activity (PubMed:8892831). May play a physiological role in feeding (PubMed:24598890).<ref>PMID:24598890</ref> <ref>PMID:24827749</ref> <ref>PMID:8892831</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double beta-barrel fold and a recently identified regulatory alpha-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms.
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Authors: Sakamoto, Y., Iizuka, I., Tateoka, C., Roppongi, S., Fujimoto, M., Nonaka, T., Ogasawara, W., Tanaka, N.
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Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.,Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Yamada M, Ohta K, Gouda H, Nonaka T, Ogasawara W, Tanaka N Sci Rep. 2015 Jun 9;5:11151. doi: 10.1038/srep11151. PMID:26057589<ref>PMID:26057589</ref>
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Description:
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Tateoka, C]]
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<div class="pdbe-citations 4y06" style="background-color:#fffaf0;"></div>
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[[Category: Roppongi, S]]
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== References ==
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[[Category: Nonaka, T]]
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<references/>
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[[Category: Sakamoto, Y]]
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__TOC__
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[[Category: Ogasawara, W]]
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</StructureSection>
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[[Category: Iizuka, I]]
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[[Category: Large Structures]]
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[[Category: Tanaka, N]]
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[[Category: Pseudoxanthomonas mexicana]]
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[[Category: Fujimoto, M]]
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[[Category: Fujimoto M]]
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[[Category: Iizuka I]]
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[[Category: Nonaka T]]
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[[Category: Ogasawara W]]
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[[Category: Roppongi S]]
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[[Category: Sakamoto Y]]
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[[Category: Tanaka N]]
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[[Category: Tateoka C]]

Current revision

Crystal structure of the DAP BII (G675R) dipeptide complex

PDB ID 4y06

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