3wor: Difference between revisions
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==Crystal structure of the DAP BII octapeptide complex== | ==Crystal structure of the DAP BII octapeptide complex== | ||
<StructureSection load='3wor' size='340' side='right' caption='[[3wor]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='3wor' size='340' side='right'caption='[[3wor]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3wor]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3wor]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700993 Atcc 700993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WOR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3woi|3woi]], [[3woj|3woj]], [[3wok|3wok]], [[3wol|3wol]], [[3wom|3wom]], [[3won|3won]], [[3woo|3woo]], [[3wop|3wop]], [[3woq|3woq]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3woi|3woi]], [[3woj|3woj]], [[3wok|3wok]], [[3wol|3wol]], [[3wom|3wom]], [[3won|3won]], [[3woo|3woo]], [[3wop|3wop]], [[3woq|3woq]]</div></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wor OCA], [https://pdbe.org/3wor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wor RCSB], [https://www.ebi.ac.uk/pdbsum/3wor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wor ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Atcc 700993]] | [[Category: Atcc 700993]] | ||
[[Category: Large Structures]] | |||
[[Category: Fujimoto, M]] | [[Category: Fujimoto, M]] | ||
[[Category: Iizuka, I]] | [[Category: Iizuka, I]] | ||
Revision as of 08:44, 3 August 2022
Crystal structure of the DAP BII octapeptide complexCrystal structure of the DAP BII octapeptide complex
Structural highlights
Publication Abstract from PubMedThe dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double beta-barrel fold and previously unreported alpha-helical domain. The structures of peptide complexes revealed that the alpha-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the alpha-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens. S46 peptidases are the first exopeptidases to be members of clan PA.,Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Masaki M, Ohta K, Okada H, Nonaka T, Morikawa Y, Nakamura KT, Ogasawara W, Tanaka N Sci Rep. 2014 May 15;4:4977. doi: 10.1038/srep04977. PMID:24827749[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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