7dkb: Difference between revisions
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<StructureSection load='7dkb' size='340' side='right'caption='[[7dkb]], [[Resolution|resolution]] 2.03Å' scene=''> | <StructureSection load='7dkb' size='340' side='right'caption='[[7dkb]], [[Resolution|resolution]] 2.03Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'> | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DKB 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]] 2.03Å</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TYR:TYROSINE'>TYR</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</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=7dkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dkb OCA], [https://pdbe.org/7dkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dkb RCSB], [https://www.ebi.ac.uk/pdbsum/7dkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dkb ProSAT]</span></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=7dkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dkb OCA], [https://pdbe.org/7dkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dkb RCSB], [https://www.ebi.ac.uk/pdbsum/7dkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dkb ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Gouda H]] | [[Category: Gouda H]] | ||
[[Category: Honma N]] | [[Category: Honma N]] | ||
Latest revision as of 16:31, 6 November 2024
Stenotrophomonas maltophilia DPP7 in complex with Val-TyrStenotrophomonas maltophilia DPP7 in complex with Val-Tyr
Structural highlights
Publication Abstract from PubMedThe emergence of drug-resistant bacteria has become a major problem worldwide. Bacterial dipeptidyl peptidases 7 and 11 (DPP7s and DPP11s), belonging to the family-S46 peptidases, are important enzymes for bacterial growth and are not present in mammals. Therefore, specific inhibitors for these peptidases are promising as potential antibiotics. While the molecular mechanisms underlining strict specificity at the S1 subsite of S46 peptidases have been well studied, those of relatively broad preference at the S2 subsite of these peptidases are unknown. In this study, we performed structural and biochemical analyses on DPP7 from Stenotrophomonas maltophilia (SmDPP7). SmDPP7 showed preference for the accommodation of hydrophobic amino acids at the S2 subsite in general, but as an exception, also for asparagine, a hydrophilic amino acid. Structural analyses of SmDPP7 revealed that this exceptional preference to asparagine is caused by a hydrogen bonding network at the bottom of the S2 subsite. The residues in the S2 subsite are well conserved among S46 peptidases as compared with those in the S1 subsite. We expect that our findings will contribute toward the development of a universal inhibitor of S46 peptidases. Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.,Nakamura A, Suzuki Y, Sakamoto Y, Roppongi S, Kushibiki C, Yonezawa N, Takahashi M, Shida Y, Gouda H, Nonaka T, Tanaka N, Ogasawara W Sci Rep. 2021 Apr 12;11(1):7929. doi: 10.1038/s41598-021-86965-x. PMID:33846449[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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