7ffp
From Proteopedia
(Difference between revisions)
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==Crystal structure of di-peptidase-E from Xenopus laevis== | ==Crystal structure of di-peptidase-E from Xenopus laevis== | ||
| - | <StructureSection load='7ffp' size='340' side='right'caption='[[7ffp]]' scene=''> | + | <StructureSection load='7ffp' size='340' side='right'caption='[[7ffp]], [[Resolution|resolution]] 1.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7c9d 7c9d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7ffp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=7c9d 7c9d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FFP FirstGlance]. <br> |
| - | </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=7ffp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffp OCA], [https://pdbe.org/7ffp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffp RCSB], [https://www.ebi.ac.uk/pdbsum/7ffp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffp ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7c9b|7c9b]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aad-a ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dipeptidase_E Dipeptidase E], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.21 3.4.13.21] </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=7ffp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ffp OCA], [https://pdbe.org/7ffp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ffp RCSB], [https://www.ebi.ac.uk/pdbsum/7ffp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ffp ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/PEPE_XENLA PEPE_XENLA]] Hydrolyzes dipeptides containing N-terminal aspartate residues. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Gene encoding aspartyl dipeptidase from Xenopus levies (PepExl) is upregulated by thyroid hormone and is proposed to play a significant role in resorption of tadpole tail during metamorphosis. However, the importance of peptidase activity for the resorption of the tail remain elusive. Here we report the crystal structures of first eukaryotic S51 peptidase, PepExl, in its ligand-free and Asp-bound states at 1.4 and 1.8 A resolutions, respectively. The active site is located at dimeric interface and the catalytic triad is found to be dissembled in ligand-free and assembled in Asp-bound state. Structural comparison and molecular dynamic simulations of ligand-free and Asp-bound states shows that distinct loop (loop-A) plays an important role in active site shielding, substrate binding and enzyme activation. This study illuminates the Asp-X dipeptide binding in PepExl is associated with ordering of the loop-A and assembly of residues of catalytic triad in active conformation for enzymatic activity. | ||
| + | |||
| + | Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly.,Kumar A, Singh R, Ghosh B, Makde RD Proteins. 2021 Aug 25. doi: 10.1002/prot.26220. PMID:34431561<ref>PMID:34431561</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7ffp" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: African clawed frog]] | ||
| + | [[Category: Dipeptidase E]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Kumar A]] | + | [[Category: Kumar, A]] |
| - | [[Category: Makde | + | [[Category: Makde, R D]] |
| - | [[Category: Singh R]] | + | [[Category: Singh, R]] |
| + | [[Category: Alpha-aspartyl dipeptidase]] | ||
| + | [[Category: Aspartyl dipeptidase]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Peptidase-e]] | ||
Revision as of 11:00, 16 February 2022
Crystal structure of di-peptidase-E from Xenopus laevis
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