2ydr: Difference between revisions

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-'''Unreleased structure'''
-The entry 2ydr is ON HOLD  until sometime in the future
+==CpOGA D298N in complex with p53-derived O-GlcNAc peptide==
+<StructureSection load='2ydr' size='340' side='right'caption='[[2ydr]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ydr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YDR 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]] 2.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=2ydr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ydr OCA], [https://pdbe.org/2ydr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ydr RCSB], [https://www.ebi.ac.uk/pdbsum/2ydr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ydr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OGA_CLOP1 OGA_CLOP1] Biological function unknown. Capable of hydrolyzing the glycosidic link of O-GlcNAcylated proteins.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Protein O-GlcNAcylation is an essential reversible posttranslational modification in higher eukaryotes. O-GlcNAc addition and removal is catalyzed by O-GlcNAc transferase and O-GlcNAcase, respectively. We report the molecular details of the interaction of a bacterial O-GlcNAcase homolog with three different synthetic glycopeptides derived from characterized O-GlcNAc sites in the human proteome. Strikingly, the peptides bind a conserved O-GlcNAcase substrate binding groove with similar orientation and conformation. In addition to extensive contacts with the sugar, O-GlcNAcase recognizes the peptide backbone through hydrophobic interactions and intramolecular hydrogen bonds, while avoiding interactions with the glycopeptide side chains. These findings elucidate the molecular basis of O-GlcNAcase substrate specificity, explaining how a single enzyme achieves cycling of the complete O-GlcNAc proteome. In addition, this work will aid development of O-GlcNAcase inhibitors that target the peptide binding site.
-Authors: Schimpl, M., Borodkin, V.S., Gray, L.J., van Aalten, D.M.F.
+Synergy of Peptide and Sugar in O-GlcNAcase Substrate Recognition.,Schimpl M, Borodkin VS, Gray LJ, van Aalten DM Chem Biol. 2012 Feb 24;19(2):173-8. PMID:22365600<ref>PMID:22365600</ref>
-Description: CpOGA D298N in complex with p53-derived O-GlcNAc peptide
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ydr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[O-GlcNAcase|O-GlcNAcase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Clostridium perfringens]]
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Borodkin VS]]
+[[Category: Gray LJ]]
+[[Category: Schimpl M]]
+[[Category: Van Aalten DMF]]