2xm2: Difference between revisions

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-[[Image:2xm2.jpg|left|200px]]
-<!--
+==BtGH84 in complex with LOGNAc==
-The line below this paragraph, containing "STRUCTURE_2xm2", creates the "Structure Box" on the page.
+<StructureSection load='2xm2' size='340' side='right'caption='[[2xm2]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2xm2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XM2 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</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=LOG:LOGNAC'>LOG</scene></td></tr>
-{{STRUCTURE_2xm2|  PDB=2xm2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xm2 OCA], [https://pdbe.org/2xm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xm2 RCSB], [https://www.ebi.ac.uk/pdbsum/2xm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xm2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OGA_BACTN OGA_BACTN] Biological function unknown. Capable of hydrolyzing the glycosidic link of O-GlcNAcylated proteins.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The dynamic, intracellular, O-GlcNAc modification is of continuing interest and one whose study through targeted "chemical genetics" approaches is set to increase. Of particular importance is the inhibition of the O-GlcNAc hydrolase, O-GlcNAcase (OGA), since this provides a route to elevate cellular O-GlcNAc levels, and subsequent phenotypic evaluation. Such a small molecule approach complements other methods and potentially avoids changes in protein-protein interactions that manifest themselves in molecular biological approaches to O-GlcNAc transferase knockout or over-expression. Here we describe the kinetic, thermodynamic and three-dimensional structural analysis of a bacterial OGA analogue from Bacteroides thetaiotaomicron, BtGH84, in complex with a lactone oxime (LOGNAc) and a lactam form of N-acetylglucosamine and compare their binding signatures with that of the more potent inhibitor O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino N-phenyl carbamate (PUGNAc). We show that both LOGNAc and the N-acetyl gluconolactam are significantly poorer inhibitors than PUGNAc, which may reflect poorer mimicry of transition state geometry and steric clashes with the enzyme upon binding; drawbacks that the phenyl carbamate adornment of PUGNAc helps mitigate. Implications for the design of future generations of inhibitors are discussed.
-===BTGH84 IN COMPLEX WITH LOGNAC===
+Inhibition of a bacterial O-GlcNAcase homologue by lactone and lactam derivatives: structural, kinetic and thermodynamic analyses.,He Y, Bubb AK, Stubbs KA, Gloster TM, Davies GJ Amino Acids. 2011 Mar;40(3):829-39. Epub 2010 Aug 6. PMID:20689974<ref>PMID:20689974</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2xm2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20689974}}, adds the Publication Abstract to the page
+*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20689974 is the PubMed ID number.
+*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
--->
+*[[O-GlcNAcase|O-GlcNAcase]]
-{{ABSTRACT_PUBMED_20689974}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[2xm2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XM2 OCA].
+</StructureSection>
+[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-==Reference==
+[[Category: Large Structures]]
-<ref group="xtra">PMID:020689974</ref><references group="xtra"/>
+[[Category: Davies GJ]]
-[[Category: Bacteria]]
+[[Category: He Y]]
-[[Category: Beta-N-acetylhexosaminidase]]
-[[Category: Davies, G J.]]
-[[Category: He, Y.]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Inhibitor]]