2chn: Difference between revisions

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-[[Image:2chn.gif|left|200px]]<br />
-<applet load="2chn" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2chn, resolution 1.95&Aring;" />
-'''BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY- NAG-THIAZOLINE COMPLEX'''<br />
-==Overview==
+==Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity- NAG-thiazoline complex==
-O-GlcNAc is an abundant post-translational modification of serine and, threonine residues of nucleocytoplasmic proteins. This modification, found, only within higher eukaryotes, is a dynamic modification that is often, reciprocal to phosphorylation. In a manner analogous to phosphatases, a, glycoside hydrolase termed O-GlcNAcase cleaves O-GlcNAc from modified, proteins. Enzymes with high sequence similarity to human O-GlcNAcase are, also found in human pathogens and symbionts. We report the, three-dimensional structure of O-GlcNAcase from the human gut symbiont, Bacteroides thetaiotaomicron both in its native form and in complex with a, mimic of the reaction intermediate. Mutagenesis and kinetics studies show, that the bacterial enzyme, very similarly to its human counterpart, operates ... [[http://ispc.weizmann.ac.il/pmbin/getpm?16565725 (full description)]]
+<StructureSection load='2chn' size='340' side='right'caption='[[2chn]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2chn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. The September 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''O-GlcNAc Transferase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_9 10.2210/rcsb_pdb/mom_2011_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CHN 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]] 1.95&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NGT:3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL'>NGT</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=2chn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2chn OCA], [https://pdbe.org/2chn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2chn RCSB], [https://www.ebi.ac.uk/pdbsum/2chn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2chn 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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ch/2chn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2chn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+O-GlcNAc is an abundant post-translational modification of serine and threonine residues of nucleocytoplasmic proteins. This modification, found only within higher eukaryotes, is a dynamic modification that is often reciprocal to phosphorylation. In a manner analogous to phosphatases, a glycoside hydrolase termed O-GlcNAcase cleaves O-GlcNAc from modified proteins. Enzymes with high sequence similarity to human O-GlcNAcase are also found in human pathogens and symbionts. We report the three-dimensional structure of O-GlcNAcase from the human gut symbiont Bacteroides thetaiotaomicron both in its native form and in complex with a mimic of the reaction intermediate. Mutagenesis and kinetics studies show that the bacterial enzyme, very similarly to its human counterpart, operates via an unusual 'substrate-assisted' catalytic mechanism, which will inform the rational design of enzyme inhibitors.
-==About this Structure==
+Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity.,Dennis RJ, Taylor EJ, Macauley MS, Stubbs KA, Turkenburg JP, Hart SJ, Black GN, Vocadlo DJ, Davies GJ Nat Struct Mol Biol. 2006 Apr;13(4):365-71. Epub 2006 Mar 26. PMID:16565725<ref>PMID:16565725</ref>
-CHN is a [[http://en.wikipedia.org/wiki/Protein_complex Protein complex]] structure of sequences from [[http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]] with CA, NGT and GOL as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CHN OCA]].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity., Dennis RJ, Taylor EJ, Macauley MS, Stubbs KA, Turkenburg JP, Hart SJ, Black GN, Vocadlo DJ, Davies GJ, Nat Struct Mol Biol. 2006 Apr;13(4):365-71. Epub 2006 Mar 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16565725 16565725]
+</div>
-[[Category: Bacteroides thetaiotaomicron]]
+<div class="pdbe-citations 2chn" style="background-color:#fffaf0;"></div>
-[[Category: Beta-N-acetylhexosaminidase]]
+== References ==
-[[Category: Protein complex]]
+<references/>
-[[Category: Black, G.N.]]
+__TOC__
-[[Category: Davies, G.J.]]
+</StructureSection>
-[[Category: Dennis, R.J.]]
+[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-[[Category: Hart, S.J.]]
+[[Category: Large Structures]]
-[[Category: Macauley, M.S.]]
+[[Category: O-GlcNAc Transferase]]
-[[Category: Stubbs, K.A.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Taylor, E.J.]]
+[[Category: Black GN]]
-[[Category: Turkenburg, J.P.]]
+[[Category: Davies GJ]]
-[[Category: Vocadlo, D.J.]]
+[[Category: Dennis RJ]]
-[[Category: CA]]
+[[Category: Hart SJ]]
-[[Category: GOL]]
+[[Category: Macauley MS]]
-[[Category: NGT]]
+[[Category: Stubbs KA]]
-[[Category: hydrolase]]
+[[Category: Taylor EJ]]
-[[Category: n-acetylglucosamibe]]
+[[Category: Turkenburg JP]]
-[[Category: o-glcnacase]]
+[[Category: Vocadlo DJ]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 13:25:30 2007''