2j7m: Difference between revisions

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-[[Image:2j7m.gif|left|200px]]<br />
-<applet load="2j7m" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2j7m, resolution 2.30&Aring;" />
-'''CHARACTERIZATION OF A FAMILY 32 CBM'''<br />
-==Overview==
+==Characterization of a Family 32 CBM==
-Clostridium perfringens is a notable colonizer of the human, gastrointestinal tract. This bacterium is quite remarkable for a human, pathogen by the number of glycoside hydrolases found in its genome. The, modularity of these enzymes is striking as is the frequent occurrence of, modules having amino acid sequence identity with family 32, carbohydrate-binding modules (CBMs), often referred to as F5/8 domains., Here we report the properties of family 32 CBMs from a C. perfringens, N-acetyl-beta-hexosaminidase. Macroarray, UV difference, and isothermal, titration calorimetry binding studies indicate a preference for the, disaccharide LacNAc (beta-d-galactosyl-1,4-beta-d-N-acetylglucosamine)., The molecular details of the interaction of this CBM with galactose, LacNAc, and the type II blood ... [[http://ispc.weizmann.ac.il/pmbin/getpm?16990278 (full description)]]
+<StructureSection load='2j7m' size='340' side='right'caption='[[2j7m]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2j7m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2j1f 2j1f]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J7M 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]] 2.3&#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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=PRD_900125:H+type+2+antigen,+alpha+anomer'>PRD_900125</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=2j7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j7m OCA], [https://pdbe.org/2j7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j7m RCSB], [https://www.ebi.ac.uk/pdbsum/2j7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j7m 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.
+== 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/j7/2j7m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2j7m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Clostridium perfringens is a notable colonizer of the human gastrointestinal tract. This bacterium is quite remarkable for a human pathogen by the number of glycoside hydrolases found in its genome. The modularity of these enzymes is striking as is the frequent occurrence of modules having amino acid sequence identity with family 32 carbohydrate-binding modules (CBMs), often referred to as F5/8 domains. Here we report the properties of family 32 CBMs from a C. perfringens N-acetyl-beta-hexosaminidase. Macroarray, UV difference, and isothermal titration calorimetry binding studies indicate a preference for the disaccharide LacNAc (beta-d-galactosyl-1,4-beta-d-N-acetylglucosamine). The molecular details of the interaction of this CBM with galactose, LacNAc, and the type II blood group H-trisaccharide are revealed by x-ray crystallographic studies at resolutions of 1.49, 2.4, and 2.3 A, respectively.
-==About this Structure==
+The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor.,Ficko-Blean E, Boraston AB J Biol Chem. 2006 Dec 8;281(49):37748-57. Epub 2006 Sep 21. PMID:16990278<ref>PMID:16990278</ref>
-J7M is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]] with CA as [[http://en.wikipedia.org/wiki/ligand ligand]]. This structure superseeds the now removed PDB entry 2J1F. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2J7M OCA]].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor., Ficko-Blean E, Boraston AB, J Biol Chem. 2006 Dec 8;281(49):37748-57. Epub 2006 Sep 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16990278 16990278]
+</div>
+<div class="pdbe-citations 2j7m" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Hyaluronidase 3D structures|Hyaluronidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Clostridium perfringens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Boraston, A.B.]]
+[[Category: Boraston AB]]
-[[Category: Ficko-Blean, E.]]
+[[Category: Ficko-Blean E]]
-[[Category: CA]]
-[[Category: carbohydrate binding]]
-[[Category: cbm]]
-[[Category: glycoside hydrolase]]
-[[Category: h-trisaccharide]]
-[[Category: hydrolase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 21:37:05 2007''