2v5c: Difference between revisions

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-{{Seed}}
-[[Image:2v5c.png|left|200px]]
-<!--
+==Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure==
-The line below this paragraph, containing "STRUCTURE_2v5c", creates the "Structure Box" on the page.
+<StructureSection load='2v5c' size='340' side='right'caption='[[2v5c]], [[Resolution|resolution]] 2.10&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'>[[2v5c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V5C 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]] 2.1&#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=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_2v5c|  PDB=2v5c  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v5c OCA], [https://pdbe.org/2v5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v5c RCSB], [https://www.ebi.ac.uk/pdbsum/2v5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v5c 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/v5/2v5c_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=2v5c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.
-===FAMILY 84 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS, 2.1 ANGSTROM STRUCTURE===
+Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens.,Ficko-Blean E, Gregg KJ, Adams JJ, Hehemann JH, Czjzek M, Smith SP, Boraston AB J Biol Chem. 2009 Apr 10;284(15):9876-84. Epub 2009 Feb 4. PMID:19193644<ref>PMID:19193644</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2v5c" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19193644}}, adds the Publication Abstract to the page
+*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19193644 is the PubMed ID number.
+*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
--->
+*[[O-GlcNAcase|O-GlcNAcase]]
-{{ABSTRACT_PUBMED_19193644}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-V5C is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V5C OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:19193644</ref><references group="xtra"/>
-[[Category: Beta-N-acetylhexosaminidase]]
 [[Category: Clostridium perfringens]]
-[[Category: Adams, J J.]]
+[[Category: Large Structures]]
-[[Category: Boraston, A B.]]
+[[Category: Adams JJ]]
-[[Category: Czjzek, M.]]
+[[Category: Boraston AB]]
-[[Category: Ficko-Blean, E.]]
+[[Category: Czjzek M]]
-[[Category: Gregg, K J.]]
+[[Category: Ficko-Blean E]]
-[[Category: Hehemann, J H.]]
+[[Category: Gregg KJ]]
-[[Category: Smith, S J.]]
+[[Category: Hehemann JH]]
-[[Category: Carbohydrate binding module]]
+[[Category: Smith SJ]]
-[[Category: Clostridium perfringen]]
-[[Category: Coiled coil]]
-[[Category: Family 84 glycoside hydrolase]]
-[[Category: Gh84]]
-[[Category: Gh84c]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:48:53 2009''