2wdb: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2wdb.png|left|200px]]
-<!--
+==A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,2) mannose==
-The line below this paragraph, containing "STRUCTURE_2wdb", creates the "Structure Box" on the page.
+<StructureSection load='2wdb' size='340' side='right'caption='[[2wdb]], [[Resolution|resolution]] 2.03&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'>[[2wdb]] is a 4 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=2WDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WDB 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]] 2.03&#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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_2wdb|  PDB=2wdb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wdb OCA], [https://pdbe.org/2wdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wdb RCSB], [https://www.ebi.ac.uk/pdbsum/2wdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wdb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAGH_CLOPE NAGH_CLOPE] Putative virulence factor which is likely to act on connective tissue during gas gangrene.
+== 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/wd/2wdb_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=2wdb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Many carbohydrate-active enzymes have complex architectures comprising multiple modules that may be involved in catalysis, carbohydrate binding, or protein-protein interactions. Carbohydrate-binding modules (CBMs) are a common ancillary module whose function is to promote the adherence of the complete enzyme to carbohydrate substrates. CBM family 32 has been proposed to be one of the most diverse CBM families classified to date, yet all of the structurally characterized CBM32s thus far recognize galactose-based ligands. Here, we report a unique binding specificity and mode of ligand binding for a family 32 CBM. NagHCBM32-2 is one of four CBM32 modules in NagH, a family 84 glycoside hydrolase secreted by Clostridium perfringens. NagHCBM32-2 has the beta-sandwich scaffold common to members of the family; however, its specificity for N-acetylglucosamine is unusual among CBMs. X-ray crystallographic analysis of the module at resolutions from 1.45 to 2.0 A and in complex with disaccharides reveals that its mode of sugar recognition is quite different from that observed for galactose-specific CBM32s. This study continues to unravel the diversity of CBMs found in family 32 and how these CBMs might impart the carbohydrate-binding specificity to the extracellular glycoside hydrolases in C. perfringens.
-===A FAMILY 32 CARBOHYDRATE-BINDING MODULE, FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH BETA-D-GLCNAC-BETA(1,2)MANNOSE===
+N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.,Ficko-Blean E, Boraston AB J Mol Biol. 2009 Jul 10;390(2):208-20. Epub 2009 May 5. PMID:19422833<ref>PMID:19422833</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wdb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19422833}}, adds the Publication Abstract to the page
+*[[Hyaluronidase 3D structures|Hyaluronidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19422833 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19422833}}
+__TOC__
+</StructureSection>
-==About this Structure==
-WDB is a 4 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=2WDB OCA].
-==Reference==
-<ref group="xtra">PMID:19422833</ref><references group="xtra"/>
 [[Category: Clostridium perfringens]]
-[[Category: Hyalurononglucosaminidase]]
+[[Category: Large Structures]]
-[[Category: Boraston, A B.]]
+[[Category: Boraston AB]]
-[[Category: Ficko-Blean, E.]]
+[[Category: Ficko-Blean E]]
-[[Category: Cbm]]
-[[Category: Clostridium perfringen]]
-[[Category: Family 32 carbohydrate binding module]]
-[[Category: Family 84 glycoside hydrolase]]
-[[Category: Glycosidase]]
-[[Category: Hexosaminidase]]
-[[Category: Hydrolase]]
-[[Category: Secreted]]
-[[Category: Toxin]]
-[[Category: Virulence]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 15:45:12 2009''