2vng: Difference between revisions

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-{{Seed}}
-[[Image:2vng.jpg|left|200px]]
-<!--
+==Family 51 carbohydrate binding module from a family 98 glycoside hydrolase produced by Clostridium perfringens in complex with blood group A-trisaccharide ligand.==
-The line below this paragraph, containing "STRUCTURE_2vng", creates the "Structure Box" on the page.
+<StructureSection load='2vng' size='340' side='right'caption='[[2vng]], [[Resolution|resolution]] 1.40&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'>[[2vng]] 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=2VNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VNG 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]] 1.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <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></td></tr>
-{{STRUCTURE_2vng|  PDB=2vng  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vng OCA], [https://pdbe.org/2vng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vng RCSB], [https://www.ebi.ac.uk/pdbsum/2vng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vng ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8XNK4_CLOPE Q8XNK4_CLOPE]
+== 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/vn/2vng_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=2vng ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The genomes of myonecrotic Clostridium perfringens isolates contain genes encoding a large and fascinating array of highly modular glycoside hydrolase enzymes. Although the catalytic activities of many of these enzymes are somewhat predictable based on their amino acid sequences, the functions of their abundant ancillary modules are not and remain poorly studied. Here, we present the structural and functional analysis of a new family of ancillary carbohydrate-binding modules (CBMs), CBM51, which was previously annotated in data bases as the novel putative CBM domain. The high resolution crystal structures of two CBM51 members, GH95CBM51 and GH98CBM51, from a putative family 95 alpha-fucosidase and from a family 98 blood group A/B antigen-specific endo-beta-galactosidase, respectively, showed them to have highly similar beta-sandwich folds. However, GH95CBM51 was shown by glycan microarray screening, isothermal titration calorimetry, and x-ray crystallography to bind galactose residues, whereas the same analyses of GH98CBM51 revealed specificity for the blood group A/B antigens through non-conserved interactions. Overall, this work identifies a new family of CBMs with many members having apparent specificity for eukaryotic glycans, in keeping with the glycan-rich environment C. perfringens would experience in its host. However, a wider bioinformatic analysis of this CBM family also indicated a large number of members in non-pathogenic environmental bacteria, suggesting a role in the recognition of environmental glycans.
-===FAMILY 51 CARBOHYDRATE BINDING MODULE FROM A FAMILY 98 GLYCOSIDE HYDROLASE PRODUCED BY CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH BLOOD GROUP A-TRISACCHARIDE LIGAND.===
+Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.,Gregg KJ, Finn R, Abbott DW, Boraston AB J Biol Chem. 2008 May 2;283(18):12604-13. Epub 2008 Feb 21. PMID:18292090<ref>PMID:18292090</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18292090}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vng" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18292090 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18292090}}
+__TOC__
+</StructureSection>
-==About this Structure==
-VNG is a [[Single protein]] structure of sequence 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=2VNG OCA].
-==Reference==
-Divergent modes of glycan recognition by a new family of carbohydrate-binding modules., Gregg KJ, Finn R, Abbott DW, Boraston AB, J Biol Chem. 2008 Feb 21;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18292090 18292090]
 [[Category: Clostridium perfringens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Abbott, D W.]]
+[[Category: Abbott DW]]
-[[Category: Boraston, A B.]]
+[[Category: Boraston AB]]
-[[Category: Finn, R.]]
+[[Category: Finn R]]
-[[Category: Gregg, K J.]]
+[[Category: Gregg KJ]]
-[[Category: A-trisaccharide]]
-[[Category: Blood group antigen]]
-[[Category: Clostridium perfringen]]
-[[Category: Family 51 carbohydrate binding module]]
-[[Category: Family 98 glycoside hydrolase]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 18:36:23 2008''