2ccr: Difference between revisions

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-{{Seed}}
-[[Image:2ccr.png|left|200px]]
-<!--
+==Structure of Beta-1,4-Galactanase==
-The line below this paragraph, containing "STRUCTURE_2ccr", creates the "Structure Box" on the page.
+<StructureSection load='2ccr' size='340' side='right'caption='[[2ccr]], [[Resolution|resolution]] 2.30&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'>[[2ccr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CCR 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]] 2.3&#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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PRD_900113:4beta-beta-galactobiose'>PRD_900113</scene>, <scene name='pdbligand=PRD_900114:4beta-beta-galactotriose'>PRD_900114</scene></td></tr>
-{{STRUCTURE_2ccr|  PDB=2ccr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ccr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ccr OCA], [https://pdbe.org/2ccr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ccr RCSB], [https://www.ebi.ac.uk/pdbsum/2ccr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ccr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GANB_BACLD GANB_BACLD] Involved in galactan degradation (PubMed:15312766). Degrades arabinose-free galactan to galactooligosaccharides, producing galactotetraose as the main product along with galactotriose, galactobiose, and galactose (PubMed:15312766). May hydrolyze the beta-1,4-galactan linkages of the galactan portion of arabinogalactan type I, a pectic plant polysaccharide from which most of the arabinose has been removed (By similarity).[UniProtKB:O07013]<ref>PMID:15312766</ref>
+== 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/cc/2ccr_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=2ccr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Microbial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycoside hydrolases, which cover many different poly- and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis beta-1,4-galactanase and its inactive nucleophile mutant have been obtained with methyl-beta(1--&gt;4)-galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the beta-1,4-galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a beta(1--&gt;4)-galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite -4 to +5. In particular, this analysis newly identified a conserved beta-turn, which contributes to subsites -2 to +3. This beta-turn is unique to family 53 beta-1,4-galactanases among all clan GH-A families that have been structurally characterized and thus might be a structural signature for endo-beta-1,4-galactanase specificity.
-===STRUCTURE OF BETA-1,4-GALACTANASE===
+Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.,Le Nours J, De Maria L, Welner D, Jorgensen CT, Christensen LL, Borchert TV, Larsen S, Lo Leggio L Proteins. 2009 Jun;75(4):977-89. PMID:19089956<ref>PMID:19089956</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ccr" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-CCR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CCR OCA].
+*[[Beta-1%2C4-galactanase|Beta-1%2C4-galactanase]]
-[[Category: Arabinogalactan endo-1,4-beta-galactosidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus licheniformis]]
-[[Category: Christensen, L L.H.]]
+[[Category: Large Structures]]
-[[Category: Jorgensen, C T.]]
+[[Category: Christensen LLH]]
-[[Category: Larsen, S.]]
+[[Category: De Maria L]]
-[[Category: Leggio, L Lo.]]
+[[Category: Jorgensen CT]]
-[[Category: Maria, L De.]]
+[[Category: Larsen S]]
-[[Category: Nours, J Le.]]
+[[Category: Le Nours J]]
-[[Category: Welner, D.]]
+[[Category: Lo Leggio L]]
-[[Category: Beta-1,4-galactanase]]
+[[Category: Welner D]]
-[[Category: Galactan]]
-[[Category: Gh-a]]
-[[Category: Glycoside hydrolase family 53]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:58:18 2009''