3eqn: Difference between revisions

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-[[Image:3eqn.png|left|200px]]
-<!--
+==Crystal structure of beta-1,3-glucanase from Phanerochaete chrysosporium (Lam55A)==
-The line below this paragraph, containing "STRUCTURE_3eqn", creates the "Structure Box" on the page.
+<StructureSection load='3eqn' size='340' side='right'caption='[[3eqn]], [[Resolution|resolution]] 1.70&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'>[[3eqn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phanerodontia_chrysosporium Phanerodontia chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EQN 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3eqn|  PDB=3eqn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eqn OCA], [https://pdbe.org/3eqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eqn RCSB], [https://www.ebi.ac.uk/pdbsum/3eqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eqn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q2Z1W1_PHACH Q2Z1W1_PHACH]
+== 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/eq/3eqn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3eqn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glycoside hydrolase family 55 consists of beta-1,3-glucanases mainly from filamentous fungi. A beta-1,3-glucanase (Lam55A) from the Basidiomycete Phanerochaete chrysosporium hydrolyzes beta-1,3-glucans in the exo-mode with inversion of anomeric configuration and produces gentiobiose in addition to glucose from beta-1,3/1,6-glucans. Here we report the crystal structure of Lam55A, establishing the three-dimensional structure of a member of glycoside hydrolase 55 for the first time. Lam55A has two beta-helical domains in a single polypeptide chain. These two domains are separated by a long linker region but are positioned side by side, and the overall structure resembles a rib cage. In the complex, a gluconolactone molecule is bound at the bottom of a pocket between the two beta-helical domains. Based on the position of the gluconolactone molecule, Glu-633 appears to be the catalytic acid, whereas the catalytic base residue could not be identified. The substrate binding pocket appears to be able to accept a gentiobiose unit near the cleavage site, and a long cleft runs from the pocket, in accordance with the activity of this enzyme toward various beta-1,3-glucan oligosaccharides. In conclusion, we provide important features of the substrate-binding site at the interface of the two beta-helical domains, demonstrating an unexpected variety of carbohydrate binding modes.
-===Crystal structure of beta-1,3-glucanase from Phanerochaete chrysosporium (Lam55A)===
+Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.,Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, Samejima M J Biol Chem. 2009 Apr 10;284(15):10100-9. Epub 2009 Feb 4. PMID:19193645<ref>PMID:19193645</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3eqn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19193645}}, adds the Publication Abstract to the page
+*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19193645 is the PubMed ID number.
+*[[Glucanase 3D structures|Glucanase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19193645}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[3eqn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Phanerochaete_chrysosporium Phanerochaete chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EQN OCA].
+[[Category: Large Structures]]
+[[Category: Phanerodontia chrysosporium]]
-==Reference==
+[[Category: Fushinobu S]]
-<ref group="xtra">PMID:19193645</ref><ref group="xtra">PMID:16614901</ref><references group="xtra"/>
+[[Category: Igarashi K]]
-[[Category: Glucan 1,3-beta-glucosidase]]
+[[Category: Ishida T]]
-[[Category: Phanerochaete chrysosporium]]
+[[Category: Kawai R]]
-[[Category: Fushinobu, S.]]
+[[Category: Kitaoka M]]
-[[Category: Igarashi, K.]]
+[[Category: Samejima M]]
-[[Category: Ishida, T.]]
-[[Category: Kawai, R.]]
-[[Category: Kitaoka, M.]]
-[[Category: Samejima, M.]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Tandem beta-helix domain]]