1z3w: Difference between revisions

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-[[Image:1z3w.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1z3w", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1z3w|  PDB=1z3w  |  SCENE=  }}
-'''Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobioimidazole'''
+==Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobioimidazole==
+<StructureSection load='1z3w' size='340' side='right'caption='[[1z3w]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1z3w]] is a 1 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=1Z3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z3W FirstGlance]. <br>
+</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=IDC:5-HYDROXYMETHYL-5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDIN-6YL-7,8-DIOL-GLUCOPYRANOSIDE'>IDC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z3w OCA], [https://pdbe.org/1z3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z3w RCSB], [https://www.ebi.ac.uk/pdbsum/1z3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z3w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7LIJ0_PHACH Q7LIJ0_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/z3/1z3w_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=1z3w ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The cellobiohydrolase Pc_Cel7D is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10% of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycoside hydrolases and, like other family members, catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration. Previous work described the apo structure of the enzyme. Here we investigate the binding of the product, cellobiose, and several inhibitors, i.e. lactose, cellobioimidazole, Tris/HCl, calcium and a thio-linked substrate analogue, methyl 4-S-beta-cellobiosyl-4-thio-beta-cellobioside (GG-S-GG). The three disaccharides bind in the glucosyl-binding subsites +1 and +2, close to the exit of the cellulose-binding tunnel/cleft. Pc_Cel7D binds to lactose more strongly than cellobiose, while the opposite is true for the homologous Trichoderma reesei cellobiohydrolase Tr_Cel7A. Although both sugars bind Pc_Cel7D in a similar fashion, the different preferences can be explained by varying interactions with nearby loops. Cellobioimidazole is bound at a slightly different position, displaced approximately 2 A toward the catalytic centre. Thus the Pc_Cel7D complexes provide evidence for two binding modes of the reducing-end cellobiosyl moiety; this conclusion is confirmed by comparison with other available structures. The combined results suggest that hydrolysis of the glycosyl-enzyme intermediate may not require the prior release of the cellobiose product from the enzyme. Further, the structure obtained in the presence of both GG-S-GG and cellobiose revealed electron density for Tris at the catalytic centre. Inhibition experiments confirm that both Tris and calcium are effective inhibitors at the conditions used for crystallization.
-==Overview==
+Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors.,Ubhayasekera W, Munoz IG, Vasella A, Stahlberg J, Mowbray SL FEBS J. 2005 Apr;272(8):1952-64. PMID:15819888<ref>PMID:15819888</ref>
-The cellobiohydrolase Pc_Cel7D is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10% of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycoside hydrolases and, like other family members, catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration. Previous work described the apo structure of the enzyme. Here we investigate the binding of the product, cellobiose, and several inhibitors, i.e. lactose, cellobioimidazole, Tris/HCl, calcium and a thio-linked substrate analogue, methyl 4-S-beta-cellobiosyl-4-thio-beta-cellobioside (GG-S-GG). The three disaccharides bind in the glucosyl-binding subsites +1 and +2, close to the exit of the cellulose-binding tunnel/cleft. Pc_Cel7D binds to lactose more strongly than cellobiose, while the opposite is true for the homologous Trichoderma reesei cellobiohydrolase Tr_Cel7A. Although both sugars bind Pc_Cel7D in a similar fashion, the different preferences can be explained by varying interactions with nearby loops. Cellobioimidazole is bound at a slightly different position, displaced approximately 2 A toward the catalytic centre. Thus the Pc_Cel7D complexes provide evidence for two binding modes of the reducing-end cellobiosyl moiety; this conclusion is confirmed by comparison with other available structures. The combined results suggest that hydrolysis of the glycosyl-enzyme intermediate may not require the prior release of the cellobiose product from the enzyme. Further, the structure obtained in the presence of both GG-S-GG and cellobiose revealed electron density for Tris at the catalytic centre. Inhibition experiments confirm that both Tris and calcium are effective inhibitors at the conditions used for crystallization.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Z3W is a [[Single protein]] structure of 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=1Z3W OCA].
+</div>
+<div class="pdbe-citations 1z3w" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors., Ubhayasekera W, Munoz IG, Vasella A, Stahlberg J, Mowbray SL, FEBS J. 2005 Apr;272(8):1952-64. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15819888 15819888]
+*[[Cellobiohydrolase 3D structures|Cellobiohydrolase 3D structures]]
-[[Category: Cellulose 1,4-beta-cellobiosidase]]
+== References ==
-[[Category: Phanerochaete chrysosporium]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Mowbray, S L.]]
+</StructureSection>
-[[Category: Stahlberg, J.]]
+[[Category: Large Structures]]
-[[Category: Ubhayasekera, W.]]
+[[Category: Phanerodontia chrysosporium]]
-[[Category: Vasella, A.]]
+[[Category: Mowbray SL]]
-[[Category: Beta sandwich]]
+[[Category: Stahlberg J]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 17:09:15 2008''
+[[Category: Ubhayasekera W]]
+[[Category: Vasella A]]