1dy4: Difference between revisions

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-[[Image:1dy4.png|left|200px]]
-<!--
+==CBH1 IN COMPLEX WITH S-PROPRANOLOL==
-The line below this paragraph, containing "STRUCTURE_1dy4", creates the "Structure Box" on the page.
+<StructureSection load='1dy4' size='340' side='right'caption='[[1dy4]], [[Resolution|resolution]] 1.90&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'>[[1dy4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei_QM9414 Trichoderma reesei QM9414]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DY4 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SNP:1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL'>SNP</scene></td></tr>
-{{STRUCTURE_1dy4|  PDB=1dy4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dy4 OCA], [https://pdbe.org/1dy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dy4 RCSB], [https://www.ebi.ac.uk/pdbsum/1dy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dy4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GUX1_HYPJE GUX1_HYPJE] The biological conversion of cellulose to glucose generally requires three types of hydrolytic enzymes: (1) Endoglucanases which cut internal beta-1,4-glucosidic bonds; (2) Exocellobiohydrolases that cut the dissaccharide cellobiose from the non-reducing end of the cellulose polymer chain; (3) Beta-1,4-glucosidases which hydrolyze the cellobiose and other short cello-oligosaccharides to glucose.
+== 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/dy/1dy4_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=1dy4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cellobiohydrolase Cel7A (previously called CBH 1), the major cellulase produced by the mould fungus Trichoderma reesei, has been successfully exploited as a chiral selector for separation of stereo-isomers of some important pharmaceutical compounds, e.g. adrenergic beta-blockers. Previous investigations, including experiments with catalytically deficient mutants of Cel7A, point unanimously to the active site as being responsible for discrimination of enantiomers.In this work the structural basis for enantioselectivity of basic drugs by Cel7A has been studied by X-ray crystallography. The catalytic domain of Cel7A was co-crystallised with the (S)-enantiomer of a common beta-blocker, propranolol, at pH 7, and the structure of the complex was determined and refined at 1. 9 A resolution. Indeed, (S)-propranolol binds at the active site, in glucosyl-binding subsites -1/+1. The catalytic residues Glu212 and Glu217 make tight salt links with the secondary amino group of (S)-propranolol. The oxygen atom attached to the chiral centre of (S)-propranolol forms hydrogen bonds to the nucleophile Glu212 O(epsilon1) and to Gln175 N(epsilon2), whereas the aromatic naphthyl moiety stacks with the indole ring of Trp376 in site +1. The bidentate charge interaction with the catalytic glutamate residues is apparently crucial, since no enantioselectivity has been obtained with the catalytically deficient mutants E212Q and E217Q.Activity inhibition experiments with wild-type Cel7A were performed in conditions close to those used for crystallisation. Competitive inhibition constants for (R)- and (S)-propranolol were determined at 220 microM and 44 microM, respectively, corresponding to binding free energies of 20 kJ/mol and 24 kJ/mol, respectively. The K(i) value for (R)-propranolol was 57-fold lower than the highest concentration, 12.5 mM, used in co-crystallisation experiments. Still several attempts to obtain a complex with the (R)-enantiomer have failed.By using cellobiose as a selective competing ligand, the retention of the enantiomers of propranolol on the chiral stationary phase (CSP) based on Cel7A mutant D214N were resolved into enantioselective and non- selective binding. The enantioselective binding was weaker for both enantiomers on D214N-CSP than on wild-type-CSP.
-===CBH1 IN COMPLEX WITH S-PROPRANOLOL===
+Structural basis for enantiomer binding and separation of a common beta-blocker: crystal structure of cellobiohydrolase Cel7A with bound (S)-propranolol at 1.9 A resolution.,Stahlberg J, Henriksson H, Divne C, Isaksson R, Pettersson G, Johansson G, Jones TA J Mol Biol. 2001 Jan 5;305(1):79-93. PMID:11114249<ref>PMID:11114249</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_11114249}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1dy4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11114249 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11114249}}
-==About this Structure==
-[[1dy4]] is a 1 chain structure of [[Glucanase]] with sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DY4 OCA].
 ==See Also==
-*[[Glucanase]]
+*[[Cellobiohydrolase 3D structures|Cellobiohydrolase 3D structures]]
+*[[Glucanase 3D structures|Glucanase 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:011114249</ref><ref group="xtra">PMID:009466911</ref><ref group="xtra">PMID:008036495</ref><references group="xtra"/>
+<references/>
-[[Category: Cellulose 1,4-beta-cellobiosidase]]
+__TOC__
-[[Category: Hypocrea jecorina]]
+</StructureSection>
-[[Category: Divne, C.]]
+[[Category: Large Structures]]
-[[Category: Henriksson, H.]]
+[[Category: Trichoderma reesei QM9414]]
-[[Category: Isaksson, R.]]
+[[Category: Divne C]]
-[[Category: Johansson, G.]]
+[[Category: Henriksson H]]
-[[Category: Jones, T A.]]
+[[Category: Isaksson R]]
-[[Category: Pettersson, G.]]
+[[Category: Johansson G]]
-[[Category: Stahlberg, J.]]
+[[Category: Jones TA]]
-[[Category: Cellulose deagradation]]
+[[Category: Pettersson G]]
-[[Category: Chiral separation]]
+[[Category: Stahlberg J]]
-[[Category: Glycoprotein]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]