2bod: Difference between revisions

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-[[Image:2bod.gif|left|200px]]<br /><applet load="2bod" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2bod, resolution 1.50&Aring;" />
-'''CATALYTIC DOMAIN OF ENDO-1,4-GLUCANASE CEL6A FROM THERMOBIFIDA FUSCA IN COMPLEX WITH METHYL CELLOBIOSYL-4-THIO-BETA-CELLOBIOSIDE'''<br />
-==Overview==
+==Catalytic domain of endo-1,4-glucanase Cel6A from Thermobifida fusca in complex with methyl cellobiosyl-4-thio-beta-cellobioside==
-Endoglucanase Cel6A from Thermobifida fusca hydrolyzes the beta-1,4, linkages in cellulose at accessible points along the polymer. The, structure of the catalytic domain of Cel6A from T. fusca in complex with a, nonhydrolysable substrate analogue that acts as an inhibitor, methylcellobiosyl-4-thio-beta-cellobioside (Glc(2)-S-Glc(2)), has been, determined to 1.5 A resolution. The glycosyl unit in subsite -1 was, sterically hindered by Tyr73 and forced into a distorted (2)S(o), conformation. In the enzyme where Tyr73 was mutated to a serine residue, the hindrance was removed and the glycosyl unit in subsite -1 had a, relaxed (4)C(1) chair conformation. The relaxed conformation was seen in, two complex structures of the mutated enzyme, with cellotetrose (Glc(4)), at 1.64 A and Glc(2)-S-Glc(2) at 1.04 A resolution.
+<StructureSection load='2bod' size='340' side='right'caption='[[2bod]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2bod]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobifida_fusca Thermobifida fusca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BOD 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=MGL:O1-METHYL-GLUCOSE'>MGL</scene>, <scene name='pdbligand=SGC:4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE'>SGC</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=2bod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bod OCA], [https://pdbe.org/2bod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bod RCSB], [https://www.ebi.ac.uk/pdbsum/2bod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bod ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GUN2_THEFU GUN2_THEFU]
+== 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/bo/2bod_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=2bod ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Endoglucanase Cel6A from Thermobifida fusca hydrolyzes the beta-1,4 linkages in cellulose at accessible points along the polymer. The structure of the catalytic domain of Cel6A from T. fusca in complex with a nonhydrolysable substrate analogue that acts as an inhibitor, methylcellobiosyl-4-thio-beta-cellobioside (Glc(2)-S-Glc(2)), has been determined to 1.5 A resolution. The glycosyl unit in subsite -1 was sterically hindered by Tyr73 and forced into a distorted (2)S(o) conformation. In the enzyme where Tyr73 was mutated to a serine residue, the hindrance was removed and the glycosyl unit in subsite -1 had a relaxed (4)C(1) chair conformation. The relaxed conformation was seen in two complex structures of the mutated enzyme, with cellotetrose (Glc(4)) at 1.64 A and Glc(2)-S-Glc(2) at 1.04 A resolution.
-==About this Structure==
+Crystal structure of Thermobifida fusca endoglucanase Cel6A in complex with substrate and inhibitor: the role of tyrosine Y73 in substrate ring distortion.,Larsson AM, Bergfors T, Dultz E, Irwin DC, Roos A, Driguez H, Wilson DB, Jones TA Biochemistry. 2005 Oct 4;44(39):12915-22. PMID:16185060<ref>PMID:16185060</ref>
-BOD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermobifida_fusca Thermobifida fusca]. Active as [http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] Known structural/functional Site: <scene name='pdbsite=AC1:Bgc+Binding+Site+For+Chain+X'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BOD OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of Thermobifida fusca endoglucanase Cel6A in complex with substrate and inhibitor: the role of tyrosine Y73 in substrate ring distortion., Larsson AM, Bergfors T, Dultz E, Irwin DC, Roos A, Driguez H, Wilson DB, Jones TA, Biochemistry. 2005 Oct 4;44(39):12915-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16185060 16185060]
+</div>
-[[Category: Cellulase]]
+<div class="pdbe-citations 2bod" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+==See Also==
+*[[Glucanase 3D structures|Glucanase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermobifida fusca]]
-[[Category: Bergfors, T.]]
+[[Category: Bergfors T]]
-[[Category: Driguez, H.]]
+[[Category: Driguez H]]
-[[Category: Dultz, E.]]
+[[Category: Dultz E]]
-[[Category: Irwin, D.C.]]
+[[Category: Irwin DC]]
-[[Category: Jones, T.A.]]
+[[Category: Jones TA]]
-[[Category: Larsson, A.M.]]
+[[Category: Larsson AM]]
-[[Category: Roos, A.]]
+[[Category: Roos A]]
-[[Category: Wilson, D.B.]]
+[[Category: Wilson DB]]
-[[Category: carbohydrate metabolism]]
-[[Category: cellulose degradation]]
-[[Category: endoglucanase]]
-[[Category: glycosidase]]
-[[Category: glycoside hydrolase family 6]]
-[[Category: hydrolase]]
-[[Category: methyl cellobiosyl-4-thio-beta-cellobioside]]
-[[Category: polysaccharide degradation]]
-[[Category: thermobifida fusca]]
-[[Category: tim a/b fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:26:18 2008''