1e6q: Difference between revisions

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-[[Image:1e6q.png|left|200px]]
-<!--
+==MYROSINASE FROM SINAPIS ALBA with the bound transition state analogue gluco-tetrazole==
-The line below this paragraph, containing "STRUCTURE_1e6q", creates the "Structure Box" on the page.
+<StructureSection load='1e6q' size='340' side='right'caption='[[1e6q]], [[Resolution|resolution]] 1.35&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'>[[1e6q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinapis_alba Sinapis alba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6Q 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]] 1.35&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NTZ:NOJIRIMYCINE+TETRAZOLE'>NTZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1e6q|  PDB=1e6q  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6q OCA], [https://pdbe.org/1e6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6q RCSB], [https://www.ebi.ac.uk/pdbsum/1e6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6q ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYRA_SINAL MYRA_SINAL] Degradation of glucosinolates (glucose residue linked by a thioglucoside bound to an amino acid derivative) to glucose, sulfate and any of the products: thiocyanates, isothiocyanates, nitriles, epithionitriles or oxazolidine-2-thiones.
+== 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/e6/1e6q_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=1e6q ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Myrosinase, an S-glycosidase, hydrolyzes plant anionic 1-thio-beta-d-glucosides (glucosinolates) considered part of the plant defense system. Although O-glycosidases are ubiquitous, myrosinase is the only known S-glycosidase. Its active site is very similar to that of retaining O-glycosidases, but one of the catalytic residues in O-glycosidases, a carboxylate residue functioning as the general base, is replaced by a glutamine residue. Myrosinase is strongly activated by ascorbic acid. Several binary and ternary complexes of myrosinase with different transition state analogues and ascorbic acid have been analyzed at high resolution by x-ray crystallography along with a 2-deoxy-2-fluoro-glucosyl enzyme intermediate. One of the inhibitors, d-gluconhydroximo-1,5-lactam, binds simultaneously with a sulfate ion to form a mimic of the enzyme-substrate complex. Ascorbate binds to a site distinct from the glucose binding site but overlapping with the aglycon binding site, suggesting that activation occurs at the second step of catalysis, i.e. hydrolysis of the glycosyl enzyme. A water molecule is placed perfectly for activation by ascorbate and for nucleophilic attack on the covalently trapped 2-fluoro-glucosyl-moiety. Activation of the hydrolysis of the glucosyl enzyme intermediate is further evidenced by the observation that ascorbate enhances the rate of reactivation of the 2-fluoro-glycosyl enzyme, leading to the conclusion that ascorbic acid substitutes for the catalytic base in myrosinase.
-===MYROSINASE FROM SINAPIS ALBA WITH THE BOUND TRANSITION STATE ANALOGUE GLUCO-TETRAZOLE===
+High resolution X-ray crystallography shows that ascorbate is a cofactor for myrosinase and substitutes for the function of the catalytic base.,Burmeister WP, Cottaz S, Rollin P, Vasella A, Henrissat B J Biol Chem. 2000 Dec 15;275(50):39385-93. PMID:10978344<ref>PMID:10978344</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_10978344}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1e6q" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10978344 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10978344}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1e6q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinapis_alba Sinapis alba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6Q OCA].
-==Reference==
-<ref group="xtra">PMID:10978344</ref><ref group="xtra">PMID:9195886</ref><references group="xtra"/>
 [[Category: Sinapis alba]]
-[[Category: Thioglucosidase]]
+[[Category: Burmeister WP]]
-[[Category: Burmeister, W P.]]
-[[Category: 5-lactone]]
-[[Category: D-glucono-1]]
-[[Category: Family 1 glycosyl hydrolase]]
-[[Category: Glucosinolate]]
-[[Category: Hydrolase]]
-[[Category: Myrosinase]]
-[[Category: Tim barrel]]
-[[Category: Transition state]]