1kqy: Difference between revisions

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-{{Seed}}
-[[Image:1kqy.png|left|200px]]
-<!--
+==Hevamine Mutant D125A/E127A/Y183F in Complex with Penta-NAG==
-The line below this paragraph, containing "STRUCTURE_1kqy", creates the "Structure Box" on the page.
+<StructureSection load='1kqy' size='340' side='right'caption='[[1kqy]], [[Resolution|resolution]] 1.92&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'>[[1kqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQY 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]] 1.92&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1kqy|  PDB=1kqy  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqy OCA], [https://pdbe.org/1kqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqy RCSB], [https://www.ebi.ac.uk/pdbsum/1kqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CHLY_HEVBR CHLY_HEVBR] Bifunctional enzyme with lysozyme / chitinase activity. May have a role in plugging the latex vessel and cessation of latex flow.
+== 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/kq/1kqy_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=1kqy ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the -1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli. After refolding and purification they were characterized by both structural and enzyme kinetic studies. Mutation of Tyr183 to phenylalanine produced an enzyme with a lower k(cat) and a slightly higher K(m) than the wild-type enzyme. Mutating Asp125 and Glu127 to alanine gave mutants with approximately 2% residual activity. In contrast, the Asp125Asn mutant retained substantial activity, with an approximately twofold lower k(cat) and an approximately twofold higher K(m) than the wild-type enzyme. More interestingly, it showed activity to higher pH values than the other variants. The X-ray structure of the Asp125Ala/Glu127Ala double mutant soaked with chitotetraose shows that, compared with wild-type hevamine, the carbonyl oxygen atom of the N-acetyl group of the -1 sugar residue has rotated away from the C1 atom of that residue. The combined structural and kinetic data show that Asp125 and Tyr183 contribute to catalysis by positioning the carbonyl oxygen of the N-acetyl group near to the C1 atom. This allows the stabilization of a positively charged transient intermediate, in agreement with a previous proposal that the enzyme makes use of substrate-assisted catalysis.
-===Hevamine Mutant D125A/E127A/Y183F in Complex with Penta-NAG===
+Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis.,Bokma E, Rozeboom HJ, Sibbald M, Dijkstra BW, Beintema JJ Eur J Biochem. 2002 Feb;269(3):893-901. PMID:11846790<ref>PMID:11846790</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_11846790}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1kqy" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11846790 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11846790}}
+__TOC__
+</StructureSection>
-==About this Structure==
-KQY is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Hevea_brasiliensis Hevea brasiliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQY OCA].
-==Reference==
-<ref group="xtra">PMID:11846790</ref><references group="xtra"/>
 [[Category: Hevea brasiliensis]]
-[[Category: Dijkstra, B W.]]
+[[Category: Large Structures]]
-[[Category: Rozeboom, H J.]]
+[[Category: Dijkstra BW]]
-[[Category: Chitinase/lysozyme]]
+[[Category: Rozeboom HJ]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:49:07 2009''