3a4a: Difference between revisions

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-[[Image:3a4a.png|left|200px]]
-<!--
+==Crystal structure of isomaltase from Saccharomyces cerevisiae==
-The line below this paragraph, containing "STRUCTURE_3a4a", creates the "Structure Box" on the page.
+<StructureSection load='3a4a' size='340' side='right'caption='[[3a4a]], [[Resolution|resolution]] 1.60&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'>[[3a4a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A4A 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
-{{STRUCTURE_3a4a|  PDB=3a4a  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4a OCA], [https://pdbe.org/3a4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a4a RCSB], [https://www.ebi.ac.uk/pdbsum/3a4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4a ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MALX3_YEAST MALX3_YEAST] Major isomaltase (alpha-1,6-glucosidase) required for isomaltose utilization. Preferentially hydrolyzes isomaltose, palatinose, and methyl-alpha-glucoside, with little activity towards isomaltotriose or longer oligosaccharides. Does not hydrolyze maltose.<ref>PMID:15291818</ref> <ref>PMID:20562106</ref>
+== 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/a4/3a4a_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3a4a ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of isomaltase from Saccharomyces cerevisiae and in complex with maltose were determined at resolutions of 1.30 and 1.60 A, respectively. Isomaltase contains three domains, namely, A, B, and C. Domain A consists of the (beta/alpha)(8) -barrel common to glycoside hydrolase family 13. However, the folding of domain C is rarely seen in other glycoside hydrolase family 13 enzymes. An electron density corresponding to a nonreducing end glucose residue was observed in the active site of isomaltase in complex with maltose; however, only incomplete density was observed for the reducing end. The active site pocket contains two water chains. One water chain is a water path from the bottom of the pocket to the surface of the protein, and may act as a water drain during substrate binding. The other water chain, which consists of six water molecules, is located near the catalytic residues Glu277 and Asp352. These water molecules may act as a reservoir that provides water for subsequent hydrolytic events. The best substrate for oligo-1,6-glucosidase is isomaltotriose; other, longer-chain, oligosaccharides are also good substrates. However, isomaltase shows the highest activity towards isomaltose and very little activity towards longer oligosaccharides. This is because the entrance to the active site pocket of isomaltose is severely narrowed by Tyr158, His280, and loop 310-315, and because the isomaltase pocket is shallower than that of other oligo-1,6-glucosidases. These features of the isomaltase active site pocket prevent isomalto-oligosaccharides from binding to the active site effectively.
-===Crystal structure of isomaltase from Saccharomyces cerevisiae===
+Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.,Yamamoto K, Miyake H, Kusunoki M, Osaki S FEBS J. 2010 Oct;277(20):4205-14. doi: 10.1111/j.1742-4658.2010.07810.x., Epub 2010 Aug 31. PMID:20812985<ref>PMID:20812985</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3a4a" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20812985}}, adds the Publication Abstract to the page
+*[[Alpha-glucosidase|Alpha-glucosidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20812985 is the PubMed ID number.
+*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_20812985}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[3a4a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4A OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:20812985</ref><references group="xtra"/>
-[[Category: Oligo-1,6-glucosidase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Kusunoki, M.]]
+[[Category: Kusunoki M]]
-[[Category: Miyake, H.]]
+[[Category: Miyake H]]
-[[Category: Osaki, S.]]
+[[Category: Osaki S]]
-[[Category: Yamamoto, K.]]
+[[Category: Yamamoto K]]