2jkp: Difference between revisions

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-{{Seed}}
-[[Image:2jkp.jpg|left|200px]]
-<!--
+==Structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron in complex with castanospermine==
-The line below this paragraph, containing "STRUCTURE_2jkp", creates the "Structure Box" on the page.
+<StructureSection load='2jkp' size='340' side='right'caption='[[2jkp]], [[Resolution|resolution]] 1.99&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'>[[2jkp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JKP 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]] 1.99&#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=CTS:CASTANOSPERMINE'>CTS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-{{STRUCTURE_2jkp|  PDB=2jkp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jkp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jkp OCA], [https://pdbe.org/2jkp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jkp RCSB], [https://www.ebi.ac.uk/pdbsum/2jkp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jkp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUSB_BACTN SUSB_BACTN] Glucoamylase that hydrolyzes alpha-1,4-glucosidic linkages, alpha-1,6-, alpha-1,3- and alpha-1,2-glucosidic linkages during starch degradation.<ref>PMID:8955399</ref> <ref>PMID:18981178</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/jk/2jkp_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=2jkp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining alpha-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron alpha-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining alpha-galactosidase.
-===STRUCTURE OF A FAMILY 97 ALPHA-GLUCOSIDASE FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH CASTANOSPERMINE===
+Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.,Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ Chem Biol. 2008 Oct 20;15(10):1058-67. Epub 2008 Oct 9. PMID:18848471<ref>PMID:18848471</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jkp" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-JKP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JKP OCA].
+*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
-[[Category: Alpha-glucosidase]]
+== References ==
-[[Category: Bacteroides thetaiotaomicron]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Davies, G J.]]
+</StructureSection>
-[[Category: Gloster, T M.]]
+[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-[[Category: Henrissat, B.]]
+[[Category: Large Structures]]
-[[Category: Potts, J R.]]
+[[Category: Davies GJ]]
-[[Category: Turkenburg, J P.]]
+[[Category: Gloster TM]]
-[[Category: Alpha-glucosidase]]
+[[Category: Henrissat B]]
-[[Category: Bacteroides thetaiotaomicron]]
+[[Category: Potts JR]]
-[[Category: Castanospermine]]
+[[Category: Turkenburg JP]]
-[[Category: Family 97]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  1 21:33:06 2008''