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2jka

From Proteopedia

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{{Seed}}
 
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[[Image:2jka.png|left|200px]]
 
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<!--
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==Native structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron==
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The line below this paragraph, containing "STRUCTURE_2jka", creates the "Structure Box" on the page.
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<StructureSection load='2jka' size='340' side='right'caption='[[2jka]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2jka]] 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=2JKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JKA FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
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{{STRUCTURE_2jka| PDB=2jka | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jka OCA], [https://pdbe.org/2jka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jka RCSB], [https://www.ebi.ac.uk/pdbsum/2jka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jka ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/2jka_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2jka ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===NATIVE STRUCTURE OF A FAMILY 97 ALPHA-GLUCOSIDASE FROM BACTEROIDES THETAIOTAOMICRON===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2jka" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18848471}}, adds the Publication Abstract to the page
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*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18848471 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18848471}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Bacteroides thetaiotaomicron VPI-5482]]
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2JKA is a 2 chains structure of sequences 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=2JKA OCA].
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[[Category: Large Structures]]
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[[Category: Davies GJ]]
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==Reference==
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[[Category: Gloster TM]]
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<ref group="xtra">PMID:18848471</ref><references group="xtra"/>
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[[Category: Henrissat B]]
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[[Category: Alpha-glucosidase]]
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[[Category: Potts JR]]
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[[Category: Bacteroides thetaiotaomicron]]
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[[Category: Turkenburg JP]]
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[[Category: Davies, G J.]]
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[[Category: Gloster, T M.]]
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[[Category: Henrissat, B.]]
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[[Category: Potts, J R.]]
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[[Category: Turkenburg, J P.]]
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[[Category: Alpha-glucosidase]]
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[[Category: Bacteroides thetaiotaomicron]]
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[[Category: Family 97]]
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[[Category: Glycoside hydrolase]]
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[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:39:30 2009''
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Current revision

Native structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron

PDB ID 2jka

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