2jke: Difference between revisions

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{{Seed}}
[[Image:2jke.png|left|200px]]


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==Structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron in complex with deoxynojirimycin==
The line below this paragraph, containing "STRUCTURE_2jke", creates the "Structure Box" on the page.
<StructureSection load='2jke' size='340' side='right'caption='[[2jke]], [[Resolution|resolution]] 1.70&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'>[[2jke]] 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=2JKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JKE 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]] 1.7&#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>, <scene name='pdbligand=NOJ:1-DEOXYNOJIRIMYCIN'>NOJ</scene></td></tr>
{{STRUCTURE_2jke|  PDB=2jke  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jke OCA], [https://pdbe.org/2jke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jke RCSB], [https://www.ebi.ac.uk/pdbsum/2jke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jke 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/2jke_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=2jke 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 DEOXYNOJIRIMYCIN===
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 2jke" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18848471}}, adds the Publication Abstract to the page
*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18848471 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18848471}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Bacteroides thetaiotaomicron VPI-5482]]
2JKE 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=2JKE OCA].
[[Category: Large Structures]]
 
[[Category: Davies GJ]]
==Reference==
[[Category: Gloster TM]]
<ref group="xtra">PMID:18848471</ref><references group="xtra"/>
[[Category: Henrissat B]]
[[Category: Alpha-glucosidase]]
[[Category: Potts JR]]
[[Category: Bacteroides thetaiotaomicron]]
[[Category: Turkenburg JP]]
[[Category: Davies, G J.]]
[[Category: Gloster, T M.]]
[[Category: Henrissat, B.]]
[[Category: Potts, J R.]]
[[Category: Turkenburg, J P.]]
[[Category: Alpha-glucosidase]]
[[Category: Bacteroides thetaiotaomicron]]
[[Category: Deoxynojirimycin]]
[[Category: Family 97]]
[[Category: Glycoside hydrolase]]
[[Category: Hydrolase]]
 
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Retrieved from "https://proteopedia.org/2jke"