2jkp: Difference between revisions

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{{Seed}}
[[Image:2jkp.png|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>


<!--
==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]]
2JKP 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=2JKP 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: Castanospermine]]
[[Category: Family 97]]
[[Category: Glycoside hydrolase]]
[[Category: Hydrolase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:34:00 2009''

Latest revision as of 17:53, 13 December 2023

Structure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron in complex with castanospermineStructure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron in complex with castanospermine

Structural highlights

2jkp is a 2 chain structure with sequence from Bacteroides thetaiotaomicron VPI-5482. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.99Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ D'Elia JN, Salyers AA. Contribution of a neopullulanase, a pullulanase, and an alpha-glucosidase to growth of Bacteroides thetaiotaomicron on starch. J Bacteriol. 1996 Dec;178(24):7173-9. PMID:8955399
  2. ↑ Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J Biol Chem. 2008 Dec 26;283(52):36328-37. Epub 2008 Nov 3. PMID:18981178 doi:10.1074/jbc.M806115200
  3. ↑ Gloster TM, Turkenburg JP, Potts JR, Henrissat B, Davies GJ. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Chem Biol. 2008 Oct 20;15(10):1058-67. Epub 2008 Oct 9. PMID:18848471 doi:10.1016/j.chembiol.2008.09.005

2jkp, resolution 1.99Å

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