3a24: Difference between revisions
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< | ==Crystal structure of BT1871 retaining glycosidase== | ||
<StructureSection load='3a24' size='340' side='right'caption='[[3a24]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3a24]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A24 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a24 OCA], [https://pdbe.org/3a24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a24 RCSB], [https://www.ebi.ac.uk/pdbsum/3a24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a24 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AGAL_BACTN AGAL_BACTN] Galactosidase that is able to hydrolyze the alpha-1,6 disaccharide melibiose and the synthetic p-nitrophenyl alpha-galactoside substrate (pNP-Gal), with retention of the anomeric configuration. Does not hydrolyze DNP-Glc or pNP-Glc.<ref>PMID:18848471</ref> <ref>PMID:19646996</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/a2/3a24_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=3a24 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Glycoside hydrolase family 97 (GH 97) is a unique glycoside family that contains inverting and retaining glycosidases. Of these, BtGH97a (SusB) and BtGH97b (UniProtKB/TrEMBL entry Q8A6L0), derived from Bacteroides thetaiotaomicron, have been characterized as an inverting alpha-glucoside hydrolase and a retaining alpha-galactosidase, respectively. Previous studies on the three-dimensional structures of BtGH97a and site-directed mutagenesis indicated that Glu532 acts as an acid catalyst and that Glu439 and Glu508 function as the catalytic base in the inverting mechanism. However, BtGH97b lacks base catalysts but possesses a putative catalytic nucleophilic residue, Asp415. Here, we report that Asp415 in BtGH97b is the nucleophilic catalyst based on the results of crystal structure analysis and site-directed mutagenesis study. Structural comparison between BtGH97b and BtGH97a indicated that OD1 of Asp415 in BtGH97b is located at a position spatially identical with the catalytic water molecule of BtGH97a, which attacks on the anomeric carbon from the beta-face (i.e., Asp415 is poised for nucleophilic attack on the anomeric carbon). Site-directed mutagenesis of Asp415 leads to inactivation of the enzyme, and the activity is rescued by an external nucleophilic azide ion. That is, Asp415 functions as a nucleophilic catalyst. The multiple amino acid sequence alignment of GH 97 members indicated that almost half of the GH 97 enzymes possess base catalyst residues at the end of beta-strands 3 and 5, while the other half of the family show a conserved nucleophilic residue at the end of beta-strand 4. The different positions of functional groups on the beta-face of the substrate, which seem to be due to "hopping of the functional group" during evolution, have led to divergence of catalytic mechanism within the same family. | |||
Catalytic mechanism of retaining alpha-galactosidase belonging to glycoside hydrolase family 97.,Okuyama M, Kitamura M, Hondoh H, Kang MS, Mori H, Kimura A, Tanaka I, Yao M J Mol Biol. 2009 Oct 9;392(5):1232-41. Epub 2009 Jul 30. PMID:19646996<ref>PMID:19646996</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3a24" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]] | |||
*[[Galactosidase 3D structures|Galactosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
== | </StructureSection> | ||
== | |||
< | |||
[[Category: Bacteroides thetaiotaomicron]] | [[Category: Bacteroides thetaiotaomicron]] | ||
[[Category: Hondoh | [[Category: Large Structures]] | ||
[[Category: Kitamura | [[Category: Hondoh H]] | ||
[[Category: Okuyama | [[Category: Kitamura M]] | ||
[[Category: Tanaka | [[Category: Okuyama M]] | ||
[[Category: Yao | [[Category: Tanaka I]] | ||
[[Category: Yao M]] | |||
Latest revision as of 17:08, 1 November 2023
Crystal structure of BT1871 retaining glycosidaseCrystal structure of BT1871 retaining glycosidase
Structural highlights
FunctionAGAL_BACTN Galactosidase that is able to hydrolyze the alpha-1,6 disaccharide melibiose and the synthetic p-nitrophenyl alpha-galactoside substrate (pNP-Gal), with retention of the anomeric configuration. Does not hydrolyze DNP-Glc or pNP-Glc.[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 PubMedGlycoside hydrolase family 97 (GH 97) is a unique glycoside family that contains inverting and retaining glycosidases. Of these, BtGH97a (SusB) and BtGH97b (UniProtKB/TrEMBL entry Q8A6L0), derived from Bacteroides thetaiotaomicron, have been characterized as an inverting alpha-glucoside hydrolase and a retaining alpha-galactosidase, respectively. Previous studies on the three-dimensional structures of BtGH97a and site-directed mutagenesis indicated that Glu532 acts as an acid catalyst and that Glu439 and Glu508 function as the catalytic base in the inverting mechanism. However, BtGH97b lacks base catalysts but possesses a putative catalytic nucleophilic residue, Asp415. Here, we report that Asp415 in BtGH97b is the nucleophilic catalyst based on the results of crystal structure analysis and site-directed mutagenesis study. Structural comparison between BtGH97b and BtGH97a indicated that OD1 of Asp415 in BtGH97b is located at a position spatially identical with the catalytic water molecule of BtGH97a, which attacks on the anomeric carbon from the beta-face (i.e., Asp415 is poised for nucleophilic attack on the anomeric carbon). Site-directed mutagenesis of Asp415 leads to inactivation of the enzyme, and the activity is rescued by an external nucleophilic azide ion. That is, Asp415 functions as a nucleophilic catalyst. The multiple amino acid sequence alignment of GH 97 members indicated that almost half of the GH 97 enzymes possess base catalyst residues at the end of beta-strands 3 and 5, while the other half of the family show a conserved nucleophilic residue at the end of beta-strand 4. The different positions of functional groups on the beta-face of the substrate, which seem to be due to "hopping of the functional group" during evolution, have led to divergence of catalytic mechanism within the same family. Catalytic mechanism of retaining alpha-galactosidase belonging to glycoside hydrolase family 97.,Okuyama M, Kitamura M, Hondoh H, Kang MS, Mori H, Kimura A, Tanaka I, Yao M J Mol Biol. 2009 Oct 9;392(5):1232-41. Epub 2009 Jul 30. PMID:19646996[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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