4xps: Difference between revisions
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==Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside== | ==Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside== | ||
<StructureSection load='4xps' size='340' side='right' caption='[[4xps]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='4xps' size='340' side='right'caption='[[4xps]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4xps]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPS FirstGlance]. <br> | <table><tr><td colspan='2'>[[4xps]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ccug_39354 Ccug 39354]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPS FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xpo|4xpo]], [[4xpp|4xpp]], [[4xpq|4xpq]], [[4xpr|4xpr]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xpo|4xpo]], [[4xpp|4xpp]], [[4xpq|4xpq]], [[4xpr|4xpr]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-galactosidase Alpha-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.22 3.2.1.22] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xps OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xps RCSB], [http://www.ebi.ac.uk/pdbsum/4xps PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xps OCA], [http://pdbe.org/4xps PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xps RCSB], [http://www.ebi.ac.uk/pdbsum/4xps PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xps ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4xps" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]] | |||
*[[Galactosidase|Galactosidase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Alpha-galactosidase]] | [[Category: Alpha-galactosidase]] | ||
[[Category: Ccug 39354]] | |||
[[Category: Large Structures]] | |||
[[Category: Ichikawa, M]] | [[Category: Ichikawa, M]] | ||
[[Category: Ishizaki, Y]] | [[Category: Ishizaki, Y]] | ||
Revision as of 03:27, 6 June 2019
Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranosideCrystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside
Structural highlights
Publication Abstract from PubMedGlycoside hydrolase family 31 (GH31) proteins have been reportedly identified as exo-alpha-glycosidases with activity for alpha-glucosides and alpha-xylosides. We focused on a GH31 subfamily, which contains proteins with low sequence identity (<24%) to the previously reported GH31 glycosidases, and characterized two enzymes from Pedobacter heparinus and Pedobacter saltans, respectively. The enzymes unexpectedly exhibited alpha-galactosidase activity, but were not active on alpha-glucosides and alpha-xylosides. The crystal structures of one of the enzymes, PsGal31A, in unliganded form and in complexes with D-galactose or L-fucose, and the catalytic nucleophile mutant in unliganded form and in complex with p-nitrophenyl-alpha-D-galactopyranoside, were determined at 1.85-2.30 A resolution. The overall structure of PsGal31A contains four domains, and the catalytic domain adopts a (beta/alpha)8-barrel fold that resembles the structures of other GH31 enzymes. Two catalytic aspartic acid residues are structurally conserved in the enzymes, whereas most residues forming the active site differ from those of GH31 alpha-glucosidases and alpha-xylosidases. PsGal31A forms a dimer via a unique loop that is not conserved in other reported GH31 enzymes; this loop is involved in its aglycone specificity and in binding L-fucose. Considering potential genes for alpha-L-fucosidases and carbohydrate-related proteins within the vicinity of Pedobacter Gal31, the identified Gal31 enzymes are likely to function in a novel sugar degradation system. This is the first report of alpha-galactosidases which belong to GH31 family. Structural and biochemical characterization of novel bacterial alpha-galactosidases belonging to glycoside hydrolase family 31.,Miyazaki T, Ishizaki Y, Ichikawa M, Nishikawa A, Tonozuka T Biochem J. 2015 May 5. PMID:25942325[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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