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4fnt

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Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose

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 ==Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose==
-<StructureSection load='4fnt' size='340' side='right' caption='[[4fnt]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='4fnt' size='340' side='right'caption='[[4fnt]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fnt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FNT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FNT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fnt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FNT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RAF:RAFFINOSE'>RAF</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fnp|4fnp]], [[4fnq|4fnq]], [[4fnr|4fnr]], [[4fns|4fns]], [[4fnu|4fnu]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900002:raffinose'>PRD_900002</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">agaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=4fnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fnt OCA], [https://pdbe.org/4fnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fnt RCSB], [https://www.ebi.ac.uk/pdbsum/4fnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fnt ProSAT]</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=4fnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fnt OCA], [http://pdbe.org/4fnt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fnt RCSB], [http://www.ebi.ac.uk/pdbsum/4fnt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fnt ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/AGAA_GEOSE AGAA_GEOSE] Hydrolyzes the short-chain alpha-galactosaccharides raffinose and stachyose.<ref>PMID:23012371</ref>
-The alpha-galactosidase AgaA from the thermophilic microorganism Geobacillus stearothermophilus has great industrial potential because it is fully active at 338 K against raffinose and can increase the yield of manufactured sucrose. AgaB has lower affinity for its natural substrates but is a powerful tool for the enzymatic synthesis of disaccharides by transglycosylation. These two enzymes have 97% identity and belong to the glycoside hydrolase (GH) family GH36 for which few structures are available. To understand the structural basis underlying the differences between these two enzymes, we determined the crystal structures of AgaA and AgaB by molecular replacement at 3.2- and 1.8 A-resolution, respectively. We also solved a 2.8-A structure of the AgaA(A355E) mutant, which has enzymatic properties similar to those of AgaB. We observe that residue 355 is located 20 A away from the active site and that the A355E substitution causes structural rearrangements resulting in a significant displacement of the invariant Trp(336) at catalytic subsite -1. Hence, the active cleft of AgaA is narrowed in comparison with AgaB, and AgaA is more efficient than AgaB against its natural substrates. The structure of AgaA(A355E) complexed with 1-deoxygalactonojirimycin reveals an induced fit movement; there is a rupture of the electrostatic interaction between Glu(355) and Asn(335) and a return of Trp(336) to an optimal position for ligand stacking. The structures of two catalytic mutants of AgaA(A355E) complexed with raffinose and stachyose show that the binding interactions are stronger at subsite -1 to enable the binding of various alpha-galactosides.
-The molecular mechanism of thermostable alpha-galactosidases AgaA and AgaB explained by x-ray crystallography and mutational studies.,Merceron R, Foucault M, Haser R, Mattes R, Watzlawick H, Gouet P J Biol Chem. 2012 Nov 16;287(47):39642-52. doi: 10.1074/jbc.M112.394114. Epub, 2012 Sep 25. PMID:23012371<ref>PMID:23012371</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4fnt" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Galactosidase|Galactosidase]]
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Alpha-galactosidase]]
+[[Category: Geobacillus stearothermophilus]]
-[[Category: Atcc 12980]]
+[[Category: Large Structures]]
-[[Category: Foucault, M]]
+[[Category: Foucault M]]
-[[Category: Gouet, P]]
+[[Category: Gouet P]]
-[[Category: Haser, R]]
+[[Category: Haser R]]
-[[Category: Mattes, R]]
+[[Category: Mattes R]]
-[[Category: Merceron, R]]
+[[Category: Merceron R]]
-[[Category: Watzlawick, H]]
+[[Category: Watzlawick H]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]

4fnt

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Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose

Structural highlights

Function

See Also

References

Contents

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