6tp2: Difference between revisions
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==Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrin== | ==Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrin== | ||
<StructureSection load='6tp2' size='340' side='right'caption='[[6tp2]]' scene=''> | <StructureSection load='6tp2' size='340' side='right'caption='[[6tp2]], [[Resolution|resolution]] 1.94Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TP2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TP2 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6tp2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_licheniforme"_weigmann_1898 "clostridium licheniforme" weigmann 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TP2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TP2 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tp2 OCA], [http://pdbe.org/6tp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6tp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tp2 ProSAT]</span></td></tr> | </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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">amy ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1402 "Clostridium licheniforme" Weigmann 1898])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tp2 OCA], [http://pdbe.org/6tp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tp2 RCSB], [http://www.ebi.ac.uk/pdbsum/6tp2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tp2 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
alpha-Amylase from Bacillus paralicheniformis (BliAmy), belonging to GH13_5 subfamily of glycoside hydrolases, was proven to be a highly efficient raw starch digesting enzyme. The ability of some alpha-amylases to hydrolyze raw starch is related to the existence of surface binding sites (SBSs) for polysaccharides that can be distant from the active site. Crystallographic studies performed on BliAmy in the apo form and of enzyme bound with different oligosaccharides and oligosaccharide precursors revealed binding of these ligands to one SBS with two amino acids F257 and Y358 mainly involved in complex formation. The role of this SBS in starch binding and degradation was probed by designing enzyme variants mutated in this region (F257A and Y358A). Kinetic studies with different substrates show that starch binding through the SBS is disrupted in the mutants and that F257 and Y358 contributed cumulatively to binding and hydrolysis. Mutation of both sites (F257A/Y358A) resulted in a 5-fold lower efficacy with raw starch as substrate and at least 5.5-fold weaker binding compared to the wild type BliAmy, suggesting that the ability of BliAmy to hydrolyze raw starch with high efficiency is related to the level of its adsorption onto starch granules. | |||
Characterization of the starch surface binding site on Bacillus paralicheniformis alpha-amylase.,Bozic N, Rozeboom HJ, Loncar N, Slavic MS, Janssen DB, Vujcic Z Int J Biol Macromol. 2020 Oct 12. pii: S0141-8130(20)34647-X. doi:, 10.1016/j.ijbiomac.2020.10.025. PMID:33058974<ref>PMID:33058974</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6tp2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Clostridium licheniforme weigmann 1898]] | |||
[[Category: Alpha-amylase]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Janssen | [[Category: Janssen, D B]] | ||
[[Category: Rozeboom | [[Category: Rozeboom, H J]] | ||
[[Category: Amylase]] | |||
[[Category: Cyclodextrin]] | |||
[[Category: Hydrolase]] | |||
[[Category: Starch binding site]] | |||
Revision as of 23:48, 28 October 2020
Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrinCrystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrin
Structural highlights
Publication Abstract from PubMedalpha-Amylase from Bacillus paralicheniformis (BliAmy), belonging to GH13_5 subfamily of glycoside hydrolases, was proven to be a highly efficient raw starch digesting enzyme. The ability of some alpha-amylases to hydrolyze raw starch is related to the existence of surface binding sites (SBSs) for polysaccharides that can be distant from the active site. Crystallographic studies performed on BliAmy in the apo form and of enzyme bound with different oligosaccharides and oligosaccharide precursors revealed binding of these ligands to one SBS with two amino acids F257 and Y358 mainly involved in complex formation. The role of this SBS in starch binding and degradation was probed by designing enzyme variants mutated in this region (F257A and Y358A). Kinetic studies with different substrates show that starch binding through the SBS is disrupted in the mutants and that F257 and Y358 contributed cumulatively to binding and hydrolysis. Mutation of both sites (F257A/Y358A) resulted in a 5-fold lower efficacy with raw starch as substrate and at least 5.5-fold weaker binding compared to the wild type BliAmy, suggesting that the ability of BliAmy to hydrolyze raw starch with high efficiency is related to the level of its adsorption onto starch granules. Characterization of the starch surface binding site on Bacillus paralicheniformis alpha-amylase.,Bozic N, Rozeboom HJ, Loncar N, Slavic MS, Janssen DB, Vujcic Z Int J Biol Macromol. 2020 Oct 12. pii: S0141-8130(20)34647-X. doi:, 10.1016/j.ijbiomac.2020.10.025. PMID:33058974[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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