5ynh
From Proteopedia
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==Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin== | ==Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin== | ||
| - | <StructureSection load='5ynh' size='340' side='right' caption='[[5ynh]], [[Resolution|resolution]] 2.05Å' scene=''> | + | <StructureSection load='5ynh' size='340' side='right'caption='[[5ynh]], [[Resolution|resolution]] 2.05Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[5ynh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YNH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.05Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <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=GOL:GLYCEROL'>GOL</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=5ynh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ynh OCA], [https://pdbe.org/5ynh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ynh RCSB], [https://www.ebi.ac.uk/pdbsum/5ynh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ynh ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/W9BQ28_KLEPN W9BQ28_KLEPN] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with alpha-cyclodextrin (alpha-CD), beta-cyclodextrin (beta-CD) and gamma-cyclodextrin (gamma-CD) were refined at around 1.98-2.59 A resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM alpha-CD or gamma-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM beta-CD or with 10 mM alpha-CD or gamma-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to alpha-CD and gamma-CD, one beta-CD molecule was found at the active site only in the presence of 0.1 mM beta-CD. These results were coincident with the solution experiments, which showed that beta-CD inhibits this enzyme more than a thousand times more potently than alpha-CD and gamma-CD. The strong inhibition of beta-CD is caused by the optimized interaction between beta-CD and the side chain of Phe746. The increased Ki values of the F746A mutant for beta-CD supported the importance of Phe746 in the strong interaction of pullulanase with beta-CD. | ||
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| + | Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin.,Saka N, Iwamoto H, Malle D, Takahashi N, Mizutani K, Mikami B Acta Crystallogr D Struct Biol. 2018 Nov 1;74(Pt 11):1115-1123. doi:, 10.1107/S2059798318014523. Epub 2018 Oct 30. PMID:30387770<ref>PMID:30387770</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5ynh" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Klebsiella pneumoniae]] | [[Category: Klebsiella pneumoniae]] | ||
| - | [[Category: Iwamoto | + | [[Category: Large Structures]] |
| - | [[Category: Mikami | + | [[Category: Iwamoto H]] |
| - | [[Category: Mizutani | + | [[Category: Mikami B]] |
| - | [[Category: Saka | + | [[Category: Mizutani K]] |
| - | [[Category: Takahashi | + | [[Category: Saka N]] |
| - | + | [[Category: Takahashi N]] | |
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Current revision
Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM gamma-cyclodextrin
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