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| | ==Structural base for cyclodextrin hydrolysis== | | ==Structural base for cyclodextrin hydrolysis== |
| - | <StructureSection load='3edj' size='340' side='right' caption='[[3edj]], [[Resolution|resolution]] 1.69Å' scene=''> | + | <StructureSection load='3edj' size='340' side='right'caption='[[3edj]], [[Resolution|resolution]] 1.69Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3edj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacterium_sp._92 Flavobacterium sp. 92]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EDJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3edj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp._92 Flavobacterium sp. 92]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EDJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCD:BETA-CYCLODEXTRIN'>BCD</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.69Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3edd|3edd]], [[3ede|3ede]], [[3edf|3edf]], [[3edk|3edk]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900012:beta-cyclodextrin'>PRD_900012</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cdase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197856 Flavobacterium sp. 92])</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=3edj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3edj OCA], [https://pdbe.org/3edj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3edj RCSB], [https://www.ebi.ac.uk/pdbsum/3edj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3edj 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/Cyclomaltodextrinase Cyclomaltodextrinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.54 3.2.1.54] </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=3edj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3edj OCA], [http://pdbe.org/3edj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3edj RCSB], [http://www.ebi.ac.uk/pdbsum/3edj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3edj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8KKG0_9FLAO Q8KKG0_9FLAO] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cyclomaltodextrinase]] | |
| | [[Category: Flavobacterium sp. 92]] | | [[Category: Flavobacterium sp. 92]] |
| - | [[Category: Buedenbender, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Schulz, G E]] | + | [[Category: Buedenbender S]] |
| - | [[Category: Beta-cyclodextrin complex]] | + | [[Category: Schulz GE]] |
| - | [[Category: Glycosidase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
Q8KKG0_9FLAO
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 PubMed
Cyclodextrins resist hydrolysis by burying all bridge oxygens at their interior. Still, the rings can be opened by a small group of specialized enzymes, the cyclomaltodextrinases. Among them, the enzyme from Flavobacterium sp. no. 92 was mutated, crystallized and soaked with cyclodextrins, giving rise to four complex structures. One of them showed an alpha-cyclodextrin at the outer rim of the active center pocket. In the other complexes, alpha-, beta-and gamma-cyclodextrins were bound in a competent mode in the active center. The structures suggest that Arg464 functions as a chaperone guiding the substrates from the solvent into the active center. Over the last part of this pathway, the cyclodextrins bump on Phe274, which rotates the glucosyl group at subsite (+1) by about 120 degrees and fixes it in the new conformation. This induced fit was observed with all three major cyclodextrins. It makes the bridging oxygen between subsites (+1) and (-1) available for protonation by Glu340, which starts the hydrolysis. The mechanism resembles a spring-lock. The structural data were supplemented by activity measurements, quantifying the initial ring opening reaction for the major cyclodextrins and the transglucosylation activity for maltotetraose. Further activity data were collected for mutants splitting the tetrameric enzyme into dimers and for active center mutants.
Structural base for enzymatic cyclodextrin hydrolysis.,Buedenbender S, Schulz GE J Mol Biol. 2009 Jan 16;385(2):606-17. Epub 2008 Nov 6. PMID:19014948[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Buedenbender S, Schulz GE. Structural base for enzymatic cyclodextrin hydrolysis. J Mol Biol. 2009 Jan 16;385(2):606-17. Epub 2008 Nov 6. PMID:19014948 doi:10.1016/j.jmb.2008.10.085
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