3edd

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{{Seed}}
 
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[[Image:3edd.jpg|left|200px]]
 
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==Structural base for cyclodextrin hydrolysis==
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The line below this paragraph, containing "STRUCTURE_3edd", creates the "Structure Box" on the page.
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<StructureSection load='3edd' size='340' side='right'caption='[[3edd]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3edd]] 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=3EDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EDD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
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<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=PRD_900015:alpha-cyclodextrin'>PRD_900015</scene></td></tr>
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{{STRUCTURE_3edd| PDB=3edd | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3edd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3edd OCA], [https://pdbe.org/3edd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3edd RCSB], [https://www.ebi.ac.uk/pdbsum/3edd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3edd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8KKG0_9FLAO Q8KKG0_9FLAO]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ed/3edd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3edd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Structural base for cyclodextrin hydrolysis===
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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<ref>PMID:19014948</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19014948}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3edd" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19014948 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19014948}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3EDD is a 2 chains structure of sequences 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=3EDD OCA].
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==Reference==
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<ref group="xtra">PMID:19014948</ref><references group="xtra"/>
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[[Category: Cyclomaltodextrinase]]
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[[Category: Flavobacterium sp. 92]]
[[Category: Flavobacterium sp. 92]]
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[[Category: Buedenbender, S.]]
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[[Category: Large Structures]]
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[[Category: Schulz, G E.]]
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[[Category: Buedenbender S]]
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[[Category: Alpha-cyclodextrin binding]]
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[[Category: Schulz GE]]
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[[Category: Glycosidase]]
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[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 14:49:29 2009''
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Current revision

Structural base for cyclodextrin hydrolysis

PDB ID 3edd

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