3EDE

Structural base for cyclodextrin hydrolysis

Summary for 3EDE

• Entry DOI: 10.2210/pdb3ede/pdb
• Related: 3EDD 3EDF 3EDJ 3EDK
• Descriptor: Cyclomaltodextrinase, CALCIUM ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: contact mutant, hydrolase, glycosidase
• Biological source: Flavobacterium sp. 92
• Total number of polymer chains: 2
• Total formula weight: 136759.86

Authors

Buedenbender, S.,Schulz, G.E. (deposition date: 2008-09-03, release date: 2009-03-03, Last modification date: 2023-11-01)

Primary citation

Buedenbender, S.,Schulz, G.E.
Structural base for enzymatic cyclodextrin hydrolysis
J.Mol.Biol., 385:606-617, 2009

PubMed Abstract: 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.

PubMed: 19014948
DOI: 10.1016/j.jmb.2008.10.085

Experimental method

X-RAY DIFFRACTION (1.71 Å)