3EDF: Structural Base For Cyclodextrin Hydrolysis

Citation:
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.
PDB ID: 3EDFDownload
MMDB ID: 69967
PDB Deposition Date: 2008/9/3
Updated in MMDB: 2009/07
Experimental Method:
x-ray diffraction
Resolution: 1.65  Å
Source Organism:
Similar Structures:
Biological Unit for 3EDF: dimeric; determined by author and by software (PISA)
Molecular Components in 3EDF
Label Count Molecule
Proteins (2 molecules)
2
Cyclomaltodextrinase
Molecule annotation
Chemicals (12 molecules)
1
4
2
2
3
2
4
4
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.