PDBsum entry: 3edf

Hydrolase

PDB-id: 3edf

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PROCHECK

Protein chains

597 a.a. *

Ligands

CE6-ACX ×2

GOL ×4

Metal ions

_CA ×4

Waters ×1302

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

3edf

Name:

Hydrolase

Title:

Structural base for cyclodextrin hydrolysis

Structure:

Cyclomaltodextrinase. Chain: a, b. Synonym: fspcmd. Engineered: yes. Mutation: yes

Source:

Flavobacterium sp. 92. Organism_taxid: 197856. Gene: cdase. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B: Q8KKG0 (Q8KKG0_9FLAO)

Seq:

Struc:

Seq:

Struc:

Seq:

619 a.a.

Struc:

597 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme class:

E.C.3.2.1.54   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Cyclomaltodextrin + H₂O = linear maltodextrin (see diagram below)

Resolution:

1.65Å

R-factor:

0.167

R-free:

0.201

Authors:

S.Buedenbender,G.E.Schulz

Key ref:

S.Buedenbender and G.E.Schulz (2009). Structural base for enzymatic cyclodextrin hydrolysis.. J Mol Biol, 385, 606-617. [PubMed id: 19014948] [DOI: 10.1016/j.jmb.2008.10.085]

Date:

03-Sep-08

Release date:

03-Mar-09

Related entries:

3edd
alpha-cyclodextrin complex
3ede
contact mutant
3edj
beta-cyclodextrin complex
3edk
gamma-cyclodextrin complex

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Clefts

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Key reference

DOI no: 10.1016/j.jmb.2008.10.085

J Mol Biol 385:606-617 (2009)

PubMed id: 19014948

Structural base for enzymatic cyclodextrin hydrolysis.

S.Buedenbender, G.E.Schulz.

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.