Dextranase

 

Dextranase catalyzes the hydrolysis of the alpha-1,6-glycosidic linkage in dextran polymers. The enzyme cleaves the linkages within the dextran molecule and releases shorter isomaltosaccharides. Belongs to the glycosyl hydrolase 49 family.

 

Reference Protein and Structure

Sequence
P48845 UniProt (3.2.1.11) IPR012334 (Sequence Homologues) (PDB Homologues)
Biological species
Talaromyces minioluteus (Filamentous fungus) Uniprot
PDB
1ogo - Dex49A from Penicillium minioluteum complex with isomaltose (1.65 Å) PDBe PDBsum 1ogo
Catalytic CATH Domains
2.160.20.10 CATHdb (see all for 1ogo)
Click To Show Structure

Enzyme Reaction (EC:3.2.1.11)

isomaltose
CHEBI:28189ChEBI
+
water
CHEBI:15377ChEBI
→
alpha-D-glucose
CHEBI:17925ChEBI
+
D-glucopyranose
CHEBI:4167ChEBI
Alternative enzyme names: Alpha-D-1,6-glucan-6-glucanohydrolase, DL 2, Dextran hydrolase, Dextranase DL 2, Endo-dextranase, Endodextranase, Alpha-1,6-glucan-6-glucanohydrolase, 1,6-alpha-D-glucan 6-glucanohydrolase,

Enzyme Mechanism

Introduction

Studies show the reaction proceeds by a single displacement mechanism with anomeric inversion. In this mechanism, Asp395 functions as a general acid, donating a proton to the oxygen of the glycosidic bond between the glucose units in the -1 and +1 position. A carbonium ion intermediate subsequently forms, and is further attacked by an activated water molecule, forming the products. Asp376 acts as a general base activating the nucleophilic water molecule.

Catalytic Residues Roles

UniProt PDB* (1ogo)
Asp410 Asp376X(A) Acts as a general base activating the nucleophilic water molecule. activator, increase nucleophilicity, proton acceptor, proton donor
Asp429 Asp395X(A) Donates a proton to the oxygen of the glycosidic bond to be hydrolysed. promote heterolysis, proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, heterolysis, overall reactant used, overall product formed, electron transfer, bimolecular nucleophilic addition, native state of enzyme regenerated

References

  1. Mizuno M et al. (2008), J Mol Biol, 376, 210-220. Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49. DOI:10.1016/j.jmb.2007.11.098. PMID:18155243.
  2. Ko JA et al. (2016), J Microbiol Biotechnol, 26, 837-845. Identification of Catalytic Amino Acid Residues by Chemical Modification in Dextranase. DOI:10.4014/jmb.1601.01014. PMID:26907761.
  3. Akeboshi H et al. (2004), Eur J Biochem, 271, 4420-4427. Insights into the reaction mechanism of glycosyl hydrolase family 49. Site-directed mutagenesis and substrate preference of isopullulanase. DOI:10.1111/j.1432-1033.2004.04378.x. PMID:15560783.
  4. Larsson AM et al. (2003), Structure, 11, 1111-1121. Dextranase from Penicillium minioluteum. DOI:10.1016/s0969-2126(03)00147-3. PMID:12962629.

Step 1. Asp395 donates a proton to the oxygen of the glycosidic bond, this promotes the cleavage of the bond and the formation of a carbonium ion intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp395X(A) promote heterolysis, proton donor

Chemical Components

proton transfer, heterolysis, overall reactant used, overall product formed

Step 2. The carbonium ion intermediate can be stabilized by movement of electrons from the neighboring oxygen.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

electron transfer

Step 3. Asp376 activates a water molecule for nucleophilic attack on the ion and another glucose unit is produced.

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Catalytic Residues Roles

Residue Roles
Asp376X(A) activator, increase nucleophilicity, proton acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, overall product formed

Step 4. Inferred reaction step- native state of the enzyme is regenerated.

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Catalytic Residues Roles

Residue Roles
Asp395X(A) proton acceptor
Asp376X(A) proton donor

Chemical Components

proton transfer, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Asp395 donates a proton to the oxygen of the glycosidic bond, this promotes the cleavage of the bond and the formation of a carbonium ion intermediate.

Step 2. The carbonium ion intermediate can be stabilized by movement of electrons from the neighboring oxygen.

Step 3. Asp376 activates a water molecule for nucleophilic attack on the ion and another glucose unit is produced.

Step 4. Inferred reaction step- native state of the enzyme is regenerated.

Products.

Contributors

Gemma L. Holliday, James Willey