PDBsum entry 2zic

Hydrolase

PDB id: 2zic

Contents

Protein chain

536 a.a. *

Ligands

TRS

GOL

Metals

_CA ×3

Waters ×405

* Residue conservation analysis

PDB id:

2zic

Name:

Hydrolase

Title:

Crystal structure of streptococcus mutans dextran glucosidase

Structure:

Dextran glucosidase. Chain: a. Engineered: yes. Mutation: yes

Source:

Streptococcus mutans. Gene: dexb. Expressed in: escherichia coli.

Resolution:

2.20Å R-factor: 0.183 R-free: 0.222

Authors:

H.Hondoh,W.Saburi,H.Mori,M.Okuyama,T.Nakada,Y.Matsuura,A.Kimura

Key ref:

H.Hondoh et al. (2008). Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans. J Mol Biol, 378, 913-922. PubMed id: 18395742

Date:

14-Feb-08 Release date: 24-Jun-08

Protein chain

Q99040  (DEXB_STRMU) -  Glucan 1,6-alpha-glucosidase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

Seq: 536 a.a.

Struc: 536 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.2.1.70 - glucan 1,6-alpha-glucosidase.
• Reaction: Hydrolysis of (1->6)-alpha-D-glucosidic linkages in 1->6-alpha-D- glucans and derived oligosaccharides.

J Mol Biol 378:913-922 (2008)

PubMed id: 18395742

Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans.

H.Hondoh, W.Saburi, H.Mori, M.Okuyama, T.Nakada, Y.Matsuura, A.Kimura.

ABSTRACT

We have determined the crystal structure of Streptococcus mutans dextran glucosidase, which hydrolyzes the alpha-1,6-glucosidic linkage of isomaltooligosaccharides from their non-reducing ends to produce alpha-glucose. By using the mutant of catalytic acid Glu236-->Gln, its complex structure with the isomaltotriose, a natural substrate of this enzyme, has been determined. The enzyme has 536 amino acid residues and a molecular mass of 62,001 Da. The native and the complex structures were determined by the molecular replacement method and refined to 2.2 A resolution, resulting in a final R-factor of 18.3% for significant reflections in the native structure and 18.4% in the complex structure. The enzyme is composed of three domains, A, B and C, and has a (beta/alpha)(8)-barrel in domain A, which is common to the alpha-amylase family enzymes. Three catalytic residues are located at the bottom of the active site pocket and the bound isomaltotriose occupies subsites -1 to +2. The environment of the glucose residue at subsite -1 is similar to the environment of this residue in the alpha-amylase family. Hydrogen bonds between Asp60 and Arg398 and O4 atom of the glucose unit at subsite -1 accomplish recognition of the non-reducing end of the bound substrate. The side-chain atoms of Glu371 and Lys275 form hydrogen bonds with the O2 and O3 atoms of the glucose residue at subsite +1. The positions of atoms that compose the scissile alpha-1,6-glucosidic linkage (C1, O6 and C6 atoms) are identical with the positions of the atoms in the scissile alpha-1,4 linkage (C1, O4 and C4 atoms) of maltopentaose in the alpha-amylase structure from Bacillus subtilis. The comparison with the alpha-amylase suggests that Val195 of the dextran glucosidase and the corresponding residues of alpha-1,6-hydrolyzing enzymes participate in the determination of the substrate specificity of these enzymes.