PDBsum entry 1iew

Hydrolase

PDB id: 1iew

Contents

Protein chain

602 a.a. *

Ligands

NAG-NAG-BMA

NAG-NAG-BMA-MAN-NAG-FUL

NAG

G2F

Waters ×285

* Residue conservation analysis

PDB id:

1iew

Name:

Hydrolase

Title:

Crystal structure of barley beta-d-glucan glucohydrolase isoenzyme exo1 in complex with 2-deoxy-2-fluoro-alpha-d-glucoside

Structure:

Beta-d-glucan glucohydrolase isoenzyme exo1. Chain: a. Synonym: beta-d-glucan exohydrolase isoenzyme exoi. Ec: 3.2.1.58

Source:

Hordeum vulgare. Organism_taxid: 4513. Strain: cultivar clipper

Resolution:

2.55Å R-factor: 0.189 R-free: 0.233

Authors:

M.Hrmova,R.Degori,G.B.Fincher,B.J.Smith,J.N.Varghese

Key ref:

M.Hrmova et al. (2001). Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase. Structure, 9, 1005-1016. PubMed id: 11709165 DOI: 10.1016/S0969-2126(01)00673-6

Date:

11-Apr-01 Release date: 14-Nov-01

Protein chain

Q9XEI3  (Q9XEI3_HORVV) -  beta-glucosidase from Hordeum vulgare subsp. vulgare

Seq: 630 a.a.

Struc: 602 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.21 - beta-glucosidase.
• Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.

DOI no: 10.1016/S0969-2126(01)00673-6

Structure 9:1005-1016 (2001)

PubMed id: 11709165

Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.

M.Hrmova, J.N.Varghese, R.De Gori, B.J.Smith, H.Driguez, G.B.Fincher.

ABSTRACT

BACKGROUND: Barley beta-D-glucan glucohydrolases represent family 3 glycoside hydrolases that catalyze the hydrolytic removal of nonreducing glucosyl residues from beta-D-glucans and beta-D-glucooligosaccharides. After hydrolysis is completed, glucose remains bound in the active site. RESULTS: When conduritol B epoxide and 2', 4'-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside are diffused into enzyme crystals, they displace the bound glucose and form covalent glycosyl-enzyme complexes through the Odelta1 of D285, which is thereby identified as the catalytic nucleophile. A nonhydrolyzable S-glycosyl analog, 4(I), 4(III), 4(V)-S-trithiocellohexaose, also diffuses into the active site, and a S-cellobioside moiety positions itself at the -1 and +1 subsites. The glycosidic S atom of the S-cellobioside moiety forms a short contact (2.75 A) with the Oepsilon2 of E491, which is likely to be the catalytic acid/base. The glucopyranosyl residues of the S-cellobioside moiety are not distorted from the low-energy 4C(1) conformation, but the glucopyranosyl ring at the +1 subsite is rotated and translated about the linkage. CONCLUSIONS: X-ray crystallography is used to define the three key intermediates during catalysis by beta-D-glucan glucohydrolase. Before a new hydrolytic event begins, the bound product (glucose) from the previous catalytic reaction is displaced by the incoming substrate, and a new enzyme-substrate complex is formed. The second stage of the hydrolytic pathway involves glycosidic bond cleavage, which proceeds through a double-displacement reaction mechanism. The crystallographic analysis of the S-cellobioside-enzyme complex with quantum mechanical modeling suggests that the complex might mimic the oxonium intermediate rather than the enzyme-substrate complex.

Selected figure(s)

Figure 4.
Figure 4. Stereo Representation of Ligands Bound in the Active Site of b Image glucan GlucohydrolaseMOLSCRIPT [47] diagrams of the nearest hydrogen bonding interactions (dashed lines) between:(a) Glucose.(b) Cyclohexitol ring.(c) 2-deoxy-2-fluoro-a- Image -glucosyl moiety.(d) S-cellobioside moiety.and the contact amino acid residues.Ligands are colored in cyan. The molecular surfaces of domains 1 and 2 are represented by transparent cyan and magenta surfaces, respectively, and are generated using GRASP [48]. Black, red, blue, yellow, and gray spheres represent carbon, oxygen, nitrogen, sulfur, and fluorine atoms, respectively. Water molecules are represented as red spheres. In (c), residues E220, E287, R291, and E491, along with Wat2 and Wat3, are not included, to improve the clarity of the data. The entrance to the active site in (b) and (c) is located perpendicularly to the page and is located toward the lower left hand corner in (a) and (d)

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 1005-1016) copyright 2001.

Figure was selected by an automated process.