PDBsum entry: 1ogo

Hydrolase

PDB-id: 1ogo

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

572 a.a. *

Ligands

BGC-GLC

Waters ×508

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1ogo

Name:

Hydrolase

Title:

Dex49a from penicillium minioluteum complex with isomaltose

Structure:

Dextranase. Chain: x. Synonym: alpha-1,6-glucan-6-glucanohydrolase. Engineered: yes. Mutation: yes

Source:

Penicillium minioluteum. Organism_taxid: 28574. Strain: hi-4. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Expression_system_variant: his3.

UniProt:

P48845 (DEXT_PENMI)

Seq:

Struc:

Seq:

Struc:

Seq:

608 a.a.

Struc:

572 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme class:

E.C.3.2.1.11   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,6-alpha-D-glucosidic linkages in dextran.

Resolution:

1.65Å

R-factor:

0.188

R-free:

0.215

Authors:

A.M.Larsson,J.Stahlberg,T.A.Jones

Key ref:

A.M.Larsson et al. (2003). Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.. Structure, 11, 1111-1121. [PubMed id: 12962629] [DOI: 10.1016/S0969-2126(03)00147-3]

Date:

08-May-03

Release date:

11-Sep-03

Related entries:

1ogm dex49a from penicillium minioluteum

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(03)00147-3

Structure 11:1111-1121 (2003)

PubMed id: 12962629

Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.

A.M.Larsson, R.Andersson, J.Ståhlberg, L.Kenne, T.A.Jones.

ABSTRACT

Dextranase catalyzes the hydrolysis of the alpha-1,6-glycosidic linkage in dextran polymers. The structure of dextranase, Dex49A, from Penicillium minioluteum was solved in the apo-enzyme and product-bound forms. The main domain of the enzyme is a right-handed parallel beta helix, which is connected to a beta sandwich domain at the N terminus. In the structure of the product complex, isomaltose was found to bind in a crevice on the surface of the enzyme. The glycosidic oxygen of the glucose unit in subsite +1 forms a hydrogen bond to the suggested catalytic acid, Asp395. By NMR spectroscopy the reaction course was shown to occur with net inversion at the anomeric carbon, implying a single displacement mechanism. Both Asp376 and Asp396 are suitably positioned to activate the water molecule that performs the nucleophilic attack. A new clan that links glycoside hydrolase families 28 and 49 is suggested.

Selected figure(s)

Figure 7.
Figure 7. The Water-Accessible Surface of the Active Site Is Shown in the Image to the LeftThe isomaltose ligand is partially visible behind Tyr463. The ball and stick image to the right is shown from the same view. A tunnel is created in the active site by the interaction between the side chains of Tyr463 and Asp317. The side chains colored in gold are located in the presumed -1 and -2 subsites and are totally conserved within GH 49.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1111-1121) copyright 2003.

Figure was selected by the author.