PDBsum entry: 1ex1

Hydrolase

PDB-id: 1ex1

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

602 a.a. *

Ligands

NAG

NAG-NAG-MAN-FCA-MAN-NAG

GLC

Waters ×220

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1ex1

Name:

Hydrolase

Title:

Beta-d-glucan exohydrolase from barley

Structure:

Protein (beta-d-glucan exohydrolase isoenzyme exo1). Chain: a. Synonym: exo1, exoglucanase. Other_details: three glycsylated sites at asn 221, 498, 600 glucose bound in putative active site

Source:

Hordeum vulgare. Organism_taxid: 4513. Organ: germinating seed

UniProt:

Q9XEI3 (Q9XEI3_HORVD)

Seq:

Struc:

Seq:

Struc:

Seq:

630 a.a.

Struc:

602 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Resolution:

2.20Å

R-factor:

0.170

R-free:

0.202

Authors:

J.N.Varghese,M.Hrmova,G.B.Fincher

Key ref:

J.N.Varghese et al. (1999). Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.. Structure, 7, 179-190. [PubMed id: 10368285] [DOI: 10.1016/S0969-2126(99)80024-0]

Date:

10-Nov-98

Release date:

17-Nov-99

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(99)80024-0

Structure 7:179-190 (1999)

PubMed id: 10368285

Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.

J.N.Varghese, M.Hrmova, G.B.Fincher.

ABSTRACT

BACKGROUND: Cell walls of the starchy endosperm and young vegetative tissues of barley (Hordeum vulgare) contain high levels of (1-->3,1-->4)-beta-D-glucans. The (1-->3,1-->4)-beta-D-glucans are hydrolysed during wall degradation in germinated grain and during wall loosening in elongating coleoptiles. These key processes of plant development are mediated by several polysaccharide endohydrolases and exohydrolases. RESULTS:. The three-dimensional structure of barley beta-D-glucan exohydrolase isoenzyme ExoI has been determined by X-ray crystallography. This is the first reported structure of a family 3 glycosyl hydrolase. The enzyme is a two-domain, globular protein of 605 amino acid residues and is N-glycosylated at three sites. The first 357 residues constitute an (alpha/beta)8 TIM-barrel domain. The second domain consists of residues 374-559 arranged in a six-stranded beta sandwich, which contains a beta sheet of five parallel beta strands and one antiparallel beta strand, with three alpha helices on either side of the sheet. A glucose moiety is observed in a pocket at the interface of the two domains, where Asp285 and Glu491 are believed to be involved in catalysis. CONCLUSIONS: The pocket at the interface of the two domains is probably the active site of the enzyme. Because amino acid residues that line this active-site pocket arise from both domains, activity could be regulated through the spatial disposition of the domains. Furthermore, there are sites on the second domain that may bind carbohydrate, as suggested by previously published kinetic data indicating that, in addition to the catalytic site, the enzyme has a second binding site specific for (1-->3, 1-->4)-beta-D-glucans.

Selected figure(s)

Figure 4.
Figure 4. A MOLSCRIPT [50] ball-and-stick stereo representation of the oligosaccharide chain (yellow bonds) that is linked to Asn498. The protein molecular surface (GRASP) [51] is in transparent green and the backbone-chain atoms are in standard colours. The C^α backbone is represented by a green ‘worm’ tube. Hydrogen-bond interactions within the oligosaccharide are represented by dashed lines. Carbon, oxygen and nitrogen atoms are represented by black, red and blue spheres, respectively, and water molecules are represented as larger red spheres.

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 179-190) copyright 1999.

Figure was selected by an automated process.