PDBsum entry: 1bg9

Hydrolase

PDB id: 1bg9

Contents

Protein chain

403 a.a. *

Ligands

DAF-BGC

AF1

Metals

_CA ×3

Waters ×148

* Residue conservation analysis

PDB id:

1bg9

Name:

Hydrolase

Title:

Barley alpha-amylase with substrate analogue acarbose

Structure:

1,4-alpha-d-glucan glucanohydrolase. Chain: a. Synonym: alpha-amylase, high pi isozyme. Ec: 3.2.1.1

Source:

Hordeum vulgare. Organism_taxid: 4513. Variant: cultivar menuet. Organ: germinated seeds

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.151 R-free: 0.249

Authors:

A.Kadziola,R.Haser

Key ref:

A.Kadziola et al. (1998). Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis. J Mol Biol, 278, 205-217. PubMed id: 9571044 DOI: 10.1006/jmbi.1998.1683

Date:

05-Jun-98 Release date: 15-Jun-99

Protein chain

P04063  (AMY2_HORVU) -  Alpha-amylase type B isozyme

Seq: 427 a.a.

Struc: 403 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.1 - Alpha-amylase.
• Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (7 terms)

DOI no: 10.1006/jmbi.1998.1683

J Mol Biol 278:205-217 (1998)

PubMed id: 9571044

Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.

A.Kadziola, M.Søgaard, B.Svensson, R.Haser.

ABSTRACT

alpha-Amylases are widely occurring, multidomain proteins with a catalytic (beta/alpha)8-barrel. In barley alpha-amylase, insight into the catalytic mechanism is gained from the X-ray crystal structure of its molecular complex with acarbose, a pseudotetrasaccharide that acts like a transition-state analogue and which is shown to bind at two specific regions of the enzyme. The structure of the complex has been refined to an R-factor of 15.1% for all observations with Fo>sigma(Fo) between 10 and 2.8 A resolution. A difference Fourier map produced after refinement of the native structure against the data of the acarbose complex clearly revealed density corresponding to two oligosaccharide-binding sites. One of these is defined as the surface-located starch granule-binding site characteristic of cereal alpha-amylases. It involves stacking of two acarbose rings on Trp276 and Trp277. The other binding region is the active site covering subsites -1, +1 and +2. Here, Glu204 is positioned to act in general acid/base catalysis protonating the glucosidic oxygen atom assisted by Asp289. A water molecule that bridges Glu204 and Asp289 is found at the entrance cavity containing a total of five water molecules. This water molecule is proposed to reprotonate Glu204 and supply the hydroxyl ion for nucleophilic attack on the glucosyl C1 atom. Asp 179 acts as the nucleophile that can bind covalently to the substrate intermediate after bond cleavage. The present complex structure together with the conservation of active-site residues among alpha-amylases and related enzymes, are consistent with a common catalytic mechanism for this class of retaining carbohydrases.

Selected figure(s)

Figure 1.
Figure 1. Topology of the acarbose molecule with ring and atom labelling as referred to in the text and in Table 1. Rings A and B constitute the acarviosine unit and ring A including the amino group the valienamine unit.

Figure 3.
Figure 3. Ribbon diagram of the AMY2 structure in complex with acarbose fragments shown as ball-and-sticks. White spheres correspond to the calcium ions. This Figure was produced with MOLSCRIPT and Raster3D [Kraulis 1991, Bacon and Anderson 1988 and Merritt and Murphy 1994].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 278, 205-217) copyright 1998.

Figures were selected by an automated process.