1BG9

BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE

Summary for 1BG9

• Entry DOI: 10.2210/pdb1bg9/pdb
• Descriptor: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE, 4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase, o-glycosyl
• Biological source: Hordeum vulgare
• Total number of polymer chains: 1
• Total formula weight: 45905.41

Authors

Kadziola, A.,Haser, R. (deposition date: 1998-06-05, release date: 1999-06-15, Last modification date: 2024-05-22)

Primary citation

Kadziola, A.,Sogaard, M.,Svensson, B.,Haser, R.
Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.
J.Mol.Biol., 278:205-217, 1998

PubMed 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.

PubMed: 9571044
DOI: 10.1006/jmbi.1998.1683

Experimental method

X-RAY DIFFRACTION (2.8 Å)