1bg9: Difference between revisions

Revision as of 12:55, 21 February 2008

BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE

OverviewOverview

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.

About this StructureAbout this Structure

1BG9 is a Single protein structure of sequence from Hordeum vulgare with and as ligands. Active as Alpha-amylase, with EC number 3.2.1.1 Full crystallographic information is available from OCA.

ReferenceReference

Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis., Kadziola A, Sogaard M, Svensson B, Haser R, J Mol Biol. 1998 Apr 24;278(1):205-17. PMID:9571044

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 '''BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE'''<br />
 ==Overview==
-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&gt;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.
+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&gt;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.
 ==About this Structure==
-BG9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare] with CA and AF1 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BG9 OCA].
+BG9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=AF1:'>AF1</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BG9 OCA].
 ==Reference==
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 [[Category: o-glycosyl]]
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