1bg9

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[[Image:1bg9.jpg|left|200px]]<br /><applet load="1bg9" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1bg9.jpg|left|200px]]
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caption="1bg9, resolution 2.8&Aring;" />
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'''BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE'''<br />
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{{Structure
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|PDB= 1bg9 |SIZE=350|CAPTION= <scene name='initialview01'>1bg9</scene>, resolution 2.8&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=AF1:4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE'>AF1</scene>
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|ACTIVITY= [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]
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|GENE=
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}}
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'''BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1BG9 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].
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1BG9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BG9 OCA].
==Reference==
==Reference==
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9571044 9571044]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/9571044 9571044]
[[Category: Alpha-amylase]]
[[Category: Alpha-amylase]]
[[Category: Hordeum vulgare]]
[[Category: Hordeum vulgare]]
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[[Category: o-glycosyl]]
[[Category: o-glycosyl]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:54:58 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:10:34 2008''

Revision as of 08:10, 20 March 2008

Image:1bg9.jpg


PDB ID 1bg9

Drag the structure with the mouse to rotate
, resolution 2.8Å
Ligands: and
Activity: Alpha-amylase, with EC number 3.2.1.1
Coordinates: save as pdb, mmCIF, xml



BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE


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>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

1BG9 is a Single protein structure of sequence from Hordeum vulgare. Full crystallographic information is available from OCA.

Reference

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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