1BG9

BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

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This is version 2.0 of the entry. See complete history


Literature

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

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

(1998) J Mol Biol 278: 205-217

  • DOI: 10.1006/jmbi.1998.1683
  • Primary Citation of Related Structures:  
    1BG9

  • 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 ...

    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.


    Related Citations: 
    • Crystal and Molecular Structure of Barley Alpha-Amylase
      Kadziola, A., Abe, J.I., Svensson, B., Haser, R.
      (1994) J Mol Biol 239: 104

    Organizational Affiliation

    UPR 9039, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier, Marseille, Cedex 20, 13402, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASEA403Hordeum vulgareMutation(s): 0 
Gene Names: AMY1.2
EC: 3.2.1.1
UniProt
Find proteins for P04063 (Hordeum vulgare)
Explore P04063 
Go to UniProtKB:  P04063
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseB2N/AN/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AF1 (Subject of Investigation/LOI)
Query on AF1

Download Ideal Coordinates CCD File 
F [auth A]4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-beta-D-glucopyranose
C13 H23 N O8
RBZIIHWPZWOIDU-MKXIPYFISA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.2α = 90
b = 135.2β = 90
c = 79.6γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
NIELSENdata reduction
XUONG)data reduction
XENGENdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary