1BG9

BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 pseudo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
A
403Hordeum vulgareGene Names: AMY1.2
EC: 3.2.1.1
Find proteins for P04063 (Hordeum vulgare)
Go to UniProtKB:  P04063
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
DAF
Query on DAF

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Download CCD File 
A
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
C13 H17 N O8
ZGWNRGISVMYHTF-KKXLKBQTSA-N
 Ligand Interaction
AF1
Query on AF1

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.151 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.200α = 90.00
b = 135.200β = 90.00
c = 79.600γ = 120.00
Software Package:
Software NamePurpose
XENGENdata reduction
XUONG)data reduction
X-PLORphasing
X-PLORmodel building
NIELSENdata reduction
XENGENdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance