1RPK

Crystal structure of barley alpha-amylase isozyme 1 (amy1) in complex with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Oligosaccharide Binding to Barley {alpha}-Amylase 1

Robert, X.Haser, R.Mori, H.Svensson, B.Aghajari, N.

(2005) J.Biol.Chem. 280: 32968-32978

  • DOI: 10.1074/jbc.M505515200
  • Primary Citation of Related Structures:  1RP8, 1RP9

  • PubMed Abstract: 
  • Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) ...

    Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough insight into the substrate binding by describing residues defining 9 subsites, namely -7 through +2. These structures support that the pseudotetrasaccharide inhibitor acarbose is hydrolyzed by the active enzymes. Moreover, sugar binding was observed to the starch granule-binding site previously determined in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site was proposed at the glycone part of the binding cleft, and the crystal structures of the catalytic nucleophile mutant (AMY1D180A) complexed with acarbose and maltoheptaose, respectively, suggest an additional role for the nucleophile in the stabilization of the Michaelis complex. Furthermore, probable roles are outlined for the surface binding sites. Our data support a model in which the two surface sites in AMY1 can interact with amylose chains in their naturally folded form. Because of the specificities of these two sites, they may locate/orient the enzyme in order to facilitate access to the active site for polysaccharide chains. Moreover, the sugar tongs surface site could also perform the unraveling of amylose chains, with the aid of Tyr-380 acting as "molecular tweezers."


    Organizational Affiliation

    Laboratoire de BioCristallographie, IFR-128 BioSciences Lyon-Gerland, Institut de Biologie et Chimie des Protéines, UMR 5086, CNRS-UCBL1, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase type 1 isozyme
A
405Hordeum vulgareGene Names: AMY1.1
EC: 3.2.1.1
Find proteins for P00693 (Hordeum vulgare)
Go to UniProtKB:  P00693
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

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

Download SDF File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.390α = 90.00
b = 72.920β = 90.00
c = 61.390γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance