1P6W

Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in complex with the substrate analogue, methyl 4I,4II,4III-tri-thiomaltotetraoside (thio-DP4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs

Robert, X.Haser, R.Gottschalk, T.E.Ratajczak, F.Driguez, H.Svensson, B.Aghajari, N.

(2003) Structure 11: 973-984

  • DOI: 10.1016/s0969-2126(03)00151-5
  • Primary Citation of Related Structures:  
    1HT6, 1P6W

  • PubMed Abstract: 
  • Though the three-dimensional structures of barley alpha-amylase isozymes AMY1 and AMY2 are very similar, they differ remarkably from each other in their affinity for Ca(2+) and when interacting with substrate analogs. A surface site recognizing maltooligosaccharides, not earlier reported for other alpha-amylases and probably associated with the different activity of AMY1 and AMY2 toward starch granules, has been identified ...

    Though the three-dimensional structures of barley alpha-amylase isozymes AMY1 and AMY2 are very similar, they differ remarkably from each other in their affinity for Ca(2+) and when interacting with substrate analogs. A surface site recognizing maltooligosaccharides, not earlier reported for other alpha-amylases and probably associated with the different activity of AMY1 and AMY2 toward starch granules, has been identified. It is located in the C-terminal part of the enzyme and, thus, highlights a potential role of domain C. In order to scrutinize the possible biological significance of this domain in alpha-amylases, a thorough comparison of their three-dimensional structures was conducted. An additional role for an earlier-identified starch granule binding surface site is proposed, and a new calcium ion is reported.


    Related Citations: 
    • Expression, purification and preliminary crystallographic studies of alpha-amylase isozyme 1 from barley seeds
      Robert, X., Gottschalk, T.E., Haser, R., Svensson, B., Aghajari, N.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 683

    Organizational Affiliation

    Laboratoire de BioCristallographie, 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (Alpha-amylase type A isozyme)A405Hordeum vulgareMutation(s): 0 
Gene Names: AMY1.1
EC: 3.2.1.1
UniProt
Find proteins for P00693 (Hordeum vulgare)
Explore P00693 
Go to UniProtKB:  P00693
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-beta-D-glucopyranosideB4N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G75417ZK
GlyCosmos:  G75417ZK
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranoseC, D2N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G09196LL
GlyCosmos:  G09196LL
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.43α = 90
b = 72.1β = 90
c = 60.88γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    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, Structure summary