1HX0

Structure of pig pancreatic alpha-amylase complexed with the "truncate" acarbose molecule (pseudotrisaccharide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 

wwPDB Validation   3D Report Full Report


This is version 4.0 of the entry. See complete history


Literature

Enzyme-catalyzed condensation reaction in a mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex

Qian, M.Nahoum, V.Bonicel, J.Bischoff, H.Henrissat, B.Payan, F.

(2001) Biochemistry 40: 7700-7709

  • DOI: 10.1021/bi0102050
  • Primary Citation of Related Structures:  
    1HX0

  • PubMed Abstract: 
  • Mammalian alpha-amylases catalyze the hydrolysis of alpha-linked glucose polymers according to a complex processive mechanism. We have determined the X-ray structures of porcine pancreatic alpha-amylase complexes with the smallest molecule of the trestatin family (acarviosine-glucose) which inhibits porcine pancreatic alpha-amylase and yet is not hydrolyzed by the enzyme ...

    Mammalian alpha-amylases catalyze the hydrolysis of alpha-linked glucose polymers according to a complex processive mechanism. We have determined the X-ray structures of porcine pancreatic alpha-amylase complexes with the smallest molecule of the trestatin family (acarviosine-glucose) which inhibits porcine pancreatic alpha-amylase and yet is not hydrolyzed by the enzyme. A structure analysis at 1.38 A resolution of this complex allowed for a clear identification of a genuine single hexasaccharide species composed of two alpha-1,4-linked original molecules bound to the active site of the enzyme. The structural results supported by mass spectrometry experiments provide evidence for an enzymatically catalyzed condensation reaction in the crystal.


    Related Citations: 
    • Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose
      Gilles, C., Astier, J.P., Marchis-Mouren, G., Cambillau, C., Payan, F.
      (1996) Eur J Biochem 238: 561
    • The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution
      Qian, M., Haser, R., Buisson, G., Duee, E., Payan, F.
      (1994) Biochemistry 33: 6284

    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universities Aix-Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA AMYLASE (PPA)A496Sus scrofaMutation(s): 0 
Gene Names: AMY2
EC: 3.2.1.1
UniProt
Find proteins for P00690 (Sus scrofa)
Explore P00690 
Go to UniProtKB:  P00690
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB5N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G53811MA
GlyCosmos:  G53811MA
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , O [auth A] , P [auth A] , 
I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], G [auth A], H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Calpha-maltoseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.28α = 90
b = 113.55β = 90
c = 117.16γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2001-01-11 
  • Released Date: 2001-08-08 
  • Deposition Author(s): Qian, M., Payan, F.

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 2.0: 2018-07-25
    Changes: Atomic model, Data collection, Source and taxonomy, Structure summary
  • Version 3.0: 2019-12-25
    Changes: Data collection, Database references, Derived calculations, Polymer sequence
  • Version 4.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary