3L2L

X-ray Crystallographic Analysis of Pig Pancreatic Alpha-Amylase with Limit Dextrin and Oligosaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.115 

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This is version 1.1 of the entry. See complete history

Literature

X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.

Larson, S.B.Day, J.S.McPherson, A.

(2010) Biochemistry 49: 3101-3115

  • DOI: 10.1021/bi902183w
  • Primary Citation of Related Structures:  3L2M

  • PubMed Abstract: 
  • Further refinement of the model using maximum likelihood procedures and reevaluation of the native electron density map has shown that crystals of pig pancreatic alpha-amylase, whose structure we reported more than 15 years ago, in fact contain a sub ...

    Further refinement of the model using maximum likelihood procedures and reevaluation of the native electron density map has shown that crystals of pig pancreatic alpha-amylase, whose structure we reported more than 15 years ago, in fact contain a substantial amount of carbohydrate. The carbohydrate fragments are the products of glycogen digestion carried out as an essential step of the protein's purification procedure. In particular, the substrate-binding cleft contains a limit dextrin of six glucose residues, one of which contains both alpha-(1,4) and alpha-(1,6) linkages to contiguous residues. The disaccharide in the original model, shared between two amylase molecules in the crystal lattice, but also occupying a portion of the substrate-binding cleft, is now seen to be a tetrasaccharide. There are, in addition, several other probable monosaccharide binding sites. Furthermore, we have further reviewed our X-ray diffraction analysis of alpha-amylase complexed with alpha-cyclodextrin. alpha-Amylase binds three cyclodextrin molecules. Glucose residues of two of the rings superimpose upon the limit dextrin and the tetrasaccharide. The limit dextrin superimposes in large part upon linear oligosaccharide inhibitors visualized by other investigators. By comprehensive integration of these complexes we have constructed a model for the binding of polysaccharides having the helical character known to be present in natural substrates such as starch and glycogen.


    Related Citations: 
    • Refined Molecular Structure of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
      Larson, S.B.,Greenwood, A.,Cascio, D.,Day, J.,McPherson, A.
      (1994) J.Mol.Biol. 235: 1560
    • X-ray Crystallographic Analysis of Swine Pancreas Alpha-Amylase
      McPherson, A.,Rich, A.
      (1972) BIOCHIM.BIOPHYS.ACTA 285: 493


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, The University of California, Irvine, California 92697-3900, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pancreatic alpha-amylase
A
496Sus scrofaGene Names: AMY2
EC: 3.2.1.1
Find proteins for P00690 (Sus scrofa)
Go to UniProtKB:  P00690
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.115 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.590α = 90.00
b = 114.820β = 90.00
c = 118.780γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SDMSdata reduction
SDMSdata collection
SDMSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance