1WO2

Crystal structure of the pig pancreatic alpha-amylase complexed with malto-oligosaacharides under the effect of the chloride ion

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

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This is version 3.0 of the entry. See complete history. 


Literature

Molecular Basis of the Effects of Chloride Ion on the Acid-Base Catalyst in the Mechanism of Pancreatic alpha-Amylase

Qian, M., Ajandouz, E.H., Payan, F., Nahoum, V.

(2005) Biochemistry 44: 3194-3201

  • DOI: https://doi.org/10.1021/bi048201t
  • Primary Citation of Related Structures:  
    1WO2

  • PubMed Abstract: 

    Pig pancreatic alpha-amylase (PPA), an enzyme belonging to the alpha-amylase family, is involved in the degradation of starch. Like some other members of this family, PPA requires chloride to reach maximum activity levels. To further explain the mechanism of chloride activation, a crystal of wild-type PPA soaked with maltopentaose using a chloride-free buffer was analyzed by X-ray crystallography. A conspicuous reorientation of the acid/base catalyst Glu233 residue was found to occur. The structural results, along with kinetic data, show that the acid/base catalyst is maintained in the active site, in an optimum position, pointing toward the scissile bond-atom, due to the presence of chloride ions. The present study therefore explains the mechanism of PPA activation by chloride ions.

    • Organizational Affiliation: 

    Department of Chemical Biology, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking University, Beijing 100871, People's Republic of China.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-amylase, pancreatic496Sus scrofaMutation(s): 0 
EC: 3.2.1.1
UniProt
Find proteins for P00690 (Sus scrofa)
Explore P00690 
Go to UniProtKB:  P00690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00690
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
B, C
3N/A
Glycosylation Resources
GlyTouCan:  G00395FS
GlyCosmos:  G00395FS
GlyGen:  G00395FS
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
D
2N/A
Glycosylation Resources
GlyTouCan:  G66120GK
GlyCosmos:  G66120GK
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA
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F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
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E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Biologically Interesting Molecules (External Reference) 2 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.09α = 90
b = 113.298β = 90
c = 117.221γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-25
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 2.0: 2019-12-25
    Changes: Data collection, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary