1WO2 | pdb_00001wo2

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

• PDB DOI: https://doi.org/10.2210/pdb1WO2/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-11 Released: 2005-03-15 
• Deposition Author(s): Qian, M., Payan, F., Nahoum, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.184 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

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

• PubMed: 15736930 
• DOI: https://doi.org/10.1021/bi048201t
• Primary Citation 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.27 kDa 
• Atom Count: 4,822 
• Modeled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase, pancreatic	A	496	Sus scrofa	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for P00690 (Sus scrofa) Explore P00690  Go to UniProtKB:  P00690

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B, C	3		N/A
Glycosylation Resources
GlyTouCan: G00395FS GlyCosmos: G00395FS GlyGen: G00395FS

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan: G66120GK GlyCosmos: G66120GK

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	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	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900065	B, C	beta-maltotriose	Oligosaccharide / Nutrient

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900018	D	beta-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.184 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.09	α = 90
b = 113.298	β = 90
c = 117.221	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
X-PLOR	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Qian, M., Payan, F., Nahoum, V.

Revision History  

• 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
• Version 3.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary