1WO2

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.

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

wwPDB Validation 3D Report Full Report

This is version 3.1 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

PubMed: 15736930 Search on PubMed
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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00690
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on 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 Query on PRD_900065	B, C	beta-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900018 Query on PRD_900018	D	beta-maltose	Oligosaccharide / Nutrient		Interactions Focus chain D Interactions & Density Focus chain D

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 = 70.09	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-03-15

Deposition Author(s):

Qian, M.

Payan, F.

Nahoum, V.

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