Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56228.04 
• Atom Count: 3962 
• Residue Count: 496 
• Unique protein chains: 1

1BSI

HUMAN PANCREATIC ALPHA-AMYLASE FROM PICHIA PASTORIS, GLYCOSYLATED PROTEIN

• DOI: 10.2210/pdb1BSI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris


• Deposited: 1998-08-28 Released: 1999-05-18 
• Deposition Author(s): Rydberg, E.H., Sidhu, G., Vo, H.C., Hewitt, J., Cote, H.C.F., Wang, Y., Numao, S., Macgillivray, R.T.A., Overall, C.M., Brayer, G.D., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.184 

Literature

Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.

Rydberg, E.H., Sidhu, G., Vo, H.C., Hewitt, J., Cote, H.C., Wang, Y., Numao, S., MacGillivray, R.T., Overall, C.M., Brayer, G.D., Withers, S.G.

(1999) Protein Sci. 8: 635-643

• PubMed: 10091666 
• DOI: 10.1110/ps.8.3.635


• PubMed Abstract: 
  

Human pancreatic alpha-amylase (HPA) was expressed in the methylotrophic yeast Pichia pastoris and two mutants (D197A and D197N) of a completely conserved active site carboxylic acid were generated. All recombinant proteins were shown by electrospray ionization mass spectrometry (ESI-MS) to be glycosylated and the site of attachment was shown to be Asn461 by peptide mapping in conjunction with ESI-MS. Treatment of these proteins with endoglycosidase F demonstrated that they contained a single N-linked oligosaccharide and yielded a protein product with a single N-acetyl glucosamine (GlcNAc), which could be crystallized. Solution of the crystal structure to a resolution of 2.0 A confirmed the location of the glycosyl group as Asn461 and showed that the recombinant protein had essentially the same conformation as the native enzyme. The kinetic parameters of the glycosylated and deglycosylated wild-type proteins were the same while the k(cat)/Km values for D197A and D197N were 10(6)-10(7) times lower than the wild-type enzyme. The decreased k(cat)/Km values for the mutants confirm that D197 plays a crucial role in the hydrolytic activity of HPA, presumably as the catalytic nucleophile.

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Organizational Affiliation: 

Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALPHA-AMYLASE	A	496	Homo sapiens	Mutation(s): 0  Gene Names: AMY2A EC: 3.2.1.1
Find proteins for P04746 (Homo sapiens) Go to Gene View: AMY2A Go to UniProtKB:  P04746

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 52.910	α = 90.00
b = 68.900	β = 90.00
c = 131.770	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-28 
• Released Date: 1999-05-18 
• Deposition Author(s): Rydberg, E.H., Sidhu, G., Vo, H.C., Hewitt, J., Cote, H.C.F., Wang, Y., Numao, S., Macgillivray, R.T.A., Overall, C.M., Brayer, G.D., Withers, S.G.

Revision History 

• Version 1.0: 1999-05-18
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance