Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.18 kDa 
• Atom Count: 4097 
• Residue Count: 496 
• Unique protein chains: 1

1KBK

Mechanistic Analyses of Catalysis in Human Pancreatic Alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids

• DOI: 10.2210/pdb1KBK/pdb

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


• Deposited: 2001-11-06 Released: 2002-04-10 
• Deposition Author(s): Rydberg, E.H., Li, C., Maurus, R., Overall, C.M., Brayer, G.D., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.177 
• R-Value Work: 0.171 

Literature

Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.

Rydberg, E.H., Li, C., Maurus, R., Overall, C.M., Brayer, G.D., Withers, S.G.

(2002) Biochemistry 41: 4492-4502

• PubMed: 11914097 
• DOI: 10.1021/bi011821z
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The roles of three conserved active site carboxylic acids (D197, E233, and D300) in the catalytic mechanism of human pancreatic alpha-amylase (HPA) were studied by utilizing site-directed mutagenesis in combination with structural and kinetic analyses of the resultant enzymes. All three residues were mutated to both alanine and the respective amide, and a double alanine mutant (E233A/D300A) was also generated. Structural analyses demonstrated that there were no significant differences in global fold for the mutant enzymes. Kinetic analyses were performed on the mutants, utilizing a range of substrates. All results suggested that D197 was the nucleophile, as virtually all activity (>10(5)-fold decrease in k(cat) values) was lost for the enzymes mutated at this position when assayed with several substrates. The significantly greater second-order rate constant of E233 mutants on "activated" substrates (k(cat)/K(m) value for alpha-maltotriosyl fluoride = 15 s(-)(1) mM(-)(1)) compared with "unactivated" substrates (k(cat)/K(m) value for maltopentaose = 0.0030 s(-)(1) mM(-)(1)) strongly suggested that E233 is the general acid catalyst, as did the pH-activity profiles. Transglycosylation was favored over hydrolysis for the reactions of several of the enzymes mutated at D300. At the least, this suggests an overall impairment of the catalytic mechanism where the reaction then proceeds using the better acceptor (oligosaccharide instead of water). This may also suggest that D300 plays a crucial role in enzymic interactions with the nucleophilic water during the hydrolysis of the glycosidic bond.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALPHA-AMYLASE, PANCREATIC	A	496	Homo sapiens	Mutation(s): 1  Gene Names: AMY2A EC: 3.2.1.1
Find proteins for P04746 (Homo sapiens) Go to UniProtKB:  P04746
NIH Common Fund Data Resources
PHAROS  P04746 GTEx  ENSG00000243480

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.177 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.88	α = 90
b = 69.52	β = 90
c = 131.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-06 
• Released Date: 2002-04-10 
Deposition Author(s): Rydberg, E.H., Li, C., Maurus, R., Overall, C.M., Brayer, G.D., Withers, S.G.

Revision History 

• Version 1.0: 2002-04-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence