3IJ9

Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic a-Amylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Directed "in situ" inhibitor elongation as a strategy to structurally characterize the covalent glycosyl-enzyme intermediate of human pancreatic alpha-amylase

Zhang, R.Li, C.Williams, L.K.Rempel, B.P.Brayer, G.D.Withers, S.G.

(2009) Biochemistry 48: 10752-10764

  • DOI: 10.1021/bi901400p
  • Primary Citation of Related Structures:  3IJ7, 3IJ8

  • PubMed Abstract: 
  • While covalent catalytic intermediates of retaining alpha-transglycosylases have been structurally characterized previously, no such information for a hydrolytic alpha-amylase has been obtained. This study presents a new "in situ" enzymatic elongatio ...

    While covalent catalytic intermediates of retaining alpha-transglycosylases have been structurally characterized previously, no such information for a hydrolytic alpha-amylase has been obtained. This study presents a new "in situ" enzymatic elongation methodology that, for the first time, has allowed the isolation and structural characterization of a catalytically competent covalent glycosyl-enzyme intermediate with human pancreatic alpha-amylase. This has been achieved by the use of a 5-fluoro-beta-l-idosyl fluoride "warhead" in conjunction with either alpha-maltotriosyl fluoride or 4'-O-methyl-alpha-maltosyl fluoride as elongation agents. This generates an oligosaccharyl-5-fluoroglycosyl fluoride that then reacts with the free enzyme. The resultant covalent intermediates are extremely stable, with hydrolytic half-lives on the order of 240 h for the trisaccharide complex. In the presence of maltose, however, they undergo turnover via transglycosylation according to a half-life of less than 1 h. Structural studies of intermediate complexes unambiguously show the covalent attachment of a 5-fluoro-alpha-l-idosyl moiety in the chair conformation to the side chain of the catalytic nucleophile D197. The elongated portions of the intermediate complexes are found to bind in the high-affinity -2 and -3 binding subsites, forming extensive hydrogen-bonding interactions. Comparative structural analyses with the related noncovalent complex formed by acarbose highlight the structural rigidity of the enzyme surface during catalysis and the key role that substrate conformational flexibility must play in this process. Taken together, the structural data provide atomic details of several key catalytic steps. The scope of this elongation approach to probe the active sites and catalytic mechanisms of alpha-amylases is further demonstrated through preliminary experiments with porcine pancreatic alpha-amylase.


    Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pancreatic alpha-amylase
A
496Homo sapiensGene 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B9D
Query on B9D

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Download CCD File 
A
(2R,3R,4R,5S,6R)-6-fluoranyl-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
C6 H11 F O6
YQZCKDSOGGIGPL-DVKNGEFBSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
B0D
Query on B0D

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Download CCD File 
A
(2R,3S,4R,5R,6R)-2,6-difluoro-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol
C6 H10 F2 O5
MGHYRMVVRYCAON-PQMKYFCFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.380α = 90.00
b = 68.000β = 90.00
c = 129.950γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance