1XD1

Acarbose Rearrangement Mechanism Implied by the Kinetic and Structural Analysis of Human Pancreatic alpha-Amylase in Complex with Analogues and Their Elongated Counterparts


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Acarbose Rearrangement Mechanism Implied by the Kinetic and Structural Analysis of Human Pancreatic alpha-Amylase in Complex with Analogues and Their Elongated Counterparts

Li, C.Begum, A.Numao, S.Park, K.H.Withers, S.G.Brayer, G.D.

(2005) Biochemistry 44: 3347-3357

  • DOI: 10.1021/bi048334e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A mechanistic study of the poorly understood pathway by which the inhibitor acarbose is enzymatically rearranged by human pancreatic alpha-amylase has been conducted by structurally examining the binding modes of the related inhibitors isoacarbose an ...

    A mechanistic study of the poorly understood pathway by which the inhibitor acarbose is enzymatically rearranged by human pancreatic alpha-amylase has been conducted by structurally examining the binding modes of the related inhibitors isoacarbose and acarviosine-glucose, and by novel kinetic measurements of all three inhibitors under conditions that demonstrate this rearrangement process. Unlike acarbose, isoacarbose has a unique terminal alpha-(1-6) linkage to glucose and is found to be resistant to enzymatic rearrangement. This terminal glucose unit is found to bind in the +3 subsite and for the first time reveals the interactions that occur in this part of the active site cleft with certainty. These results also suggest that the +3 binding subsite may be sufficiently flexible to bind the alpha-(1-6) branch points in polysaccharide substrates, and therefore may play a role in allowing efficient cleavage in the direct vicinity of such junctures. Also found to be resistant to enzymatic rearrangement was acarviosine-glucose, which has one fewer glucose unit than acarbose. Collectively, structural studies of all three inhibitors and the specific cleavage pattern of HPA make it possible to outline the simplest sequence of enzymatic reactions likely involved upon acarbose binding. Prominent features incorporated into the starting structure of acarbose to facilitate the synthesis of the final tightly bound pseudo-pentasaccharide product are the restricted availability of hydrolyzable bonds and the placement of the transition state-like acarviosine group. Additional "in situ" experiments designed to elongate and thereby optimize isoacarbose and acarviosine-glucose inhibition using the activated substrate alphaG3F demonstrate the feasibility of this approach and that the principles outlined for acarbose rearrangement can be used to predict the final products that were obtained.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase
A
496Homo sapiensMutation(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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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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
6SA
Query on 6SA

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A
ACARBOSE DERIVED HEXASACCHARIDE
4,6-DIDEOXY-4-{[(4R,5R)-4-[(4-O-ALPHA-D-ERYTHRO-HEXOPYRANOSYL-ALPHA-D-ERYTHRO-HEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}-BETA-D-LYXO-HEXOPYRANOSYL-(1->4)-ALPHA-D-XYLO-HEXOPYRANOSYL-(1->6)-BETA-D-ARABINO-HEXOPYRANOSE
C37 H63 N O28
MBNITLCAVXHYER-DHAMQIFDSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6SAKi: 12 nM (99) BINDINGDB
6SAKi: 12 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.700α = 90.00
b = 69.000β = 90.00
c = 132.300γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance