7TAA

FAMILY 13 ALPHA AMYLASE IN COMPLEX WITH ACARBOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.

Brzozowski, A.M.Davies, G.J.

(1997) Biochemistry 36: 10837-10845

  • DOI: 10.1021/bi970539i

  • PubMed Abstract: 
  • The three-dimensional structure of the Aspergillus oryzae alpha-amylase (TAKA-amylase), in complex with the inhibitor acarbose, has been determined by X-ray crystallography at a resolution of 1. 98 A. The tetrasaccharide inhibitor is present as a hex ...

    The three-dimensional structure of the Aspergillus oryzae alpha-amylase (TAKA-amylase), in complex with the inhibitor acarbose, has been determined by X-ray crystallography at a resolution of 1. 98 A. The tetrasaccharide inhibitor is present as a hexasaccharide presumably resulting from a transglycosylation event. The hexasaccharide occupies the -3 to +3 subsites of the enzyme, consistent with the known number of subsites determined by kinetic studies, with the acarbose unit itself in the -1 to +3 subsites of the enzyme. The transition state mimicking unsaturated pseudo-saccharide occupies the -1 subsite as expected and is present in a distorted 2H3 half-chair conformation. Careful refinement plus extremely well-resolved unbiased electron density suggest that the hexasaccharide represents a genuine transglycosylation product, but the possibility that this apparent species results from an overlapping network of tetrasaccharides is also discussed. Catalysis by alpha-amylase involves the hydrolysis of the alpha-1,4 linkages in amylose with a net retention of the anomeric configuration, via a double-displacement mechanism, as originally outlined by Koshland [Koshland, D. E. (1953) Biol. Rev. 28, 416-336]. The enzymatic acid/base and nucleophile, residues Glu230 and Asp206, respectively, are appropriately positioned for catalysis in this complex, and the hexasaccharide species allows mapping of all the noncovalent interactions between protein and ligand through the enzyme's six subsites.


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York YO1 5DD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAKA AMYLASE
A
478Aspergillus oryzae (strain ATCC 42149 / RIB 40)Gene Names: amy1, amy2 (amyI, Taa-G1, amyII, Taa-G2)
EC: 3.2.1.1
Find proteins for P0C1B3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  P0C1B3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
A
MODIFIED ACARBOSE HEXASACCHARIDE
C37 H63 N O26
YXELUDMUQSCWQW-HCVSURSQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.040α = 90.00
b = 67.183β = 90.00
c = 133.560γ = 90.00
Software Package:
Software NamePurpose
AGROVATAdata reduction
DENZOdata reduction
REFMACrefinement
AGROVATAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance