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


Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/bi970539i
  • Primary Citation of Related Structures:  
    7TAA

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TAKA AMYLASE478Aspergillus oryzaeMutation(s): 0 
EC: 3.2.1.1
UniProt
Find proteins for P0C1B3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P0C1B3 
Go to UniProtKB:  P0C1B3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C1B3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ABC
Query on ABC

Download Ideal Coordinates CCD File 
B [auth A]MODIFIED ACARBOSE HEXASACCHARIDE
C37 H63 N O26
YXELUDMUQSCWQW-HCVSURSQSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
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 = 51.04α = 90
b = 67.183β = 90
c = 133.56γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
AGROVATAdata reduction
REFMACrefinement
AGROVATAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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