2AAA

CALCIUM BINDING IN ALPHA-AMYLASES: AN X-RAY DIFFRACTION STUDY AT 2.1 ANGSTROMS RESOLUTION OF TWO ENZYMES FROM ASPERGILLUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus.

Boel, E.Brady, L.Brzozowski, A.M.Derewenda, Z.Dodson, G.G.Jensen, V.J.Petersen, S.B.Swift, H.Thim, L.Woldike, H.F.

(1990) Biochemistry 29: 6244-6249


  • PubMed Abstract: 
  • X-ray diffraction analysis (at 2.1-A resolution) of an acid alpha-amylase from Aspergillus niger allowed a detailed description of the stereochemistry of the calcium-binding sites. The primary site (which is essential in maintaining proper folding ar ...

    X-ray diffraction analysis (at 2.1-A resolution) of an acid alpha-amylase from Aspergillus niger allowed a detailed description of the stereochemistry of the calcium-binding sites. The primary site (which is essential in maintaining proper folding around the active site) contains a tightly bound Ca2+ with an unusually high number of eight ligands (O delta 1 and O delta 2 of Asp175, O delta of Asn121, main-chain carbonyl oxygens of Glu162 and Glu210, and three water molecules). A secondary binding site was identified at the bottom of the substrate binding cleft; it involves the residues presumed to play a catalytic role (Asp206 and Glu230). This explains the inhibitory effect of calcium observed at higher concentrations. Neutral Aspergillus oryzae (TAKA) alpha-amylase was also refined in a new crystal at 2.1-A resolution. The structure of this homologous (over 80%) enzyme and additional kinetic studies support all the structural conclusions regarding both calcium-binding sites.


    Organizational Affiliation

    Chemistry Department, University of York, Heslington, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASE
A
484Aspergillus nigerEC: 3.2.1.1
Find proteins for P56271 (Aspergillus niger)
Go to UniProtKB:  P56271
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.100α = 90.00
b = 98.300β = 90.00
c = 138.000γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-09-17
    Type: Other