1JL8

Complex of alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with beta-cyclodextrin based on a co-crystallization with methyl beta-cyclodextrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues.

Yokota, T.Tonozuka, T.Shimura, Y.Ichikawa, K.Kamitori, S.Sakano, Y.

(2001) Biosci.Biotechnol.Biochem. 65: 619-626

  • DOI: 10.1271/bbb.65.619
  • Primary Citation of Related Structures:  1JIB

  • PubMed Abstract: 
  • The structures of Thermoactinomyces vulgaris R-47 alpha-amylase II mutant (d325nTVA II) complexed with substrate analogues, methyl beta-cyclodextrin (m beta-CD) and maltohexaose (G6), were solved by X-ray diffraction at 3.2 A and 3.3 A resolution, re ...

    The structures of Thermoactinomyces vulgaris R-47 alpha-amylase II mutant (d325nTVA II) complexed with substrate analogues, methyl beta-cyclodextrin (m beta-CD) and maltohexaose (G6), were solved by X-ray diffraction at 3.2 A and 3.3 A resolution, respectively. In d325nTVA II-m beta-CD complex, the orientation and binding-position of beta-CD in TVA II were identical to those in cyclodextin glucanotransferase (CGTase). The active site residues were essentialy conserved, while there are no residues corresponding to Tyr89, Phe183, and His233 of CGTase in TVA II. In d325nTVA II-G6 complex, the electron density maps of two glucosyl units at the non-reducing end were disordered and invisible. The four glucosyl units of G6 were bound to TVA II as in CGTase, while the others were not stacked and were probably flexible. The residues of TVA II corresponding to Tyr89, Lys232, and His233 of CGTase were completely lacking. These results suggest that the lack of the residues related to alpha-glucan and CD-stacking causes the functional distinctions between CGTase and TVA II.


    Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASE II
A, B
585Thermoactinomyces vulgarisGene Names: tvaII
EC: 3.2.1.135
Find proteins for Q08751 (Thermoactinomyces vulgaris)
Go to UniProtKB:  Q08751
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCD
Query on BCD

Download SDF File 
Download CCD File 
A, B
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.019α = 90.00
b = 120.359β = 90.00
c = 113.524γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance