1JF5 | pdb_00001jf5

CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 2 MUTANT F286A

• PDB DOI: https://doi.org/10.2210/pdb1JF5/pdb

• Classification: HYDROLASE
• Organism(s): Thermoactinomyces vulgaris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-06-20 Released: 2002-05-22 
• Deposition Author(s): Ohtaki, A., Kondo, S., Shimura, Y., Tonozuka, T., Sakano, Y., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs

Ohtaki, A., Kondo, S., Shimura, Y., Tonozuka, T., Sakano, Y., Kamitori, S.

(2001) Carbohydr Res 334: 309-313

• PubMed: 11527532 
• DOI: https://doi.org/10.1016/s0008-6215(01)00190-2
• Primary Citation Related Structures: 
  1JF5, 1JF6


• PubMed Abstract: 
  

  Phe286 located in the center of the active site of alpha-amylase 2 from Thermoactinomyces vulgaris R-47 (TVAII) plays an important role in the substrate recognition for cyclomaltooligosaccharides (cyclodextrins). The X-ray structures of mutant TVAIIs with the replacement of Phe286 by Ala (F286A) and Tyr (F286Y) were determined at 3.2 A resolution. Their structures have no significant differences from that of the wild-type enzyme. The kinetic analyses of Phe286-replaced variants showed that the variants with non-aromatic residues, Ala (F286A) and Leu (F286L), have lower enzymatic activities than those with aromatic residues, Tyr (F286Y) and Trp (F286W), and the replacement of Phe286 affects enzymatic activities for CDs more than those for starch.

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Organizational Affiliation: 
• Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, 184-8588, Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 135.04 kDa 
• Atom Count: 9,542 
• Modeled Residue Count: 1,170 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA AMYLASE II	A, B	585	Thermoactinomyces vulgaris	Mutation(s): 1  EC: 3.2.1.135
UniProt
Find proteins for Q08751 (Thermoactinomyces vulgaris) Explore Q08751  Go to UniProtKB:  Q08751

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.6	α = 90
b = 118.05	β = 90
c = 113.13	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-22 
Deposition Author(s): Ohtaki, A., Kondo, S., Shimura, Y., Tonozuka, T., Sakano, Y., Kamitori, S.

Revision History  

• Version 1.0: 2002-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection