1IZJ | pdb_00001izj

Thermoactinomyces vulgaris R-47 alpha-amylase 1 mutant enzyme f313a

• PDB DOI: https://doi.org/10.2210/pdb1IZJ/pdb

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


• Deposited: 2002-10-03 Released: 2003-07-29 
• Deposition Author(s): Ohtaki, A., Iguchi, A., Mizuno, M., Tonozuka, T., Sakano, Y., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Mutual conversion of substrate specificities of Thermoactinomyces vulgaris R-47 alpha-amylases TVAI and TVAII by site-directed mutagenesis

Ohtaki, A., Iguchi, A., Mizuno, M., Tonozuka, T., Sakano, Y., Kamitori, S.

(2003) Carbohydr Res 338: 1553-1558

• PubMed: 12860426 
• DOI: https://doi.org/10.1016/s0008-6215(03)00219-2
• Primary Citation Related Structures: 
  1IZJ, 1IZK


• PubMed Abstract: 
  

  Thermoactinomyces vulgaris R-47 produces two alpha-amylases, TVAI and TVAII, differing in substrate specificity from each other. TVAI favors high-molecular-weight substrates like starch, and scarcely hydrolyzes cyclomaltooligosaccharides (cyclodextrins) with a small cavity. TVAII favors low-molecular-weight substrates like oligosaccharides, and can efficiently hydrolyze cyclodextrins with various sized cavities. To understand the relationship between the structure and substrate specificity of these enzymes, we precisely examined the roles of key residues for substrate recognition by X-ray structural and kinetic parameter analyses of mutant enzymes and successfully obtained mutants in which the substrate specificity of each enzyme is partially converted into that of another.

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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, Tokyo 184-8588, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.15 kDa 
• Atom Count: 5,346 
• Modeled Residue Count: 637 
• Deposited Residue Count: 637 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amylase	A	637	Thermoactinomyces vulgaris	Mutation(s): 1  EC: 3.2.1.1 (PDB Primary Data), 3.2.1.135 (UniProt)
UniProt
Find proteins for Q60053 (Thermoactinomyces vulgaris) Explore Q60053  Go to UniProtKB:  Q60053

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.944	α = 90
b = 50.417	β = 103.56
c = 107.92	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-29 
Deposition Author(s): Ohtaki, A., Iguchi, A., Mizuno, M., Tonozuka, T., Sakano, Y., Kamitori, S.

Revision History  

• Version 1.0: 2003-07-29
  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: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-12-27
  Changes: Data collection