1HVX

BACILLUS STEAROTHERMOPHILUS ALPHA-AMYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability.

Suvd, D.Fujimoto, Z.Takase, K.Matsumura, M.Mizuno, H.

(2001) J Biochem 129: 461-468

  • DOI: 10.1093/oxfordjournals.jbchem.a002878
  • Primary Citation of Related Structures:  
    1HVX

  • PubMed Abstract: 
  • The crystal structure of a thermostable alpha-amylase from Bacillus stearothermophilus (BSTA) has been determined at 2.0 A resolution. The main-chain fold is almost identical to that of the known crystal structure of Bacillus licheniformis alpha-amyl ...

    The crystal structure of a thermostable alpha-amylase from Bacillus stearothermophilus (BSTA) has been determined at 2.0 A resolution. The main-chain fold is almost identical to that of the known crystal structure of Bacillus licheniformis alpha-amylase (BLA). BLA is known to be more stable than BSTA. A structural comparison between the crystal structures of BSTA and BLA showed significant differences that may account for the difference in their thermostabilities, as follows. (i) The two-residue insertion in BSTA, Ile181-Gly182, pushes away the spatially contacting region including Asp207, which corresponds to Ca(2+)-coordinating Asp204 in BLA. As a result, Asp207 cannot coordinate the Ca(2+). (ii) BSTA contains nine fewer hydrogen bonds than BLA, which costs about 12 kcal/mol. This tendency is prominent in the (beta/alpha)(8)-barrel, where 10 fewer hydrogen bonds were observed in BSTA. BLA forms a denser hydrogen bond network in the inter-helical region, which may stabilize alpha-helices in the barrel. (iii) A few small voids observed in the alpha-helical region of the (beta/alpha)(8)-barrel in BSTA decrease inter-helical compactness and hydrophobic interactions. (iv) The solvent-accessible surface area of charged residues in BLA is about two times larger than that in BSTA.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray crystallographic study of alpha-amylase from Bacillus stearothermophilus.
      Suvd, D., Takase, K., Fujiimoto, Z., Matsumura, M., Mizuno, H.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 200
    • Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution.
      Machius, M., Wiegand, G., Huber, R.
      (1995) J Mol Biol 246: 545
    • ACTIVATION OF BACILLUS LICHENIFORMIS ALPHA-AMYLASE THROUGH A DISORDER-->ORDER TRANSITION OF THE SUBSTRATE-BINDING SITE MEDIATED BY A CALCIUM-SODIUM-CALCIUM METAL TRIAD
      Machius, M., Declerck, N., Huber, R., Wiegand, R.
      (1998) Structure 6: 281

    Organizational Affiliation

    Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan. mizuno@abr.affrc.go.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-AMYLASEA515Geobacillus stearothermophilusMutation(s): 0 
Gene Names: AMYT631amyS
EC: 3.2.1.1
Find proteins for P06279 (Geobacillus stearothermophilus)
Explore P06279 
Go to UniProtKB:  P06279
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.55α = 90
b = 93.119β = 109.31
c = 53.275γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-31
    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: 2012-02-15
    Changes: Database references
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references