1OB0

Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kinetic Stabilization of Bacillus Licheniformis Alpha-Amylase Through Introduction of Hydrophobic Residues at the Surface

Machius, M.Declerck, N.Huber, R.Wiegand, G.

(2003) J.Biol.Chem. 278: 11546

  • DOI: 10.1074/jbc.M212618200

  • PubMed Abstract: 
  • It is generally assumed that in proteins hydrophobic residues are not favorable at solvent-exposed sites, and that amino acid substitutions on the surface have little effect on protein thermostability. Contrary to these assumptions, we have identifie ...

    It is generally assumed that in proteins hydrophobic residues are not favorable at solvent-exposed sites, and that amino acid substitutions on the surface have little effect on protein thermostability. Contrary to these assumptions, we have identified hyperthermostable variants of Bacillus licheniformis alpha-amylase (BLA) that result from the incorporation of hydrophobic residues at the surface. Under highly destabilizing conditions, a variant combining five stabilizing mutations unfolds 32 times more slowly and at a temperature 13 degrees C higher than the wild-type. Crystal structure analysis at 1.7 A resolution suggests that stabilization is achieved through (a) extension of the concept of increased hydrophobic packing, usually applied to cavities, to surface indentations, (b) introduction of favorable aromatic-aromatic interactions on the surface, (c) specific stabilization of intrinsic metal binding sites, and (d) stabilization of a beta-sheet by introducing a residue with high beta-sheet forming propensity. All mutated residues are involved in forming complex, cooperative interaction networks that extend from the interior of the protein to its surface and which may therefore constitute "weak points" where BLA unfolding is initiated. This might explain the unexpectedly large effect induced by some of the substitutions on the kinetic stability of BLA. Our study shows that substantial protein stabilization can be achieved by stabilizing surface positions that participate in underlying cooperatively formed substructures. At such positions, even the apparently thermodynamically unfavorable introduction of hydrophobic residues should be explored.


    Related Citations: 
    • 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, G.
      (1998) Structure 6: 281
    • 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
    • Crystal Structure of Thermostable Alpha-Amylase from Bacillus Licheniformis Refined at 1.7 A Resolution
      Hwang, K.Y.,Song, H.K.,Chang, C.,Lee, J.,Lee, S.Y.,Kim, K.K.,Choe, S.,Sweet, R.M.,Suh, S.W.
      (1997) Mol.Cells 7: 251


    Organizational Affiliation

    University of Texas, Southwestern Medical Center at Dallas, Texas 75390, USA. Mischa.Machius@UTSouthwestern.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASE
A
483Bacillus licheniformisGene Names: amyS (amyL)
EC: 3.2.1.1
Find proteins for P06278 (Bacillus licheniformis)
Go to UniProtKB:  P06278
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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: 1.83 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.147 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 91.292α = 90.00
b = 91.292β = 90.00
c = 137.466γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-30
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance