2DIE

Alkaline alpha-amylase AmyK from Bacillus sp. KSM-1378


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins

Shirai, T.Igarashi, K.Ozawa, T.Hagihara, H.Kobayashi, T.Ozaki, K.Ito, S.

(2007) Proteins 66: 600-610

  • DOI: 10.1002/prot.21255
  • Primary Citation of Related Structures:  
    2DIE

  • PubMed Abstract: 
  • The crystal structure of alkaline liquefying alpha-amylase (AmyK) from the alkaliphilic Bacillus sp. KSM-1378 was determined at 2.1 A resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and ...

    The crystal structure of alkaline liquefying alpha-amylase (AmyK) from the alkaliphilic Bacillus sp. KSM-1378 was determined at 2.1 A resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys-Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg-Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling.


    Organizational Affiliation

    Department of Bioscience, Nagahama Institute of Bio-science and Technology, Nagahama 526-0829, Japan. t_shirai@nagahama-i-bio.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
amylaseA485Bacillus sp. (in: Bacteria)Mutation(s): 0 
EC: 3.2.1.1
Find proteins for O82839 (Bacillus sp)
Explore O82839 
Go to UniProtKB:  O82839
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: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.577α = 90
b = 41.467β = 92.24
c = 74.855γ = 90
Software Package:
Software NamePurpose
XPRESSdata collection
DENZOdata reduction
AMoREphasing
CNSrefinement
XPRESSdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-04-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance