2DIE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.177 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
amylase
A
485Bacillus spMutation(s): 0 
Find proteins for O82839 (Bacillus sp)
Go to UniProtKB:  O82839
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: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 174.577α = 90.00
b = 41.467β = 92.24
c = 74.855γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
XPRESSdata collection
XPRESSdata reduction
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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