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protein metals links
Hydrolase PDB id
2die
Jmol
Contents
Protein chain
481 a.a. *
Metals
_NA
_CA ×3
Waters ×280
* Residue conservation analysis
PDB id:
2die
Name: Hydrolase
Title: Alkaline alpha-amylase amyk from bacillus sp. Ksm-1378
Structure: Amylase. Chain: a. Fragment: residues 1-485. Synonym: alklaine alpha-amylase amyk. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 1409. Strain: ksm-1378. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
2.10Å     R-factor:   0.177     R-free:   0.231
Authors: T.Shirai,K.Igarashi,T.Ozawa,H.Hagihara,T.Kobayashi,K.Ozaki, S.Ito
Key ref:
T.Shirai et al. (2007). 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. Proteins, 66, 600-610. PubMed id: 17154418 DOI: 10.1002/prot.21255
Date:
29-Mar-06     Release date:   13-Feb-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
O82839  (O82839_BACSP) -  Amylase
Seq:
Struc: 		516 a.a.
481 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1002/prot.21255 Proteins 66:600-610 (2007)
PubMed id: 17154418  
 
 
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.
T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, S.Ito.
 
  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 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.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) Molecular phylogeny of amylases. The sequences from known 3D structures are shown in their PDB codes, and the names and branches for other proteins were omitted to simplify the tree presentation. The numbers in parentheses are the number of proteins omitted beyond the corresponding branches. Branch b1 (green) is the alkaline adaptation branch of amylases. Branches b1 (blue) and b1 (orange) represent the evolutionary processes of the AmyK38 and AmyK relatives, respectively. (b) The residues replaced on branches b1, b1 , and b1 are shown on the AmyK structure in green, blue, and orange (same colors as in plate a), respectively. The gray and purple spheres represent calcium and sodium ions, respectively. 		Figure 4.
Figure 4. (a) The structure of the calcium-binding sites of AmyK. The calcium and sodium ions are shown in gray and purple spheres, respectively. The red spheres are solvent molecules used to coordinate the calcium ions. The residues of AmyK38 that were replaced by Asn (orange) from mainly Asp residues are superposed. The green sphere shows the position of the sodium ion in AmyK38. The residues are labeled as amino acid and residue number in AmyK and amino acid in AmyK38. (b) The active site structure of AmyK and the superposed AmyK38 structure (orange).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 66, 600-610) copyright 2007.  
  Figures were selected by the author.  
 
 
    Author's comment    
 
  The mutations relevant to the alkaline adaptation of AmyK are mapped by using ASET method (right). According to the phylogeny (left), the green sites are responsible for the foundation of the alkaline amylase family.
T.Shirai 		 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19476481 J.Pytelková, J.Hubert, M.Lepsík, J.Sobotník, R.Sindelka, I.Krízková, M.Horn, and M.Mares (2009).
Digestive alpha-amylases of the flour moth Ephestia kuehniella--adaptation to alkaline environment and plant inhibitors.
  FEBS J, 276, 3531-3546.  
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
18398906 T.Shirai, V.S.Hung, K.Morinaka, T.Kobayashi, and S.Ito (2008).
Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria.
  Proteins, 73, 126-133.
PDB code: 2ze0
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.