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PDBsum entry 1ud2

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protein ligands metals links
Hydrolase PDB id
1ud2
Jmol
Contents
Protein chain
480 a.a. *
Ligands
GOL
Metals
_NA ×3
Waters ×298
* Residue conservation analysis
PDB id:
1ud2
Name: Hydrolase
Title: Crystal structure of calcium-free alpha-amylase from bacillu strain ksm-k38 (amyk38)
Structure: Amylase. Chain: a. Fragment: residues 1-480. Synonym: alpha-amylase. Engineered: yes
Source: Bacillus sp. Ksm-k38. Organism_taxid: 129736. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
2.13Å     R-factor:   0.196     R-free:   0.229
Authors: T.Nonaka,M.Fujihashi,A.Kita,H.Hagihara,K.Ozaki,S.Ito,K.Miki
Key ref:
T.Nonaka et al. (2003). Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites. J Biol Chem, 278, 24818-24824. PubMed id: 12719434 DOI: 10.1074/jbc.M212763200
Date:
28-Apr-03     Release date:   22-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q93I48  (Q93I48_9BACI) -  Amylase
Seq:
Struc:
501 a.a.
480 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1074/jbc.M212763200 J Biol Chem 278:24818-24824 (2003)
PubMed id: 12719434  
 
 
Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.
T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki.
 
  ABSTRACT  
 
The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Stereo view of the ribbon model of the overall structure of AmyK38. Three domains (A, B, and C) are shown in red, blue, and green, respectively. Three sodium ions, Na I, Na II, and Na III, are shown as yellow spheres. The N and C termini of AmyK38 are in the domains A and C, respectively. Domain A is the most well conserved ( / )[8]-barrel domain in -amylases. Domain C, which is composed of -strands with the socalled Greek key motif, is also conserved in amylolytic enzymes, except in barley -amylase. Na I and Na II are located at the sites corresponding to the Ca^2^+ ions (Ca I and Ca III) in the BLA structure. These figures were drawn by MOLSCRIPT and Raster3D (34, 35).
Figure 3.
FIG. 3. Stereo views of three sodium ions binding sites of AmyK38 and BLA (Protein Data Bank accession code 1bli [PDB] (1)). Pentagonal and quadrilateral bipyramidal cages surrounding metal ions are drawn by solid or broken lines. Sodium and calcium ions are drawn as yellow and sky-blue spheres, respectively. These figures were drawn by MOLSCRIPT, Raster3D, and Conscript (34-36). In a, the [A] weighted omit map (lightblue; contoured at 4.0 ) is shown, and refined models of the Na I site of wild-type AmyK38 are shown in the upper section. The model in the lower section is the calcium-sodium-calcium triad containing the Ca I site of BLA corresponding to the Na I site of AmyK38. In b, the [A] weighted omit map (light blue; contoured at 4.0 ) is shown, and refined models of the Na II site of wild-type AmyK38 are shown in the upper section. The model in the lower section is the Ca III site of BLA corresponding to the Na II site of AmyK38. In c, the [A] weighted omit map (light blue; contoured at 4.0 ) is shown, and the refined model of the Na III site of wild-type AmyK38 is shown in the upper section. The model in the lower section is the site of BLA corresponding to the Na III site of AmyK38. d, the superimposition of the refined structure of N289H AmyK38 on BLA around the corresponding site of the Na III site in wild-type AmyK38. The model of BLA is drawn transparently.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 24818-24824) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20453894 O.I.Kubrak, J.M.Storey, K.B.Storey, and V.I.Lushchak (2010).
Production and properties of alpha-amylase from Bacillus sp. BKL20.
  Can J Microbiol, 56, 279-288.  
19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
  Appl Biochem Biotechnol, 160, 2401-2414.  
17598074 R.Priyadharshini, and P.Gunasekaran (2007).
Site-directed mutagenesis of the calcium-binding site of alpha-amylase of Bacillus licheniformis.
  Biotechnol Lett, 29, 1493-1499.  
17154418 T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, and S.Ito (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.
PDB code: 2die
16710633 K.Hirasawa, K.Uchimura, M.Kashiwa, W.D.Grant, S.Ito, T.Kobayashi, and K.Horikoshi (2006).
Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens.
  Antonie Van Leeuwenhoek, 89, 211-219.  
17068753 N.Wang, Y.Zhang, Q.Wang, J.Liu, H.Wang, Y.Xue, and Y.Ma (2006).
Gene cloning and characterization of a novel alpha-amylase from alkaliphilic Alkalimonas amylolytica.
  Biotechnol J, 1, 1258-1265.  
16452622 R.Kanai, K.Haga, T.Akiba, K.Yamane, and K.Harata (2006).
Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707.
  Protein Sci, 15, 468-477.
PDB codes: 2d3l 2d3n
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