PDBsum entry 1bfn

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Hydrolase PDB id
Protein chain
490 a.a. *
Waters ×318
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Beta-amylase/beta-cyclodextrin complex
Structure: Beta-amylase. Chain: a. Engineered: yes
Source: Glycine max. Soybean. Organism_taxid: 3847. Organ: seed. Expressed in: escherichia coli. Expression_system_taxid: 562
2.07Å     R-factor:   0.158     R-free:   0.211
Authors: M.Adachi,B.Mikami,T.Katsube,S.Utsumi
Key ref:
M.Adachi et al. (1998). Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin. J Biol Chem, 273, 19859-19865. PubMed id: 9677422 DOI: 10.1074/jbc.273.31.19859
22-May-98     Release date:   28-Oct-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P10538  (AMYB_SOYBN) -  Beta-amylase
496 a.a.
490 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Beta-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     3 terms  


DOI no: 10.1074/jbc.273.31.19859 J Biol Chem 273:19859-19865 (1998)
PubMed id: 9677422  
Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.
M.Adachi, B.Mikami, T.Katsube, S.Utsumi.
In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein. The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme. The crystal structure of recombinant enzyme complexed with beta-cyclodextrin was refined at 2. 07-A resolution with a final crystallographic R value of 15.8% (Rfree = 21.1%). The root mean square deviation in the position of C-alpha atoms between this recombinant enzyme and the native enzyme was 0.22 A. These results indicate that the expression system established here is suitable for studying structure-function relationships of beta-amylase. The conformation of the bound beta-cyclodextrin takes an ellipsoid shape in contrast to the circular shape of the bound alpha-cyclodextrin. The cyclodextrins shared mainly two glucose binding sites, 3 and 4. The glucose residue 4 was slightly shifted from the maltose binding site. This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate, which enables the multiple attack mechanism of beta-amylase.
  Selected figure(s)  
Figure 1.
Fig. 1. Differences among the amino acid sequences of soybean -amylase. The terminator is indicated by three asterisks. The differences in sequence are indicated by underlining. The cDNA sequence from cv. Bonminori is reported by Totsuka et al. (1).
Figure 6.
Fig. 6. Stereo view of a hypothetical single chain attack mechanism of -amylase. Thick lines indicate the substrate and produced maltose. The structures in steps 1 and 2 and in step 3 are drawn on the basis of the structure of maltose- -amylase complex (16) and -CD· -amylase complex, respectively. Numerals 1-4 and italicized numerals 3-6 show glucose residues on the four subsites (16) and those in -CD complexed with enzyme, respectively. Broken and thin lines indicate the flexible loop composed of protein residues from Gly96 to Ile^103 and other protein residues around the active site, respectively.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 19859-19865) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17918736 L.Matilainen, K.L.Larsen, R.Wimmer, P.Keski-Rahkonen, S.Auriola, T.Järvinen, and P.Jarho (2008).
The effect of cyclodextrins on chemical and physical stability of glucagon and characterization of glucagon/gamma-CD inclusion complexes.
  J Pharm Sci, 97, 2720-2729.  
12587126 A.C.Illapakurthy, Y.A.Sabnis, B.A.Avery, M.A.Avery, and C.M.Wyandt (2003).
Interaction of artemisinin and its related compounds with hydroxypropyl-beta-cyclodextrin in solution state: experimental and molecular-modeling studies.
  J Pharm Sci, 92, 649-655.  
11733023 E.J.Van Damme, J.Hu, A.Barre, B.Hause, G.Baggerman, P.Rougé, and W.J.Peumans (2001).
Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.
  Eur J Biochem, 268, 6263-6273.  
11468361 G.Pujadas, and J.Palau (2001).
Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
  Protein Sci, 10, 1645-1657.  
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