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PDBsum entry 5bca

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
5bca
Jmol
Contents
Protein chains
516 a.a. *
Metals
_CA ×4
Waters ×752
* Residue conservation analysis
PDB id:
5bca
Name: Hydrolase
Title: Beta-amylase from bacillus cereus var. Mycoides
Structure: Protein (1,4-alpha-d-glucan maltohydrolase.). Chain: a, b, c, d. Ec: 3.2.1.2
Source: Bacillus cereus. Organism_taxid: 1396. Strain: bacillus cereus. Variant: mycoides. Cellular_location: extracellular
Resolution:
2.20Å     R-factor:   0.186     R-free:   0.240
Authors: T.Oyama,M.Kusunoki,Y.Kishimoto,Y.Takasaki,Y.Nitta
Key ref: T.Oyama et al. (1999). Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution. J Biochem, 125, 1120-1130. PubMed id: 10348915
Date:
12-Mar-99     Release date:   15-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36924  (AMYB_BACCE) -  Beta-amylase
Seq:
Struc:
 
Seq:
Struc:
546 a.a.
516 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.2  - 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   4 terms 
  Biochemical function     starch binding     5 terms  

 

 
J Biochem 125:1120-1130 (1999)
PubMed id: 10348915  
 
 
Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.
T.Oyama, M.Kusunoki, Y.Kishimoto, Y.Takasaki, Y.Nitta.
 
  ABSTRACT  
 
The crystal structure of beta-amylase from Bacillus cereus var. mycoides was determined by the multiple isomorphous replacement method. The structure was refined to a final R-factor of 0.186 for 102,807 independent reflections with F/sigma(F) > or = 2.0 at 2.2 A resolution with root-mean-square deviations from ideality in bond lengths, and bond angles of 0.014 A and 3.00 degrees, respectively. The asymmetric unit comprises four molecules exhibiting a dimer-of-dimers structure. The enzyme, however, acts as a monomer in solution. The beta-amylase molecule folds into three domains; the first one is the N-terminal catalytic domain with a (beta/alpha)8 barrel, the second one is the excursion part from the first one, and the third one is the C-terminal domain with two almost anti-parallel beta-sheets. The active site cleft, including two putative catalytic residues (Glu172 and Glu367), is located on the carboxyl side of the central beta-sheet in the (beta/alpha)8 barrel, as in most amylases. The active site structure of the enzyme resembles that of soybean beta-amylase with slight differences. One calcium ion is bound per molecule far from the active site. The C-terminal domain has a fold similar to the raw starch binding domains of cyclodextrin glycosyltransferase and glucoamylase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
16262690 M.Machovic, B.Svensson, E.A.MacGregor, and S.Janecek (2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
  FEBS J, 272, 5497-5513.  
11272837 Y.Mezaki, Y.Katsuya, M.Kubota, and Y.Matsuura (2001).
Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
  Biosci Biotechnol Biochem, 65, 222-225.
PDB code: 1gcy
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