PDBsum entry 1vem

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Hydrolase PDB id
Protein chain
516 a.a. *
Waters ×283
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure analysis of bacillus cereus beta-amylase at the optimum ph (6.5)
Structure: Beta-amylase. Chain: a. Synonym: 1,4-alpha-d-glucan maltohydrolase, glycoside hydrolase family 14. Engineered: yes
Source: Bacillus cereus. Organism_taxid: 1396. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.85Å     R-factor:   0.176     R-free:   0.205
Authors: A.Hirata,M.Adachi,S.Utsumi,B.Mikami
Key ref:
A.Hirata et al. (2004). Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type. Biochemistry, 43, 12523-12531. PubMed id: 15449941 DOI: 10.1021/bi049173h
03-Apr-04     Release date:   24-May-05    
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Protein chain
Pfam   ArchSchema ?
P36924  (AMYB_BACCE) -  Beta-amylase
546 a.a.
516 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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   4 terms 
  Biochemical function     starch binding     5 terms  


DOI no: 10.1021/bi049173h Biochemistry 43:12523-12531 (2004)
PubMed id: 15449941  
Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type.
A.Hirata, M.Adachi, S.Utsumi, B.Mikami.
The optimum pH of Bacillus cereus beta-amylase (BCB, pH 6.7) differs from that of soybean beta-amylase (SBA, pH 5.4) due to the substitution of a few amino acid residues near the catalytic base residue (Glu 380 in SBA and Glu 367 in BCB). To explore the mechanism for controlling the optimum pH of beta-amylase, five mutants of BCB (Y164E, Y164F, Y164H, Y164Q, and Y164Q/T47M/Y164E/T328N) were constructed and characterized with respect to enzymatic properties and X-ray structural crystal analysis. The optimum pH of the four single mutants shifted to 4.2-4.8, approximately 2 pH units and approximately 1 pH unit lower than those of BCB and SBA, respectively, and their k(cat) values decreased to 41-3% of that of the wild-type enzyme. The X-ray crystal analysis of the enzyme-maltose complexes showed that Glu 367 of the wild type is surrounded by two water molecules (W1 and W2) that are not found in SBA. W1 is hydrogen-bonded to both side chains of Glu 367 and Tyr 164. The mutation of Tyr 164 to Glu and Phe resulted in the disruption of the hydrogen bond between Tyr 164 Oeta and W1 and the introduction of two additional water molecules near position 164. In contrast, the triple mutant of BCB with a slightly decreased pH optimum at pH 6.0 has no water molecules (W1 and W2) around Glu 367. These results suggested that a water-mediated hydrogen bond network (Glu 367...W1...Tyr 164...Thr 328) is the primary requisite for the increased pH optimum of wild-type BCB. This strategy is completely different from that of SBA, in which a hydrogen bond network (Glu 380...Thr 340...Glu 178) reduces the optimum pH in a hydrophobic environment.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20157910 L.Zhu, K.L.Tee, D.Roccatano, B.Sonmez, Y.Ni, Z.H.Sun, and U.Schwaneberg (2010).
Directed evolution of an antitumor drug (arginine deiminase PpADI) for increased activity at physiological pH.
  Chembiochem, 11, 691-697.  
17189477 B.M.Tynan-Connolly, and J.E.Nielsen (2007).
Redesigning protein pKa values.
  Protein Sci, 16, 239-249.  
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