1B90

BACILLUS CEREUS BETA-AMYLASE APO FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.

Mikami, B.Adachi, M.Kage, T.Sarikaya, E.Nanmori, T.Shinke, R.Utsumi, S.

(1999) Biochemistry 38: 7050-7061

  • DOI: https://doi.org/10.1021/bi9829377
  • Primary Citation of Related Structures:  
    1B90, 1B9Z

  • PubMed Abstract: 

    The crystals of beta-amylase from Bacillus cereus belong to space group P21 with the following cell dimensions: a = 57.70 A, b = 92.87 A, c = 65.93 A, and beta =101.95 degrees. The structures of free and maltose-bound beta-amylases were determined by X-ray crystallography at 2.1 and 2.5 A with R-factors of 0.170 and 0.164, respectively. The final model of the maltose-bound form comprises 516 amino acid residues, four maltose molecules, 275 water molecules, one Ca2+, one acetate, and one sulfate ion. The enzyme consists of a core (beta/alpha)8-barrel domain (residues 5-434) and a C-terminal starch-binding domain (residues 435-613). Besides the active site in the core where two maltose molecules are bound in tandem, two novel maltose-binding sites were found in the core L4 region and in the C-terminal domain. The structure of the core domain is similar to that of soybean beta-amylase except for the L4 maltose-binding site, whereas the C-terminal domain has the same secondary structure as domain E of cyclodextrin glucosyltransferase. These two maltose-binding sites are 32-36 A apart from the active site. These results indicate that the ability of B. cereus beta-amylase to digest raw starch can be attributed to the additional two maltose-binding sites.


  • Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Japan. mikami@soya.food.kyoto-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (BETA-AMYLASE)516Bacillus cereusMutation(s): 0 
EC: 3.2.1.2
UniProt
Find proteins for P36924 (Bacillus cereus)
Explore P36924 
Go to UniProtKB:  P36924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36924
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.075α = 90
b = 92.103β = 101.81
c = 65.671γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-15
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Structure summary