1J0H

Crystal structure of Bacillus stearothermophilus neopullulanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional Structure and Substrate Binding of Bacillus stearothermophilus Neopullulanase

Hondoh, H.Kuriki, T.Matsuura, Y.

(2003) J Mol Biol 326: 177-188

  • DOI: https://doi.org/10.1016/s0022-2836(02)01402-x
  • Primary Citation of Related Structures:  
    1J0H, 1J0I, 1J0J, 1J0K

  • PubMed Abstract: 

    Crystal structures of Bacillus stearothermophilus TRS40 neopullulanase and its complexes with panose, maltotetraose and isopanose were determined at resolutions of 1.9, 2.4, 2.8 and 3.2A, respectively. Since the latter two carbohydrates are substrates of this enzyme, a deactivated mutant at the catalytic residue Glu357-->Gln was used for complex crystallization. The structures were refined at accuracies with r.m.s. deviations of bond lengths and bond angles ranging from 0.005A to 0.008A and 1.3 degrees to 1.4 degrees, respectively. The active enzyme forms a dimer in the crystalline state and in solution. The monomer enzyme is composed of four domains, N, A, B and C, and has a (beta/alpha)(8)-barrel in domain A. The active site lies between domain A and domain N from the other monomer. The results show that dimer formation makes the active-site cleft narrower than those of ordinary alpha-amylases, which may contribute to the unique substrate specificity of this enzyme toward both alpha-1,4 and alpha-1,6-glucosidic linkages. This specificity may be influenced by the subsite structure. Only subsites -1 and -2 are commonly occupied by the product and substrates, suggesting that equivocal recognition occurs at the other subsites, which contributes to the wide substrate specificity of this enzyme.


  • Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, 565-0871, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
neopullulanase
A, B
588Geobacillus stearothermophilusMutation(s): 0 
EC: 3.2.1.135
UniProt
Find proteins for P38940 (Geobacillus stearothermophilus)
Explore P38940 
Go to UniProtKB:  P38940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38940
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.713α = 90
b = 72.762β = 90.84
c = 123.64γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    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