1J0J

Crystal structure of neopullulanase E357Q complex with maltotetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • Primary Citation of Related Structures:  1J0H, 1J0I, 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 substrate ...

    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.


    Related Citations: 
    • Pattern of action of Bacillus stearothermophilus neopullulanase on pullulan
      Imanaka, T.,Kuriki, T.
      (1989) J.Bacteriol. 171: 369
    • Action of neopullulanase. neopullulanase catalyzes both hydrolysis and transglycosylation at alpha-(1,4)- and alpha-(1,6)-glucosidic linkages
      Takata, H.,Kuriki, T.,Okada, S.,Takesada, Y.,Iizuka, M.,Minamiura, N.,Imanaka, T.
      (1992) J.Biol.Chem. 267: 18447
    • New type of pullulanase from Bacillus stearothermophilus and molecular cloning and expression of the gene in Bacillus subtilis
      Kuriki, T.,Okada, S.,Imanaka, T.
      (1988) J.Bacteriol. 170: 1554


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
neopullulanase
A, B
588Geobacillus stearothermophilusGene Names: nplT
EC: 3.2.1.135
Find proteins for P38940 (Geobacillus stearothermophilus)
Go to UniProtKB:  P38940
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.806α = 90.00
b = 74.407β = 90.02
c = 123.330γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
AMoREphasing
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance