Ctystal structure of glycosyltrehalose trehalohydrolase (D252E)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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Substrate recognition mechanism of a glycosyltrehalose trehalohydrolase from Sulfolobus solfataricus KM1.

Okazaki, N.Tamada, T.Feese, M.D.Kato, M.Miura, Y.Komeda, T.Kobayashi, K.Kondo, K.Blaber, M.Kuroki, R.

(2012) Protein Sci 21: 539-552

  • DOI: https://doi.org/10.1002/pro.2039
  • Primary Citation of Related Structures:  
    3VGB, 3VGD, 3VGE, 3VGF, 3VGG, 3VGH

  • PubMed Abstract: 

    Glycosyltrehalose trehalohydrolase (GTHase) is an α-amylase that cleaves the α-1,4 bond adjacent to the α-1,1 bond of maltooligosyltrehalose to release trehalose. To investigate the catalytic and substrate recognition mechanisms of GTHase, two residues, Asp252 (nucleophile) and Glu283 (general acid/base), located at the catalytic site of GTHase were mutated (Asp252→Ser (D252S), Glu (D252E) and Glu283→Gln (E283Q)), and the activity and structure of the enzyme were investigated. The E283Q, D252E, and D252S mutants showed only 0.04, 0.03, and 0.6% of enzymatic activity against the wild-type, respectively. The crystal structure of the E283Q mutant GTHase in complex with the substrate, maltotriosyltrehalose (G3-Tre), was determined to 2.6-Å resolution. The structure with G3-Tre indicated that GTHase has at least five substrate binding subsites and that Glu283 is the catalytic acid, and Asp252 is the nucleophile that attacks the C1 carbon in the glycosidic linkage of G3-Tre. The complex structure also revealed a scheme for substrate recognition by GTHase. Substrate recognition involves two unique interactions: stacking of Tyr325 with the terminal glucose ring of the trehalose moiety and perpendicularly placement of Trp215 to the pyranose rings at the subsites -1 and +1 glucose.

  • Organizational Affiliation

    Molecular Biology Research Division, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malto-oligosyltrehalose trehalohydrolase558Saccharolobus solfataricusMutation(s): 1 
Gene Names: treZ
Find proteins for Q55088 (Saccharolobus solfataricus)
Explore Q55088 
Go to UniProtKB:  Q55088
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55088
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.881α = 90
b = 78.881β = 90
c = 282.53γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description