4R27

Crystal structure of beta-glycosidase BGL167


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Rational design of a beta-glycosidase with high regiospecificity for triterpenoid tailoring

Park, S.J.Choi, J.M.Kyeong, H.H.Kim, S.G.Kim, H.S.

(2015) Chembiochem 16: 854-860

  • DOI: https://doi.org/10.1002/cbic.201500004
  • Primary Citation of Related Structures:  
    4R27

  • PubMed Abstract: 

    Triterpenoids with desired glycosylation patterns have attracted considerable attention as potential therapeutics for inflammatory diseases and various types of cancer. Sugar-hydrolyzing enzymes with high substrate specificity would be far more efficient than other methods for the synthesis of such specialty triterpenoids, but they are yet to be developed. Here we present a strategy to rationally design a β-glycosidase with high regiospecificity for triterpenoids. A β-glycosidase with broad substrate specificity was isolated, and its crystal structure was determined at 2.0 Å resolution. Based on the product profiles and substrate docking simulations, we modeled the substrate binding modes of the enzyme. From the model, the substrate binding cleft of the enzyme was redesigned in a manner that preferentially hydrolyzes glycans at specific glycosylation sites of triterpenoids. The designed mutants were shown to produce a variety of specialty triterpenoids with high purity.


  • Organizational Affiliation

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daehak-ro, Yuseong-gu, Daejeon, 305-701 (Korea).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase
A, B
434Microbacterium sp. Gsoil167Mutation(s): 0 
EC: 3.2.1
UniProt
Find proteins for L0ELG0 (Microbacterium sp. Gsoil167)
Explore L0ELG0 
Go to UniProtKB:  L0ELG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0ELG0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.498α = 90
b = 146.94β = 101.99
c = 53.041γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description