3WH7

Crystal structure of GH1 beta-glucosidase Td2F2 L-fucose complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity and transglycosylation activity of metagenomic beta-glucosidase Td2F2

Matsuzawa, T.Jo, T.Uchiyama, T.Manninen, J.A.Arakawa, T.Miyazaki, K.Fushinobu, S.Yaoi, K.

(2016) Febs J. --: --

  • DOI: 10.1111/febs.13743
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Glucosidase Td2F2 isolated from a compost metagenome has high glucose tolerance and transglycosylation activity. In this study, we determined the high-resolution crystal structure of Td2F2. It has a unique structure at the -1 subsite that is import ...

    β-Glucosidase Td2F2 isolated from a compost metagenome has high glucose tolerance and transglycosylation activity. In this study, we determined the high-resolution crystal structure of Td2F2. It has a unique structure at the -1 subsite that is important for substrate specificity but not for glucose tolerance. To elucidate the mechanism(s) of glucose tolerance, we isolated a glucose-sensitive Td2F2 mutant using random mutagenesis. In this mutant, Asn223 residue located between subsites +1 and +2 was mutated. The Asn223 mutation resulted in reduced glucose tolerance and transglycosylation activity, and drastically changed substrate specificity. These results indicate that the structure between subsites +1 and +2 is critical for the glucose tolerance and substrate specificity of Td2F2. Our findings shed light on the glucose tolerance and transglycosylation activity mechanisms of glycoside hydrolase family 1 β-glucosidases.


    Related Citations: 
    • Characterization of a novel beta-glucosidase from a compost microbial metagenome with strong transglycosylation activity
      Uchiyama, T.,Miyazaki, K.,Yaoi, K.
      (2013) J.Biol.Chem. 288: 18325


    Organizational Affiliation

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.,Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.,Department of Biotechnology, The University of Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta-glucosidase
A
457N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download SDF File 
Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
FCB
Query on FCB

Download SDF File 
Download CCD File 
A
BETA-D-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-FPRJBGLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.113 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.050α = 90.00
b = 69.693β = 90.00
c = 96.209γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references