4HZ7

Crystal structure of BglB with glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into the substrate recognition properties of beta-glucosidase.

Nam, K.H.Sung, M.W.Hwang, K.Y.

(2010) Biochem.Biophys.Res.Commun. 391: 1131-1135

  • DOI: 10.1016/j.bbrc.2009.12.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beta-glucosidase enzymes (EC 3.2.1-3.2.3) hydrolyze sugars and are implicated in a wide spectrum of biological processes. Recently, we reported that beta-glucosidase has varied kinetic parameters for the natural and synthetic substrates [K.H Nam, S.J ...

    Beta-glucosidase enzymes (EC 3.2.1-3.2.3) hydrolyze sugars and are implicated in a wide spectrum of biological processes. Recently, we reported that beta-glucosidase has varied kinetic parameters for the natural and synthetic substrates [K.H Nam, S.J. Kim, M.Y. Kim, J.H. Kim, T.S. Yeo, C.M. Lee, H.K Jun, K.Y. Hwang. Crystal structure of engineered beta-glucosidase from a soil metagenome, Proteins 73 (2008) 788-793]. However, an understanding of the kinetic values of beta-glucosidase has not yet enabled the elucidation of its molecular function. Here, we report the X-ray crystal structure of beta-glucosidase with a glucose and cellobiose fragment from uncultured soil metagenome. From the various crystals, we obtained the pre-reaction (native), intermediate (disaccharide cleavage) and post-reaction (glucose binding) states of the active site pocket. These structures provide snapshots of the catalytic processing of beta-glucosidase. In addition, the intermediate state of the crystal structure provides insight into the substrate specificity of beta-glucosidase. These structural studies will facilitate elucidation of the architectural mechanism responsible for the substrate recognition of beta-glucosidase.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta-glucosidase
A
444uncultured bacteriumMutation(s): 8 
Gene Names: bglA
EC: 3.2.1.21
Find proteins for Q0GMU3 (uncultured bacterium)
Go to UniProtKB:  Q0GMU3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.384α = 90.00
b = 71.340β = 90.00
c = 86.981γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-14 
  • Released Date: 2012-12-19 
  • Deposition Author(s): Hwang, K.Y., Nam, K.H.
  • This entry supersedes: 3FIZ

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release