4HZ7

Crystal structure of BglB with glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bbrc.2009.12.038
  • Primary Citation of Related Structures:  
    4HZ6, 4HZ7, 4HZ8

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-glucosidase444uncultured bacteriumMutation(s): 8 
Gene Names: bglA
UniProt
Find proteins for Q0GMU3 (uncultured bacterium)
Explore Q0GMU3 
Go to UniProtKB:  Q0GMU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0GMU3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
B [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.384α = 90
b = 71.34β = 90
c = 86.981γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary