4HZ6 | pdb_00004hz6

crystal structure of BglB

• PDB DOI: https://doi.org/10.2210/pdb4HZ6/pdb
• Entry: 4HZ6 supersedes: 3FIY

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-11-14 Released: 2012-12-19 
• Deposition Author(s): Hwang, K.Y., Nam, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.179 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

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

• PubMed: 20005197 
• DOI: https://doi.org/10.1016/j.bbrc.2009.12.038
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.39 kDa 
• Atom Count: 3,980 
• Modeled Residue Count: 441 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	444	uncultured bacterium	Mutation(s): 8  Gene Names: bglA
UniProt
Find proteins for A0ACD6B8B8 (uncultured bacterium) Explore A0ACD6B8B8  Go to UniProtKB:  A0ACD6B8B8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.179 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.697	α = 90
b = 71.143	β = 90
c = 87.373	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description