3AXD

The truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase V18Y/W203Y in apo-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational design to improve thermostability and specific activity of the truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase

Huang, J.W.Cheng, Y.S.Ko, T.P.Lin, C.Y.Lai, H.L.Chen, C.C.Ma, Y.Zheng, Y.Huang, C.H.Zou, P.Liu, J.R.Guo, R.T.

(2012) Appl.Microbiol.Biotechnol. 94: 111-121

  • DOI: 10.1007/s00253-011-3586-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1,3-1,4-β-D-Glucanase has been widely used as a feed additive to help non-ruminant animals digest plant fibers, with potential in increasing nutrition turnover rate and reducing sanitary problems. Engineering of enzymes for better thermostability is ...

    1,3-1,4-β-D-Glucanase has been widely used as a feed additive to help non-ruminant animals digest plant fibers, with potential in increasing nutrition turnover rate and reducing sanitary problems. Engineering of enzymes for better thermostability is of great importance because it not only can broaden their industrial applications, but also facilitate exploring the mechanism of enzyme stability from structural point of view. To obtain enzyme with higher thermostability and specific activity, structure-based rational design was carried out in this study. Eleven mutants of Fibrobacter succinogenes 1,3-1,4-β-D-glucanase were constructed in attempt to improve the enzyme properties. In particular, the crude proteins expressed in Pichia pastoris were examined firstly to ensure that the protein productions meet the need for industrial fermentation. The crude protein of V18Y mutant showed a 2 °C increment of Tm and W203Y showed ∼30% increment of the specific activity. To further investigate the structure-function relationship, some mutants were expressed and purified from P. pastoris and Escherichia coli. Notably, the specific activity of purified W203Y which was expressed in E. coli was 63% higher than the wild-type protein. The double mutant V18Y/W203Y showed the same increments of Tm and specific activity as the single mutants did. When expressed and purified from E. coli, V18Y/W203Y showed similar pattern of thermostability increment and 75% higher specific activity. Furthermore, the apo-form and substrate complex structures of V18Y/W203Y were solved by X-ray crystallography. Analyzing protein structure of V18Y/W203Y helps elucidate how the mutations could enhance the protein stability and enzyme activity.


    Organizational Affiliation

    Genozyme Biotechnology Inc., Taipei 106, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucanase
A, B
249Fibrobacter succinogenes (strain ATCC 19169 / S85)Mutation(s): 4 
EC: 3.2.1.73
Find proteins for P17989 (Fibrobacter succinogenes (strain ATCC 19169 / S85))
Go to UniProtKB:  P17989
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.391α = 90.00
b = 69.963β = 100.98
c = 81.242γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
XTALVIEWrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references