3WDV

The complex structure of PtLic16A with cellotetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.936 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and mutagenetic analyses of a 1,3-1,4-beta-glucanase from Paecilomyces thermophila

Cheng, Y.S.Huang, C.H.Chen, C.C.Huang, T.Y.Ko, T.P.Huang, J.W.Wu, T.H.Liu, J.R.Guo, R.T.

(2014) Biochim.Biophys.Acta 1844: 366-373

  • DOI: 10.1016/j.bbapap.2013.11.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The thermostable 1,3-1,4-β-glucanase PtLic16A from the fungus Paecilomyces thermophila catalyzes stringent hydrolysis of barley β-glucan and lichenan with an outstanding efficiency and has great potential for broad industrial applications. Here, we r ...

    The thermostable 1,3-1,4-β-glucanase PtLic16A from the fungus Paecilomyces thermophila catalyzes stringent hydrolysis of barley β-glucan and lichenan with an outstanding efficiency and has great potential for broad industrial applications. Here, we report the crystal structures of PtLic16A and an inactive mutant E113A in ligand-free form and in complex with the ligands cellobiose, cellotetraose and glucotriose at 1.80Å to 2.25Å resolution. PtLic16A adopts a typical β-jellyroll fold with a curved surface and the concave face forms an extended ligand binding cleft. These structures suggest that PtLic16A might carry out the hydrolysis via retaining mechanism with E113 and E118 serving as the nucleophile and general acid/base, respectively. Interestingly, in the structure of E113A/1,3-1,4-β-glucotriose complex, the sugar bound to the -1 subsite adopts an intermediate-like (α-anomeric) configuration. By combining all crystal structures solved here, a comprehensive binding mode for a substrate is proposed. These findings not only help understand the 1,3-1,4-β-glucanase catalytic mechanism but also provide a basis for further enzymatic engineering.


    Organizational Affiliation

    Genozyme Biotechnology Inc., Taipei 106, Taiwan; AsiaPac Biotechnology Co., Ltd., Dongguan 523808, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-1,3-1,4-glucanase
A, B, C, D
298Paecilomyces sp. 'thermophila'Mutation(s): 0 
EC: 3.2.1.73
Find proteins for E0XN39 (Paecilomyces sp. 'thermophila')
Go to UniProtKB:  E0XN39
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CBI
Query on CBI

Download SDF File 
Download CCD File 
A, B, C, D
CELLOBIOSE
C12 H22 O11
GUBGYTABKSRVRQ-QRZGKKJRSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BGC
Query on BGC

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.936 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 88.241α = 90.00
b = 172.960β = 90.00
c = 167.426γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release