3EQO

Crystal structure of beta-1,3-glucanase from Phanerochaete chrysosporium (Lam55A) gluconolactone complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of glycoside hydrolase family 55 beta -1,3-glucanase from the basidiomycete Phanerochaete chrysosporium

Ishida, T.Fushinobu, S.Kawai, R.Kitaoka, M.Igarashi, K.Samejima, M.

(2009) J.Biol.Chem. 284: 10100-10109

  • DOI: 10.1074/jbc.M808122200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycoside hydrolase family 55 consists of beta-1,3-glucanases mainly from filamentous fungi. A beta-1,3-glucanase (Lam55A) from the Basidiomycete Phanerochaete chrysosporium hydrolyzes beta-1,3-glucans in the exo-mode with inversion of anomeric confi ...

    Glycoside hydrolase family 55 consists of beta-1,3-glucanases mainly from filamentous fungi. A beta-1,3-glucanase (Lam55A) from the Basidiomycete Phanerochaete chrysosporium hydrolyzes beta-1,3-glucans in the exo-mode with inversion of anomeric configuration and produces gentiobiose in addition to glucose from beta-1,3/1,6-glucans. Here we report the crystal structure of Lam55A, establishing the three-dimensional structure of a member of glycoside hydrolase 55 for the first time. Lam55A has two beta-helical domains in a single polypeptide chain. These two domains are separated by a long linker region but are positioned side by side, and the overall structure resembles a rib cage. In the complex, a gluconolactone molecule is bound at the bottom of a pocket between the two beta-helical domains. Based on the position of the gluconolactone molecule, Glu-633 appears to be the catalytic acid, whereas the catalytic base residue could not be identified. The substrate binding pocket appears to be able to accept a gentiobiose unit near the cleavage site, and a long cleft runs from the pocket, in accordance with the activity of this enzyme toward various beta-1,3-glucan oligosaccharides. In conclusion, we provide important features of the substrate-binding site at the interface of the two beta-helical domains, demonstrating an unexpected variety of carbohydrate binding modes.


    Related Citations: 
    • Gene cloning and heterologous expression of glycoside hydrolase family 55 beta-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium
      Kawai, R.,Igarashi, K.,Samejima, M.
      (2006) Biotechnol.Lett. 28: 365


    Organizational Affiliation

    Departments of Biomaterials Sciences and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucan 1,3-beta-glucosidase
A, B
758Phanerochaete chrysosporiumMutation(s): 0 
Gene Names: lam55A
EC: 3.2.1.58
Find proteins for Q2Z1W1 (Phanerochaete chrysosporium)
Go to UniProtKB:  Q2Z1W1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
LGC
Query on LGC

Download SDF File 
Download CCD File 
A, B
(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
GLUCONOLACTONE
C6 H10 O6
PHOQVHQSTUBQQK-SQOUGZDYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.142 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.534α = 93.94
b = 67.146β = 106.76
c = 109.778γ = 97.08
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance