3DGT

The 1.5 A crystal structure of endo-1,3-beta-glucanase from Streptomyces sioyaensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.5 A structure of endo-1,3-beta-glucanase from Streptomyces sioyaensis: evolution of the active-site structure for 1,3-beta-glucan-binding specificity and hydrolysis

Hong, T.-Y.Hsiao, Y.-Y.Meng, M.Li, T.T.

(2008) Acta Crystallogr.,Sect.D 64: 964-970

  • DOI: 10.1107/S0907444908021550

  • PubMed Abstract: 
  • The catalytic domain structure of Streptomyces sioyaensis 1,3-beta-glucanase (278 amino acids), a member of glycosyl hydrolase family 16 (GHF16), was determined to 1.5 A resolution in space group P2(1)2(1)2(1). The enzyme specifically hydrolyzes the ...

    The catalytic domain structure of Streptomyces sioyaensis 1,3-beta-glucanase (278 amino acids), a member of glycosyl hydrolase family 16 (GHF16), was determined to 1.5 A resolution in space group P2(1)2(1)2(1). The enzyme specifically hydrolyzes the glycosidic bond of the 1,3-beta-linked glucan substrate. The overall structure contains two antiparallel six-and seven-stranded beta-sheets stacked in a beta-sandwich jelly-roll motif similar to the fold of GHF16 1,3-1,4-beta-glucanases. The active-site cleft of the enzyme is distinct, with the closure of one end primarily caused by two protruding loop insertions and two key residues, Tyr38 and Tyr134. The current known structures of 1,3-1,4-beta-glucanases and 1,3-beta-glucanase from Nocardiopsis sp., on the other hand, have open-channel active-site clefts that can accommodate six beta-D-glucopyranosyl units. The active-site structure of 1,3-beta-glucanase was compared with those of other homologous structures in order to address the binding and enzymatic specificity for 1,3-beta-linked glucans in Streptomyces. This information could be helpful in the development of specific antifungal agents.


    Organizational Affiliation

    Department of Biotechnology, Tajen University, Pingtung 907, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,3-beta-glucanase
A
280Streptomyces sioyaensisMutation(s): 0 
Find proteins for Q9L816 (Streptomyces sioyaensis)
Go to UniProtKB:  Q9L816
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.509α = 90.00
b = 75.967β = 90.00
c = 79.663γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
SHELXCDphasing
CrystalCleardata collection
DENZOdata reduction
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-06-16 
  • Released Date: 2008-09-02 
  • Deposition Author(s): Li, T.H.

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description