6IMW

The complex structure of endo-beta-1,2-glucanase mutant (E262Q) from Talaromyces funiculosus with beta-1,2-glucan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.

Tanaka, N.Nakajima, M.Narukawa-Nara, M.Matsunaga, H.Kamisuki, S.Aramasa, H.Takahashi, Y.Sugimoto, N.Abe, K.Terada, T.Miyanaga, A.Yamashita, T.Sugawara, F.Kamakura, T.Komba, S.Nakai, H.Taguchi, H.

(2019) J.Biol.Chem. 294: 7942-7965

  • DOI: 10.1074/jbc.RA118.007087
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>endo </i>-β-1,2-Glucanase (SGL) is an enzyme that hydrolyzes β-1,2-glucans, which play important physiological roles in some bacteria as a cyclic form. To date, no eukaryotic SGL has been identified. We purified an SGL from <i>Talaromyces funicu ...

    endo -β-1,2-Glucanase (SGL) is an enzyme that hydrolyzes β-1,2-glucans, which play important physiological roles in some bacteria as a cyclic form. To date, no eukaryotic SGL has been identified. We purified an SGL from Talaromyces funiculosus ( Tf SGL), a soil fungus, to homogeneity and then cloned the complementary DNA encoding the enzyme. Tf SGL shows no significant sequence similarity to any known glycoside hydrolase (GH) families, but shows significant similarity to certain eukaryotic proteins with unknown functions. The recombinant Tf SGL ( Tf SGLr) specifically hydrolyzed linear and cyclic β-1,2-glucans to sophorose (Glc-β-1,2-Glc) as a main product. Tf SGLr hydrolyzed reducing-end-modified β-1,2-gluco-oligosaccharides to release a sophoroside with the modified moiety. These results indicate that Tf SGL is an endo -type enzyme that preferably releases sophorose from the reducing end of substrates. Stereochemical analysis demonstrated that Tf SGL is an inverting enzyme. The overall structure of Tf SGLr includes an (α/α) 6 toroid fold. The substrate-binding mode was revealed by the structure of a Michaelis complex of an inactive Tf SGLr mutant with a β-1,2-glucoheptasaccharide. Mutational analysis and action pattern analysis of β-1,2-gluco-oligosaccharide derivatives revealed an unprecedented catalytic mechanism for substrate hydrolysis. Glu-262 (general acid) indirectly protonates the anomeric oxygen at subsite -1 via the 3-hydroxy group of the Glc moiety at subsite +2, and Asp-446 (general base) activates the nucleophilic water via another water. Tf SGLr is apparently different from a GH144 SGL in the reaction and substrate recognition mechanism based on structural comparison. Overall, we propose that Tf SGL and closely-related enzymes can be classified into a new family, GH162.


    Organizational Affiliation

    the Faculty of Agriculture, Niigata University, Niigata 950-2181.,the Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657.,the Food Component Analysis Unit, Food Research Institute, National Agriculture and Food Research Organization, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan.,From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, m-nakajima@rs.tus.ac.jp.,the Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551.,the Faculty of Agriculture, Iwate University, Iwate 020-8550, and.,the School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5201.,From the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-beta-1,2-glucanase
A, B
505Talaromyces funiculosusMutation(s): 0 
EC: 3.2.1.71
Find proteins for A0A4V8H013 (Talaromyces funiculosus)
Go to UniProtKB:  A0A4V8H013
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.169α = 90.00
b = 117.924β = 90.00
c = 93.284γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references