7EEE | pdb_00007eee

Complex structure of glycoside hydrolase family 12 beta-1,3-1,4-glucanase with gentiobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural and biochemical insights into the substrate-binding mechanism of a glycoside hydrolase family 12 beta-1,3-1,4-glucanase from Chaetomium sp.

Ma, J.Li, Y.Han, S.Jiang, Z.Yan, Q.Yang, S.

(2021) J Struct Biol 213: 107774-107774

  • DOI: https://doi.org/10.1016/j.jsb.2021.107774
  • Primary Citation Related Structures: 
    7EE2, 7EEE, 7EEJ

  • PubMed Abstract: 

    β-1,3-1,4-Glucanases are a type of hydrolytic enzymes capable of catalyzing the strict cleavage of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in β-D-glucans and have exhibited great potential in food and feed industrials. In this study, a novel glycoside hydrolase (GH) family 12 β-1,3-1,4-glucanase (CtGlu12A) from the thermophilic fungus Chaetomium sp. CQ31 was identified and biochemically characterized. CtGlu12A was most active at pH 7.5 and 65 °C, respectively, and exhibited a high specific activity of 999.9 U mg -1 towards lichenin. It maintained more than 80% of its initial activity in a wide pH range of 5.0-11.0, and up to 60 °C after incubation at 55 °C for 60 min. Moreover, the crystal structures of CtGlu12A with gentiobiose and tetrasccharide were resolved. CtGlu12A had a β-jellyroll fold, and performed retaining mechanism with two glutamic acids severing as the catalytic residues. In the complex structure, cellobiose molecule showed two binding modes, occupying subsites -2 to -1 and subsites + 1 to + 2, respectively. The concave cleft made mixed β-1,3-1,4-glucan substrates maintain a bent conformation to fit into the active site. Overall, this study is not only helpful for the understanding of the substrate-binding model and catalytic mechanism of GH 12 β-1,3-1,4-glucanases, but also provides a basis for further enzymatic engineering of β-1,3-1,4-glucanases.


  • Organizational Affiliation
    • Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China.

Macromolecule Content 

  • Total Structure Weight: 26.1 kDa 
  • Atom Count: 2,036 
  • Modeled Residue Count: 223 
  • Deposited Residue Count: 227 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
glycoside hydrolase family 12 beta-1,3-1,4-glucanase227Chaetomium sp.Mutation(s): 0 
EC: 3.2.1.73
UniProt
Find proteins for A0A915Q9D1 (Chaetomium sp)
Explore A0A915Q9D1 
Go to UniProtKB:  A0A915Q9D1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A915Q9D1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G48547LV
GlyCosmos: G48547LV
GlyGen: G48547LV

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.354α = 90
b = 63.354β = 90
c = 137.962γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing
PHENIXrefinement

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary