5GM9

Crystal structure of a glycoside hydrolase in complex with cellobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Characterization and crystal structure of a thermostable glycoside hydrolase family 45 1,4-beta-endoglucanase from Thielavia terrestris

Gao, J.Huang, J.W.Li, Q.Liu, W.D.Ko, T.P.Zheng, Y.Y.Xiao, X.Kuo, C.J.Chen, C.C.Guo, R.T.

(2017) Enzyme Microb Technol 99: 32-37

  • DOI: https://doi.org/10.1016/j.enzmictec.2017.01.005
  • Primary Citation of Related Structures:  
    5GLX, 5GLY, 5GM9

  • PubMed Abstract: 

    1,4-β-Endoglucanase is one of the most important biocatalysts in modern industries. Here, a glycoside hydrolase (GH) family 45 endoglucanase from thermophilic fungus Theilavia terrestris (TtCel45A) was expressed in Pichia pastoris. The recombinant protein shows optimal activity at 60°C, pH 4-5. The enzyme exhibits extraordinary thermostability that more than 80% activity was detected after heating at 80°C for 2.5h. The high resolution crystal structures of apo-form enzyme and that in complex with cellobiose and cellotetraose were solved to 1.36-1.58Å. The protein folds into two overall regions: one is a six-stranded β-barrel, and the other one consists of several extended loops. Between the two regions lies the substrate-binding channel, which is an open cleft spanning across the protein surface. A continuous substrate-binding cleft from subsite -4 to +3 were clearly identified in the complex structures. Notably, the flexible V-VI loop ( 113 Gly- 114 Gly- 115 Asp- 116 Leu- 117 Gly- 118 Ser) is found to open in the presence of -1 sugar, with D115 and L116 swung away to yield a space to accommodate the catalytic acid D122 and the 2,5 B boat conformation of -1 sugar during transition state. Collectively, we characterized the enzyme properties of P. pastoris-expressed TtCel45A and solved high-resolution crystal structures of the enzyme. These results are of great interests in industrial applications and provide new insights into the fundamental understanding of enzyme catalytic mechanism of GH45 endoglucanases.


  • Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 45 protein213Thermothielavioides terrestris NRRL 8126Mutation(s): 0 
Gene Names: THITE_2110957
EC: 3.2.1.4
UniProt
Find proteins for G2QVH7 (Thermothielavioides terrestris (strain ATCC 38088 / NRRL 8126))
Explore G2QVH7 
Go to UniProtKB:  G2QVH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2QVH7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G86802XL
GlyCosmos:  G86802XL
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G84824ZO
GlyCosmos:  G84824ZO
Biologically Interesting Molecules (External Reference) 2 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.337α = 90
b = 54.315β = 90
c = 84.848γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary