8ZVK | pdb_00008zvk

Crystal structure of the GH5 domain from a processive endoglucanase of Acetivibrio alkalicellulosi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

His 70 of Acetivibrio alkalicellulosi Cel5A is important for efficient hydrolysis of short cellodextrins.

Jia, M.Chen, Y.Wang, J.Wang, J.Ma, Y.Wang, Y.Ma, Q.Zhang, Y.Liu, W.Liu, K.

(2025) AMB Express 15: 53-53

  • DOI: https://doi.org/10.1186/s13568-025-01858-w
  • Primary Citation of Related Structures:  
    8ZVK

  • PubMed Abstract: 

    Cellulose, a linear glucan linked by β-1,4 glycosidic bonds, is the most abundant renewable polysaccharide on earth. Complete enzymatic hydrolysis of cellulose liberates the readily metabolizable glucose that could be further converted to valuable biocommodities, and essential to this process are cellulases that hydrolyze the β-1,4 glycosidic bonds. Cellulases are among the most intensively studied and best understood enzymes, and many key residues have been uncovered and interrogated with respect to their functions in catalysis and/or substrate binding. However, it remains to be explored whether additional residues, especially in many poorly characterized cellulases such as processive endoglucanases, might also be functionally important. Here, we investigated a processive endoglucanase from an alkaliphilic bacterium Acetivibrio alkalicellulosi AaCel5A that consists of a glycohydrolase family 5 (GH5) domain and two tandem carbohydrate-binding module family 6 (CBM6) domains. Via structure-guided engineering, we uncovered the functional importance of a previously underexplored but relatively conserved histidine (histidine70 or His 70 ). His 70 itself appears to be largely dispensable for hydrolyzing β-1,4 glycosidic bonds, but it is important for efficient hydrolysis of short cellodextrins such as cellotriose, cellotetraose, and cellopentaose, likely through its ability to coordinate substrate binding. Our work thus provides important mechanistic insights into how processive endoglucanases may act on short cellodextrins.


  • Organizational Affiliation
    • Department of Bioengineering, Tianjin University of Science and Technology, Tianjin, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AaBgIC785Acetivibrio alkalicellulosiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.775α = 90
b = 80.775β = 90
c = 82.167γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release