The X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural diversity and substrate preferences of three tannase enzymes encoded by the anaerobic bacterium Clostridium butyricum.

Ristinmaa, A.S.Coleman, T.Cesar, L.Langborg Weinmann, A.Mazurkewich, S.Branden, G.Hasani, M.Larsbrink, J.

(2022) J Biol Chem 298: 101758-101758

  • DOI: https://doi.org/10.1016/j.jbc.2022.101758
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Tannins are secondary metabolites that are enriched in the bark, roots, and knots in trees and are known to hinder microbial attack. The biological degradation of water-soluble gallotannins, such as tannic acid, is initiated by tannase enzymes (EC, which are esterases able to liberate gallic acid from aromatic-sugar complexes. However, only few tannases have previously been studied in detail. Here, for the first time, we biochemically and structurally characterize three tannases from a single organism, the anaerobic bacterium Clostridium butyricum, which inhabits both soil and gut environments. The enzymes were named CbTan1-3, and we show that each one exhibits a unique substrate preference on a range of galloyl ester model substrates; CbTan1 and 3 demonstrated preference toward galloyl esters linked to glucose, while CbTan2 was more promiscuous. All enzymes were also active on oak bark extractives. Furthermore, we solved the crystal structure of CbTan2 and produced homology models for CbTan1 and 3. In each structure, the catalytic triad and gallate-binding regions in the core domain were found in very similar positions in the active site compared with other bacterial tannases, suggesting a similar mechanism of action among these enzymes, though large inserts in each enzyme showcase overall structural diversity. In conclusion, the varied structural features and substrate specificities of the C. butyricum tannases indicate that they have different biological roles and could further be used in development of new valorization strategies for renewable plant biomass.

  • Organizational Affiliation

    Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha/beta hydrolase
A, B
490Clostridium butyricumMutation(s): 0 
Gene Names: CBLFYP62_01769FF104_18625
Find proteins for A0A6M0U600 (Clostridium butyricum)
Explore A0A6M0U600 
Go to UniProtKB:  A0A6M0U600
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6M0U600
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
H [auth A],
I [auth A],
M [auth A],
P [auth B]
C4 H10 O3
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
Q [auth B],
R [auth B]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.22 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.675α = 90
b = 95.003β = 90
c = 131.586γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Energy AgencySweden2018-004339
Swedish Research CouncilSweden2018-004339
Carl Trygger FoundationSwedenCTS 19:195

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description