4J0J

Tannin acyl hydrolase in complex with ethyl 3,5-dihydroxybenzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of tannase from Lactobacillus plantarum.

Ren, B.Wu, M.Wang, Q.Peng, X.Wen, H.McKinstry, W.J.Chen, Q.

(2013) J Mol Biol 425: 2737-2751

  • DOI: 10.1016/j.jmb.2013.04.032
  • Primary Citation of Related Structures:  
    4J0C, 4J0D, 4J0G, 4J0H, 4J0I, 4J0J, 4J0K, 4JUI

  • PubMed Abstract: 
  • Tannins are water-soluble polyphenolic compounds in plants. Hydrolyzable tannins are derivatives of gallic acid (3,4,5-trihydroxybenzoic acid) or its meta-depsidic forms that are esterified to polyol, catechin, or triterpenoid units. Tannases are a family of esterases that catalyze the hydrolysis of the galloyl ester bond in hydrolyzable tannins to release gallic acid ...

    Tannins are water-soluble polyphenolic compounds in plants. Hydrolyzable tannins are derivatives of gallic acid (3,4,5-trihydroxybenzoic acid) or its meta-depsidic forms that are esterified to polyol, catechin, or triterpenoid units. Tannases are a family of esterases that catalyze the hydrolysis of the galloyl ester bond in hydrolyzable tannins to release gallic acid. The enzymes have found wide applications in food, feed, beverage, pharmaceutical, and chemical industries since their discovery more than a century ago, although little is known about them at the molecular level, including the details of the catalytic and substrate binding sites. Here, we report the first three-dimensional structure of a tannase from Lactobacillus plantarum. The enzyme displays an α/β structure, featured by a large cap domain inserted into the classical serine hydrolase fold. A catalytic triad was identified in the structure, which is composed of Ser163, His451, and Asp419. During the binding of gallic acid, the carboxyl group of the molecule forges hydrogen-bonding interactions with the catalytic triad of the enzyme while the three hydroxyl groups make contacts with Asp421, Lys343, and Glu357 to form another hydrogen-bonding network. Mutagenesis studies demonstrated that these residues are indispensable for the activity of the enzyme. Structural studies of the enzyme in complex with a number of substrates indicated that the interactions at the galloyl binding site are the determinant force for the binding of substrates. The single galloyl binding site is responsible for the esterase and depsidase activities of the enzyme.


    Organizational Affiliation

    Materials Science and Engineering, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia. bin.ren@csiro.au



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TannaseA, B491Lactiplantibacillus plantarumMutation(s): 0 
Gene Names: tanLpl
UniProt
Find proteins for B3Y018 (Lactiplantibacillus plantarum)
Explore B3Y018 
Go to UniProtKB:  B3Y018
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y018
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E35
Query on E35

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ethyl 3,5-dihydroxybenzoate
C9 H10 O4
APHYVLPIZUVDTK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.251α = 70.47
b = 62.726β = 86.55
c = 83.466γ = 79.13
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations