9J3U | pdb_00009j3u

Crystal structure of tyrosine phenol-lyase in complex with 3,5-dihydroxybenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

3,5-Dihydroxybenzoic Acid as a Potent Inhibitor of Tyrosine Phenol-Lyase Decreases Fecal Phenol Levels in Mice.

Kobayashi, T.Oishi, S.Hara, K.Matsui, M.Mena, P.Hashimoto, H.Watanabe, K.Miyoshi, N.

(2025) J Med Chem 68: 8786-8795

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00418
  • Primary Citation of Related Structures:  
    9J3U

  • PubMed Abstract: 

    Phenol is produced by β-elimination of l-tyrosine (Tyr) catalyzed by tyrosine phenol-lyase (TPL) during intestinal bacterial metabolism. Phenol and its conjugate, phenyl sulfate (PhS), are protein-bound uremic toxins (PBUTs). Elevated levels of phenol and PhS are strongly implicated in the etiology and outcomes of uremia. Because hemodialysis is insufficient in removing phenol and PhS, novel methods are necessary for inhibiting phenol production during bacterial metabolism. We explored TPL inhibitors and found that dietary polyphenols, particularly gallic acid (GA), strongly inhibited TPL-catalyzed phenol production. A GA derivative, 3,5-dihydroxybenzoic acid (3,5DHBA), competitively inhibited TPL and significantly decreased phenol levels in TPL-expressing bacteria ( Morganella morganii and Citrobacter koseri ) and Tyr-rich-diet-fed C57BL/6J mouse feces. Our findings suggested that 3,5DHBA was the most promising polyphenol in decreasing phenol levels. Therefore, dietary intake of 3,5DHBA or its phenolic precursors may be useful in minimizing PBUT levels by targeting intestinal bacteria.


  • Organizational Affiliation

    Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine phenol-lyase
A, B
458Morganella morganii subsp. morganiiMutation(s): 0 
Gene Names: tplMU9_2951
EC: 4.1.99.2
UniProt
Find proteins for J7TAF3 (Morganella morganii subsp. morganii KT)
Explore J7TAF3 
Go to UniProtKB:  J7TAF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7TAF3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.422α = 90
b = 155.664β = 90
c = 58.919γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references