8VMK | pdb_00008vmk

A crystal structure of heme-dependent tyrosine hydroxylase complexed with a substrate analog, 3-(4-hydroxyphenyl)propionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Substrate Analogs Implicate a Free Radical Pathway in Tyrosine Hydroxylase Catalysis.

Traore, E.S.Wang, Y.Griffith, W.P.Liu, A.

(2025) ACS Catal 15: 18270-18281

  • DOI: https://doi.org/10.1021/acscatal.5c05776
  • Primary Citation Related Structures: 
    8VMK

  • PubMed Abstract: 

    Heme-dependent tyrosine hydroxylases (TyrH) are critical enzymes in catecholamine biosynthesis, yet the role of the substrate's α -amino group in their monooxygenation mechanism has been unclear. Using 3-(4-hydroxyphenyl)propionic acid (HPPA), an l-tyrosine analog lacking the α -amino group, we observed a distinct dimerization pathway that competes with the expected hydroxylation reaction. Several lines of evidence confirm that this process originates from a radical intermediate. First, the formation of this (HPPA) 2 dimer is selectively inhibited by a free radical scavenger. Second, 18 O-labeling experiments show phenolic oxygen scrambling, indicating a disruption of substrate aromaticity during catalysis. Finally, EPR spectroscopy using nitrosobenzene as a substrate analog revealed a substrate-based free radical. This mechanistic divergence clarifies the role of the α -amino group. Its absence in HPPA creates a kinetic bottleneck for the final O atom transfer step, allowing a fraction of the substrate radical to form the off-pathway dimer. Thus, the native substrate's α -amino group acts as a crucial kinetic modulator, ensuring the rapid and efficient commitment of the substrate radical to productive hydroxylation. These results collectively establish a peroxidase-like free radical pathway for TyrH and reveal the nonessential yet significant role the amino group plays in controlling reaction outcomes.


  • Organizational Affiliation
    • Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States.

Macromolecule Content 

  • Total Structure Weight: 71.06 kDa 
  • Atom Count: 5,417 
  • Modeled Residue Count: 604 
  • Deposited Residue Count: 632 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heme-dependent L-tyrosine hydroxylase
A, B
316Streptomyces sclerotialusMutation(s): 0 
UniProt
Find proteins for A0ACD6BA76 (Streptomyces sp. ICBB 8177)
Explore A0ACD6BA76 
Go to UniProtKB:  A0ACD6BA76
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BA76
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
HPP
(Subject of Investigation/LOI)

Query on HPP



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
HYDROXYPHENYL PROPIONIC ACID
C9 H10 O3
NMHMNPHRMNGLLB-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.634α = 90
b = 129.819β = 93.86
c = 48.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108988

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references