8IN2 | pdb_00008in2

4,5-DOPA-extradiol-dioxygenase from Beta vulgaris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural Insights into 4,5-DOPA Extradiol Dioxygenase from Beta vulgaris : Unraveling the Key Step in Versatile Betalain Biosynthesis.

Chiang, C.C.Lu, Y.J.Liu, J.W.Lin, S.W.Chou, C.C.Lin, C.H.Chien, I.W.Hsu, C.H.

(2025) J Agric Food Chem 73: 6785-6794

  • DOI: https://doi.org/10.1021/acs.jafc.4c09501
  • Primary Citation Related Structures: 
    8IN2

  • PubMed Abstract: 

    Betalains, a group of pigments widely distributed in various plants, are extensively applied in the food, beverage, and medicinal industries. The biosynthesis of betalains involves the enzymatic action of 4,5-DOPA-dioxygenase, which catalyzes the key ring-opening reaction of DOPA to produce betalamic acid, a crucial intermediate in the pathway. The crystal structure of a 4,5-DOPA-dioxygenase from Beta vulgaris (BvDOD) was determined in this study. The structural analysis revealed that BvDOD exhibited a structural fold similar to that of other members of the extradiol dioxygenase family. Moreover, the Fe-ligand residues His15, His53, and His229 indicated the enzyme's reliance on nonheme iron for catalyzing the ring-opening reaction. Molecular docking and mutational analysis identified two conserved residues, His119 and His175, in the active site essential for the catalytic reaction. In addition, Thr17, Asp254, and Tyr260 contributed to properly positioning the substrate in the active site. This study has provided structural insights into substrate recognition and catalytic mechanisms of BvDOD, which can be applied to develop enzymes for improved betalain production.


  • Organizational Affiliation
    • Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 61.56 kDa 
  • Atom Count: 4,120 
  • Modeled Residue Count: 526 
  • Deposited Residue Count: 552 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4,5-DOPA dioxygenase extradiol
A, B
276Beta vulgarisMutation(s): 0 
Gene Names: DODA
EC: 1.13.11.29
UniProt
Find proteins for Q70FG7 (Beta vulgaris)
Explore Q70FG7 
Go to UniProtKB:  Q70FG7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70FG7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.873α = 90
b = 95.873β = 90
c = 124.908γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan111-2113-M-002-015-MY3
Ministry of Science and Technology (MoST, Taiwan)Taiwan111-2311-B-002-008-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references, Structure summary