7VBQ | pdb_00007vbq

Heterodimer structure of Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxIJ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis.

Li, X.Awakawa, T.Mori, T.Ling, M.Hu, D.Wu, B.Abe, I.

(2021) J Am Chem Soc 143: 21425-21432

  • DOI: https://doi.org/10.1021/jacs.1c11548
  • Primary Citation Related Structures: 
    7VBQ, 7VBR

  • PubMed Abstract: 

    Talaromyolides ( 1 - 6 ) are a group of unusual 6/6/6/6/6/6 hexacyclic meroterpenoids with (3 R )-6-hydroxymellein and 4,5-seco-drimane substructures, isolated from the marine fungus Talaromyces purpureogenus . We have identified the biosynthetic gene cluster tlxA-J by heterologous expression in Aspergillus , in vitro enzyme assays, and CRISPR-Cas9-based gene inactivation. Remarkably, the heterodimer of non-heme iron (NHI) enzymes, TlxJ-TlxI, catalyzes three steps of oxidation including a key reaction, hydroxylation at C-5 and C-9 of 12 , the intermediate with 3-ketohydroxydrimane scaffold, to facilitate a retro-aldol reaction, leading to the construction of the 4,5-secodrimane skeleton and characteristic ketal scaffold of 1 - 6 . The products of TlxJ-TlxI, 1 and 4 , were further hydroxylated at C-4'β by another NHI heterodimer, TlxA-TlxC, and acetylated by TlxB to yield the final products, 3 and 6 . The X-ray structural analysis coupled with site-directed mutagenesis provided insights into the heterodimer TlxJ-TlxI formation and its catalysis. This is the first report to show that two NHI proteins form a heterodimer for catalysis and utilizes a novel methodology to create functional oxygenase structures in secondary metabolite biosynthesis.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 67.9 kDa 
  • Atom Count: 4,773 
  • Modeled Residue Count: 547 
  • Deposited Residue Count: 600 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxJ318Talaromyces purpureogenusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI282Talaromyces purpureogenusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.933α = 90
b = 75.335β = 90
c = 133.611γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description