8YXS | pdb_00008yxs

X-ray structure of non-heme iron dioxygenase from Aspergillus brunneoviolaceus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 
    0.312 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.276 (Depositor), 0.278 (DCC) 
  • R-Value Observed: 
    0.278 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YXS

This is version 1.1 of the entry. See complete history

Literature

Regioselectivity switches between anthraquinone precursor fissions involved in bioactive xanthone biosynthesis.

Lv, X.J.Ai, C.Z.Zhang, L.R.Ma, X.X.Zhang, J.J.Zhu, J.P.Tan, R.X.

(2024) Chem Sci 15: 19534-19545

  • DOI: https://doi.org/10.1039/d4sc06369d
  • Primary Citation Related Structures: 
    8YXS

  • PubMed Abstract: 

    Xanthone-based polyketides with complex molecular frameworks and potent bioactivities distribute and function in different biological kingdoms, yet their biosynthesis remains under-investigated. In particular, nothing is known regarding how to switch between the C 4a -C 10 (C 4a -selective) and C 10a -C 10 bond (C 10a -selective) cleavages of anthraquinone intermediates involved in biosynthesizing strikingly different frameworks of xanthones and their siblings. Enabled by our characterization of antiosteoporotic brunneoxanthones, a subfamily of polyketides from Aspergillus brunneoviolaceus FB-2, we present herein the brunneoxanthone biosynthetic gene cluster and the C 10a -selective cleavage of anthraquinone (chrysophanol) hydroquinone leading ultimately to the bioactive brunneoxanthones under the catalysis of BruN (an undescribed atypical non-heme iron dioxygenase) in collaboration with BruM as a new oxidoreductase that reduces the anthraquinone into its hydroquinone using NADPH as a cofactor. The insights into the driving force that determines whether the C 10a - or C 4a -selective cleavages of anthraquinone hydroquinones take place were achieved by a combination of multiprotein sequence alignment, directed protein evolution, theoretical simulation, chemical capture of hydroquinone tautomer, 18 O chasing, and X-ray crystal structure of the BruN N441M mutant, eventually allowing for the protocol establishment for the on-demand switch between the two ways of anthraquinone openings. Collectively, the work paves the way for the synthetic biology-based regeneration of uniquely structured high-value xanthones present in low abundance in complex mixtures, and helps to deepen the understanding on why and how such xanthones and their congeners are biosynthesized by different (micro)organisms in nature.


  • Organizational Affiliation
    • State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine Nanjing 210023 China rxtan@nju.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 256.72 kDa 
  • Atom Count: 17,736 
  • Modeled Residue Count: 2,230 
  • Deposited Residue Count: 2,280 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxidoreductase AflY
A, B, C, D, E
456Aspergillus brunneoviolaceusMutation(s): 1 
Gene Names: BO72DRAFT_450687
UniProt
Find proteins for A0A1L9WLE0 (Aspergillus aculeatus (strain ATCC 16872 / CBS 172.66 / WB 5094))
Explore A0A1L9WLE0 
Go to UniProtKB:  A0A1L9WLE0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L9WLE0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free:  0.312 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.276 (Depositor), 0.278 (DCC) 
  • R-Value Observed: 0.278 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 256.987α = 90
b = 109.736β = 93.39
c = 179.891γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-04-09 
  • Deposition Author(s): Lv, X., Ma, X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81991524

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references