8IS2

Crystal structure of a polyketide aromatase/cyclase Abx(+)D from Actinomycetes sp. MA7150.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Literature

An unusual aromatase/cyclase programs the formation of the phenyldimethylanthrone framework in anthrabenzoxocinones and fasamycin.

Jiang, K.Chen, X.Yan, X.Li, G.Lin, Z.Deng, Z.Luo, S.Qu, X.

(2024) Proc Natl Acad Sci U S A 121: e2321722121-e2321722121

  • DOI: https://doi.org/10.1073/pnas.2321722121
  • Primary Citation of Related Structures:  
    8IS2

  • PubMed Abstract: 

    Aromatic polyketides are renowned for their wide-ranging pharmaceutical activities. Their structural diversity is mainly produced via modification of limited types of basic frameworks. In this study, we characterized the biosynthesis of a unique basic aromatic framework, phenyldimethylanthrone (PDA) found in (+)/(-)-anthrabenzoxocinones (ABXs) and fasamycin (FAS). Its biosynthesis employs a methyltransferase (Abx (+) M/Abx (-) M/FasT) and an unusual TcmI-like aromatase/cyclase (ARO/CYC, Abx (+) D/Abx (-) D/FasL) as well as a nonessential helper ARO/CYC (Abx (+) C/Abx (-) C/FasD) to catalyze the aromatization/cyclization of polyketide chain, leading to the formation of all four aromatic rings of the PDA framework, including the C9 to C14 ring and a rare angular benzene ring. Biochemical and structural analysis of Abx (+) D reveals a unique loop region, giving rise to its distinct acyl carrier protein-dependent specificity compared to other conventional TcmI-type ARO/CYCs, all of which impose on free molecules. Mutagenic analysis discloses critical residues of Abx (+) D for its catalytic activity and indicates that the size and shape of its interior pocket determine the orientation of aromatization/cyclization. This study unveils the tetracyclic and non-TcmN type C9 to C14 ARO/CYC, significantly expanding our cognition of ARO/CYCs and the biosynthesis of aromatic polyketide framework.


  • Organizational Affiliation

    State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclase
A, B
117uncultured actinomyceteMutation(s): 0 
Gene Names: abxD
UniProt
Find proteins for A0A2U3TEK9 (Actinomycetes bacterium)
Explore A0A2U3TEK9 
Go to UniProtKB:  A0A2U3TEK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2U3TEK9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.945α = 90
b = 50.945β = 90
c = 74.75γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
MoRDaphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references