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 8IS2 | pdb_00008is2

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 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.227 (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

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 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.

Macromolecule Content 

  • Total Structure Weight: 26.88 kDa 
  • Atom Count: 1,829 
  • Modeled Residue Count: 204 
  • Deposited Residue Count: 234 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclase
A, B
117uncultured actinomyceteMutation(s): 0 
Gene Names: abxD
UniProt
Find proteins for A0A1R1S9S3 (Streptomyces sparsogenes DSM 40356)
Explore A0A1R1S9S3 
Go to UniProtKB:  A0A1R1S9S3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1R1S9S3
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 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
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