7XSI | pdb_00007xsi

SdnG, a Diels Alderase catalyzed the formation of norbornene skeleton in Sordarin biosynthetic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biosynthesis of Sordarin Revealing a Diels-Alderase for the Formation of the Norbornene Skeleton.

Liu, S.H.Sun, J.L.Hu, Y.L.Zhang, L.Zhang, X.Yan, Z.Y.Guo, X.Guo, Z.K.Jiao, R.H.Zhang, B.Tan, R.X.Ge, H.M.

(2022) Angew Chem Int Ed Engl 61: e202205577-e202205577

  • DOI: https://doi.org/10.1002/anie.202205577
  • Primary Citation of Related Structures:  
    7XSI

  • PubMed Abstract: 

    Sordarin (1) is a fungal diterpene glycoside that displays potent antifungal bioactivity through inhibition of elongation factor 2. The structures of sordarin and related compounds feature a highly rearranged tetracyclic diterpene core. In this study, we identified a concise pathway in the biosynthesis of sordarin. A diterpene cyclase (SdnA) generates the 5/8/5 cycloaraneosene framework, which is decorated by a set of P450s that catalyze a series of oxidation reactions, including hydroxylation, desaturation, and C-C bond oxidative cleavage, to give a carboxylate intermediate with a terminal alkene and a cyclopentadiene moiety. A novel Diels-Alderase SdnG catalyzes an intramolecular Diels-Alder (IMDA) reaction on this intermediate to forge the sordarin core structure. Subsequent methyl hydroxylation and glycosylation complete the biosynthesis of sordarin. Our work discloses a new strategy used by nature for the formation of the rearranged diterpene skeleton.


  • Organizational Affiliation
    • State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sordarin/hypoxysordarin biosynthesis cluster protein G163Sordaria araneosaMutation(s): 0 
Gene Names: sdnG
UniProt
Find proteins for A0A1B4XBH4 (Sordaria araneosa)
Explore A0A1B4XBH4 
Go to UniProtKB:  A0A1B4XBH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B4XBH4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.87α = 70.58
b = 64.92β = 72.43
c = 83.99γ = 88.01
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81991524, 81991522

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Advisory, Data collection, Refinement description