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 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), 0.277 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 145.23 kDa 
  • Atom Count: 8,133 
  • Modeled Residue Count: 1,040 
  • Deposited Residue Count: 1,304 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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), 0.277 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.227 (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

View Full Validation Report



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