8YJ4 | pdb_00008yj4

The complex structure of SdnG with its analogue of substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Iminium Catalysis in Natural Diels-Alderase.

Sun, Z.Zang, X.Zhou, Q.Ohashi, M.Houk, K.N.Zhou, J.Tang, Y.

(2025) Nat Catal 8: 218-228

  • DOI: https://doi.org/10.1038/s41929-025-01294-w
  • Primary Citation Related Structures: 
    8YHG, 8YHM, 8YI8, 8YIA, 8YJ4

  • PubMed Abstract: 

    Iminium-catalyzed cycloaddition is one of the most prominent examples of organocatalysis, yet a biological counterpart has not been reported despite the wide-spread occurrence of iminium adducts in enzymes. Here, we present biochemical, structural, and computational evidence for iminium catalysis by the natural Diels-Alderase SdnG that catalyzes norbornene formation in sordarin biosynthesis. A Schiff base adduct between the ε-nitrogen of active site K127 and the aldehyde group of the enal dienophile was revealed by structural analysis and captured under catalytic conditions via borohydride reduction. This Schiff base adduct positions the substrate into near-attack conformation and decreases the transition state barrier of Diels-Alder cyclization by 8.3 kcal/mol via dienophile activation. A hydrogen bond network consisting of a catalytic triad is proposed to facilitate proton transfer required for iminium formation. This work establishes a new mode of catalysis for Diels-Alderases and points the way to the design of novel iminium based (bio)catalysts.


  • Organizational Affiliation
    • Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States.

Macromolecule Content 

  • Total Structure Weight: 99.71 kDa 
  • Atom Count: 6,825 
  • Modeled Residue Count: 804 
  • Deposited Residue Count: 882 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sordarin/hypoxysordarin biosynthesis cluster protein G
A, B, C, D, E
A, B, C, D, E, F
147Sordaria 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: 2.20 Å
  • R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.96α = 90
b = 111.21β = 113.026
c = 81.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2025-10-22
    Type: Initial release