8R1R | pdb_00008r1r

Structure of the Diels Alderase TedJ, in complex with cofactor FAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.244 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Chemoenzymatic total synthesis of the antibiotic (-)-13-deoxytetrodecamycin using the Diels-Alderase TedJ.

Russell, S.J.Back, C.R.Perry, C.Cheung, K.A.Maschio, L.Charlton, S.N.Lees, N.R.Manzo-Ruiz, M.Hayes, M.A.van der Kamp, M.W.Race, P.R.Willis, C.L.

(2025) Chem Sci 16: 16993-16999

  • DOI: https://doi.org/10.1039/d5sc05480j
  • Primary Citation Related Structures: 
    8R1R

  • PubMed Abstract: 

    The tetrodecamycins are tetracyclic natural products that exhibit potent antimicrobial activity against a multitude of drug-resistant pathogens. These compounds are structurally distinguished by the presence of a tetronate ring and trans -decalin with six contiguous asymmetric centres united by a seven-membered oxygen heterocycle. Herein we describe the first total synthesis of the antibiotic (-)-13-deoxytetrodecamycin. Our strategy is predicated on an enantioselective [4 + 2]-cycloaddition catalysed by the FAD-dependent Diels-Alderase TedJ, forming the trans -decalin with concomitant creation of two rings and four contiguous stereocenters with exquisite selectivity under mild conditions. In complementary studies, in vitro enzyme assays, X-ray crystallography and computational modelling are used to provide molecular insights into the TedJ catalysed reaction. These studies illustrate the power of adopting a chemoenzymatic approach for the enantioselective synthesis of a target compound which would be difficult to achieve using non-biological methods and provide a practical demonstration of the use of Diels-Alder biocatalysts in total synthesis. This approach has potentially widespread value in the global challenge of discovery and development of new antibiotics.


  • Organizational Affiliation
    • School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK chris.willis@bristol.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 53.8 kDa 
  • Atom Count: 3,825 
  • Modeled Residue Count: 492 
  • Deposited Residue Count: 510 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Short-chain dehydrogenase/reductase510StreptomycesMutation(s): 0 
Gene Names: tedJ

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.244 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.25α = 90
b = 70.25β = 90
c = 203.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T001968/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M012107/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Database references