8STB | pdb_00008stb

The structure of abxF, an enzyme catalyzing the formation of the chiral spiroketal of an anthrabenzoxocinone antibiotic, (-)-ABX

• PDB DOI: https://doi.org/10.2210/pdb8STB/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2024-05-22 
• Deposition Author(s): Luo, Z., Jia, X., Yan, X., Qu, X., Kobe, B.
• Funding Organization(s): Australian Research Council (ARC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

An enzymatic dual-oxa Diels-Alder reaction constructs the oxygen-bridged tricyclic acetal unit of (-)-anthrabenzoxocinone.

Yan, X., Jia, X., Luo, Z., Ji, S., Zhang, M.J., Zhang, H., Yu, M., Orts, J., Jiang, K., Lin, Z., Deng, Z., Kong, X.D., Kobe, B., Zhao, Y.L., Mobli, M., Qu, X.

(2025) Nat Chem 

• PubMed: 40263633 
• DOI: https://doi.org/10.1038/s41557-025-01804-0
• Primary Citation of Related Structures:  
  8STB, 9JT3


• PubMed Abstract: 
  

  The hetero-Diels-Alder (HDA) reaction is a key method for synthesizing six-membered heterocyclic rings in natural products and bioactive compounds. Despite its importance in synthetic chemistry, naturally occurring enzymatic HDA reactions are rare and limited to a single heteroatom. Here we report Abx _(-) F, a bifunctional vicinal oxygen chelate (VOC)-like protein that catalyses dehydration and dual-oxa Diels-Alder reactions to stereoselectively form the oxygen-bridged tricyclic acetal of (-)-anthrabenzoxocinone ((-)-ABX). Isotope assays and density functional theory calculations reveal a dehydration-coordinated, concerted HDA mechanism. The crystal structure of Abx _(-) F and NMR complex structures of Abx _(-) F with its substrate analogue and (-)-ABX define the reaction's structural basis. Mutational analysis identifies Asp17 as a general base that mediates dehydration, forming an o-quinone methide intermediate for stereoselective dual-oxa HDA. This work establishes the molecular and structural basis of a polyheteroatomic Diels-Alderase, paving the way for designing polyheteroatomic DA enzymatic tools.

---

Organizational Affiliation: 
• State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China.
Department of Biochemistry, National University of Singapore, Singapore, Singapore.
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia.
School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia.
Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, Australia. [e-mail].
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. [e-mail].
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. [e-mail].
Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints, gel filtration

Macromolecule Content 

• Total Structure Weight: 48.31 kDa 
• Atom Count: 3,219 
• Modeled Residue Count: 428 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase	A [auth B], B [auth A]	234	Streptomyces sp.	Mutation(s): 0  Gene Names: abxF

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.029	α = 90
b = 76.029	β = 90
c = 166.752	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Luo, Z., Jia, X., Yan, X., Qu, X., Kobe, B.

---

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FL180100109

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release
  
• Version 2.0: 2025-06-04
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary