9LSD | pdb_00009lsd

Crystal structure of a polyketide cyclase FasU from Streptomyces kanamyceticus

• PDB DOI: https://doi.org/10.2210/pdb9LSD/pdb

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


• Deposited: 2025-02-04 Released: 2025-03-12 
• Deposition Author(s): Luo, S., Zhu, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: in silico

Literature

A Stereoselective Decarboxylative Aromatase/Cyclase Directs the Biosynthesis of an Axially Chiral Biphenyl Framework in Fasamycin.

Jiang, K., Zhu, C., Yan, X., Li, G., Lin, Z., Deng, Z., Luo, S., Qu, X.

(2025) J Am Chem Soc 147: 5596-5601

• PubMed: 39910892 
• DOI: https://doi.org/10.1021/jacs.4c18376
• Primary Citation of Related Structures:  
  9LSD


• PubMed Abstract: 
  

  Aromatic polyketides are an important class of natural products with various bioactivities, and their structural diversity arises from modifications to their aromatic frameworks. In this study, we identify a stereoselective aromatase/cyclase (ARO/CYC) FasU, which is responsible for forming the axial chiral biphenyl framework in fasamycin. FasU catalyzes sequential decarboxylation and cyclization/aromatization with strict S -stereospecificity on a previously unidentified biosynthetic intermediate. Through crystal structure analysis and site-directed mutagenesis, we reveal the enzyme's substrate binding mode, stereospecificity, and the key residues involved in catalysis. This discovery introduces a novel class of ARO/CYC enzymes in type II polyketide biosynthesis, advancing the development of biocatalysts for chiral aromatic polyketides.

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Organizational Affiliation: 
• State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China.
Abiochem Biotechnology Co. Ltd., Shanghai 200240, China.

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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.94 kDa 
• Atom Count: 1,923 
• Modeled Residue Count: 214 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibiotic biosynthesis monooxygenase	A, B	123	Streptomyces kanamyceticus	Mutation(s): 0  Gene Names: CP970_07265
UniProt
Find proteins for A0A5J6G7S2 (Streptomyces kanamyceticus) Explore A0A5J6G7S2  Go to UniProtKB:  A0A5J6G7S2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AE3	C [auth A], E [auth B]	2-(2-ETHOXYETHOXY)ETHANOL C6 H14 O3 XXJWXESWEXIICW-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.669	α = 90
b = 85.669	β = 90
c = 63.359	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Luo, S., Zhu, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release