9JHX | pdb_00009jhx

Versatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP

• PDB DOI: https://doi.org/10.2210/pdb9JHX/pdb
• EM Map EMD-61491: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Penicillium solitum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-10 Released: 2025-02-05 
• Deposition Author(s): Li, D., Zhang, Y., Wang, W., Wang, P.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Characterization and structural analysis of a versatile aromatic prenyltransferase for imidazole-containing diketopiperazines.

Wang, W., Wang, P., Ma, C., Li, K., Wang, Z., Liu, Y., Wang, L., Zhang, G., Che, Q., Zhu, T., Zhang, Y., Li, D.

(2025) Nat Commun 16: 144-144

• PubMed: 39747040 
• DOI: https://doi.org/10.1038/s41467-024-55537-8
• Primary Citation of Related Structures:  
  8Y9D, 8Y9E, 8Y9G, 9JHX


• PubMed Abstract: 
  

  Prenylation modifications of natural products play essential roles in chemical diversity and bioactivities, but imidazole modification prenyltransferases are not well investigated. Here, we discover a dimethylallyl tryptophan synthase family prenyltransferase, AuraA, that catalyzes the rare dimethylallylation on the imidazole moiety in the biosynthesis of aurantiamine. Biochemical assays validate that AuraA could accept both cyclo-(L-Val-L-His) and cyclo-(L-Val-DH-His) as substrates, while the prenylation modes are completely different, yielding C2-regular and C5-reverse products, respectively. Cryo-electron microscopy analysis of AuraA and its two ternary complex structures reveal two distinct modes for receptor binding, demonstrating a tolerance for altered orientations of highly similar receptors. The mutation experiments further demonstrate the promiscuity of AuraA towards imidazole-C-dimethylallylation. In this work, we also characterize a case of AuraA mutant-catalyzed dimethylallylation of imidazole moiety, offering available structural insights into the utilization and engineering of dimethylallyl tryptophan synthase family prenyltransferases.

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Organizational Affiliation: 
• Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, P R China.
Laboratory for Marine Drugs and Bioproducts & Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, P R China.
MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, P R China.
Sanya Oceanographic Institute, Ocean University of China, Sanya, P R China.
Laboratory for Marine Drugs and Bioproducts & Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, P R China. [e-mail].
MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, P R China. [e-mail].
State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, P R China. [e-mail].
Key Laboratory of Marine Drugs Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, P R China. [e-mail].
Laboratory for Marine Drugs and Bioproducts & Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, P R China. [e-mail].
Sanya Oceanographic Institute, Ocean University of China, Sanya, P R China. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 196.58 kDa 
• Atom Count: 13,104 
• Modeled Residue Count: 1,640 
• Deposited Residue Count: 1,736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Versatile Aromatic Prenyltransferase auraA	A, B, C, D	434	Penicillium solitum	Mutation(s): 0
UniProt
Find proteins for A0A117NS29 (Penicillium freii) Explore A0A117NS29  Go to UniProtKB:  A0A117NS29

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DST (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C5 H12 O6 P2 S ZWFWSISPSBLNGO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-05 
Deposition Author(s): Li, D., Zhang, Y., Wang, W., Wang, P.

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Funding Organization	Location	Grant Number
Other government	China	Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City (Grant No: 2021CXLH0012)
Other government	China	Major Basic Research Programs of Natural Science Foundation of Shandong Province (ZR2019ZD18)
Other government	China	Qingdao Marine Science and Technology Center (No.2022QNLM030003-1)

Revision History  

• Version 1.0: 2025-02-05
  Type: Initial release