9LPB | pdb_00009lpb

Terpene cyclase AriE mutant-D128A

• PDB DOI: https://doi.org/10.2210/pdb9LPB/pdb
• Entry: 9LPB supersedes: 8ITQ

• Classification: METAL BINDING PROTEIN
• Organism(s): Amycolatopsis arida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-01-24 Released: 2025-05-07 
• Deposition Author(s): Li, F.R., Yang, Q., He, J.Y., Sun, X.R., Pan, X.M., Xu, H.M., Rudolf, J.D., Dong, L.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Catalytic Mechanism of the cis-Eunicellane Cyclase AriE.

Li, F.R., Yang, Q., He, J., Sun, X., Pan, X., Xu, H.M., Rudolf, J.D., Dong, L.B.

(2025) Chemistry 31: e202500012-e202500012

• PubMed: 40265331 
• DOI: https://doi.org/10.1002/chem.202500012
• Primary Citation Related Structures: 
  9LPB


• PubMed Abstract: 
  

  Eunicellane diterpenoids, with over 360 known examples characterized by a cis- or trans-6/10-bicyclic carbon skeleton, exhibit diverse biological activities. To date, five eunicellane cyclases (ECs) have been reported: cis-ECs (Bnd4, CpDTS2 and EcTPS1) and trans-ECs (AlbS and MicA), yet the structural basis and molecular mechanisms governing their distinct cis- or trans-cyclization modes remain unsolved. Here, we present the crystal structure of a cis-EC AriE from Amycolatopsis arida, which catalyzes geranylgeranyl diphosphate to form cis-6/10-fused bicyclic benditerpe-2,6,15-triene (1) in aridacin biosynthesis. Through surface entropy reduction, we obtained the 1.87 Å resolution structure of AriED128A. Structure-guided mutagenesis identified W73 as a key regulatory hotspot controlling product diversity, with its variants generating diverse diterpene products. Y203A converted AriE into a highly specific (-)-(R)-cembrene A synthase. Our findings provide the first structural insights into this type of terpene synthase and demonstrate the feasibility of engineering EC variants for selective product formation.

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Organizational Affiliation: 
• China Pharmaceutical University, School of Traditional Chinese Pharmacy, CHINA.
China Pharmaceutical University, The Public Laboratory Platform, CHINA.
University of Florida, Department of Chemistry, UNITED STATES OF AMERICA.
China Pharmaceutical University, State key Laboratory of Natural Medicines, Longmian Avenue #639, Jiangning District, 211198, Nanjiing, CHINA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.46 kDa 
• Atom Count: 3,096 
• Modeled Residue Count: 354 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase	A	369	Amycolatopsis arida	Mutation(s): 1  Gene Names: SAMN05421810_102118 EC: 4.2.3
UniProt
Find proteins for A0A1I5P1T3 (Amycolatopsis arida) Explore A0A1I5P1T3  Go to UniProtKB:  A0A1I5P1T3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.815	α = 90
b = 83.815	β = 90
c = 163.673	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Li, F.R., Yang, Q., He, J.Y., Sun, X.R., Pan, X.M., Xu, H.M., Rudolf, J.D., Dong, L.B.
• This entry supersedes: 8ITQ

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82073746

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release
  
• Version 1.1: 2025-06-11
  Changes: Database references