7VTB | pdb_00007vtb

Partially closed conformation of talaropentaene synthase cyclase domain

• PDB DOI: https://doi.org/10.2210/pdb7VTB/pdb

• Classification: TRANSFERASE
• Organism(s): Talaromyces verruculosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-28 Released: 2022-06-08 
• Deposition Author(s): Hui, T., Mori, T., Abe, I.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Discovery of non-squalene triterpenes.

Tao, H., Lauterbach, L., Bian, G., Chen, R., Hou, A., Mori, T., Cheng, S., Hu, B., Lu, L., Mu, X., Li, M., Adachi, N., Kawasaki, M., Moriya, T., Senda, T., Wang, X., Deng, Z., Abe, I., Dickschat, J.S., Liu, T.

(2022) Nature 606: 414-419

• PubMed: 35650436 
• DOI: https://doi.org/10.1038/s41586-022-04773-3
• Primary Citation Related Structures: 
  7VTA, 7VTB, 7WIJ


• PubMed Abstract: 
  

  All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene ¹ . This approach is fundamentally different from the biosynthesis of short-chain (C ₁₀ -C ₂₅ ) terpenes that are formed from polyisoprenyl diphosphates ^2-4 . In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature.

---

Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
PRESTO, Japan Science and Technology Agency, Saitama, Japan.
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan. [e-mail].
Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany. [e-mail].
Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. [e-mail].
Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China. [e-mail].
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China. [e-mail].

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: 37.05 kDa 
• Atom Count: 2,426 
• Modeled Residue Count: 287 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TvTS cyclase domain	A	328	Talaromyces verruculosus	Mutation(s): 0  EC: 4.2.3.220 (UniProt), 2.5.1.158 (UniProt)
UniProt
Find proteins for P9WER5 (Talaromyces verruculosus) Explore P9WER5  Go to UniProtKB:  P9WER5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.809	α = 90
b = 61.942	β = 116.298
c = 81.297	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: 2022-06-08 
Deposition Author(s): Hui, T., Mori, T., Abe, I.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2022-06-15
  Changes: Database references
• Version 1.2: 2022-06-22
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description