7XRU

Drimenyl diphosphate synthase D303E from Streptomyces showdoensis in complex with 2-fluorofarnesyl diphosphate (2F-FPP) and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Literature

Discovery, Structure, and Mechanism of a Class II Sesquiterpene Cyclase.

Pan, X.Du, W.Zhang, X.Lin, X.Li, F.R.Yang, Q.Wang, H.Rudolf, J.D.Zhang, B.Dong, L.B.

(2022) J Am Chem Soc 144: 22067-22074

  • DOI: https://doi.org/10.1021/jacs.2c09412
  • Primary Citation of Related Structures:  
    7XQ4, 7XQZ, 7XR7, 7XRA, 7XRU

  • PubMed Abstract: 

    Terpene cyclases (TCs), extraordinary enzymes that create the structural diversity seen in terpene natural products, are traditionally divided into two classes, class I and class II. Although the structural and mechanistic features of class I TCs are well-known, the corresponding details in class II counterparts have not been fully characterized. Here, we report the genome mining discovery and structural characterization of two class II sesquiterpene cyclases (STCs) from Streptomyces . These drimenyl diphosphate synthases (DMSs) are the first STCs shown to possess β,γ-didomain architecture. High-resolution X-ray crystal structures of DMS from Streptomyces showdoensis (SsDMS) in complex with both a farnesyl diphosphate and Mg 2+ unveiled an induced-fit mechanism, with an unprecedented Mg 2+ binding mode, finally solving one of the lingering questions in class II TC enzymology. This study supports continued genome mining for novel bacterial TCs and provides new mechanistic insights into canonical class II TCs that will lead to advances in TC engineering and synthetic biology.


  • Organizational Affiliation

    State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, Jiangsu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SQHop_cyclase_C domain-containing protein514Streptomyces showdoensisMutation(s): 1 
Gene Names: VO63_21045
UniProt
Find proteins for A0A2P2GK84 (Streptomyces showdoensis)
Explore A0A2P2GK84 
Go to UniProtKB:  A0A2P2GK84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P2GK84
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.35α = 90
b = 113.78β = 90
c = 179.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82073746

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description