4OMG

Crystal structure of the bacterial diterpene cyclase COTB2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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This is version 1.4 of the entry. See complete history


Literature

The first structure of a bacterial diterpene cyclase: CotB2.

Janke, R.Gorner, C.Hirte, M.Bruck, T.Loll, B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1528-1537

  • DOI: https://doi.org/10.1107/S1399004714005513
  • Primary Citation of Related Structures:  
    4OMG, 4OMH

  • PubMed Abstract: 

    Sesquiterpenes and diterpenes are a diverse class of secondary metabolites that are predominantly derived from plants and some prokaryotes. The properties of these natural products encompass antitumor, antibiotic and even insecticidal activities. Therefore, they are interesting commercial targets for the chemical and pharmaceutical industries. Owing to their structural complexity, these compounds are more efficiently accessed by metabolic engineering of microbial systems than by chemical synthesis. This work presents the first crystal structure of a bacterial diterpene cyclase, CotB2 from the soil bacterium Streptomyces melanosporofaciens, at 1.64 Å resolution. CotB2 is a diterpene cyclase that catalyzes the cyclization of the linear geranylgeranyl diphosphate to the tricyclic cyclooctat-9-en-7-ol. The subsequent oxidation of cyclooctat-9-en-7-ol by two cytochrome P450 monooxygenases leads to bioactive cyclooctatin. Plasticity residues that decorate the active site of CotB2 have been mutated, resulting in alternative monocyclic, dicyclic and tricyclic compounds that show bioactivity. These new compounds shed new light on diterpene cyclase reaction mechanisms. Furthermore, the product of mutant CotB2(W288G) produced the new antibiotic compound (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene, which acts specifically against multidrug-resistant Staphylococcus aureus. This opens a sustainable route for the industrial-scale production of this bioactive compound.


  • Organizational Affiliation

    Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl diphosphate cyclase
A, B
318Streptomyces melanosporofaciensMutation(s): 0 
EC: 4.2.3.146
UniProt
Find proteins for C9K1X5 (Streptomyces melanosporofaciens)
Explore C9K1X5 
Go to UniProtKB:  C9K1X5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC9K1X5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.06α = 90
b = 100.65β = 90
c = 108.73γ = 90
Software Package:
Software NamePurpose
DNAdata collection
SHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2015-01-07
    Changes: Structure summary
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations