Crystal structure of CotB2 C-terminal truncation

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis.

Driller, R.Janke, S.Fuchs, M.Warner, E.Mhashal, A.R.Major, D.T.Christmann, M.Bruck, T.Loll, B.

(2018) Nat Commun 9: 3971-3971

  • DOI: https://doi.org/10.1038/s41467-018-06325-8
  • Primary Citation of Related Structures:  
    6GGI, 6GGJ, 6GGK, 6GGL

  • PubMed Abstract: 

    Terpenes constitute the largest and structurally most diverse natural product family. Most terpenoids exhibit a stereochemically complex macrocyclic core, which is generated by C-C bond forming of aliphatic oligo-prenyl precursors. This reaction is catalysed by terpene synthases (TPSs), which are capable of chaperoning highly reactive carbocation intermediates through an enzyme-specific reaction. Due to the instability of carbocation intermediates, the proteins' structural dynamics and enzyme:substrate interactions during TPS catalysis remain elusive. Here, we present the structure of the diterpene synthase CotB2, in complex with an in crystallo cyclised abrupt reaction product and a substrate-derived diphosphate. We captured additional snapshots of the reaction to gain an overview of CotB2's catalytic mechanism. To enhance insights into catalysis, structural information is augmented with multiscale molecular dynamic simulations. Our data represent fundamental TPS structure dynamics during catalysis, which ultimately enable rational engineering towards tailored terpene macrocycles that are inaccessible by conventional chemical synthesis.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclooctat-9-en-7-ol synthase
A, B
293Streptomyces melanosporofaciensMutation(s): 0 
Gene Names: CotB2
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.01α = 90
b = 99.714β = 90
c = 107.718γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description