4MC3

Hedycaryol synthase in complex with Nerolidol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Hedycaryol synthase in complex with nerolidol reveals terpene cyclase mechanism.

Baer, P.Rabe, P.Citron, C.A.de Oliveira Mann, C.C.Kaufmann, N.Groll, M.Dickschat, J.S.

(2014) Chembiochem 15: 213-216

  • DOI: 10.1002/cbic.201300708
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biosynthesis of terpenes is catalysed by class I and II terpene cyclases. Here we present structural data from a class I hedycaryol synthase in complex with nerolidol, serving as a surrogate for the reaction intermediate nerolidyl diphosphate. Th ...

    The biosynthesis of terpenes is catalysed by class I and II terpene cyclases. Here we present structural data from a class I hedycaryol synthase in complex with nerolidol, serving as a surrogate for the reaction intermediate nerolidyl diphosphate. This prefolded ligand allows mapping of the active site and hence the identification of a key carbonyl oxygen of Val179, a highly conserved helix break (G1/2) and its corresponding helix dipole. Stabilising the carbocation at the substrate's C1 position, these elements act in concert to catalyse the 1,10 ring closure, thereby exclusively generating the anti-Markovnikov product. The delineation of a general mechanistic scaffold was confirmed by site-specific mutations. This work serves as a basis for understanding carbocation chemistry in enzymatic reactions and should contribute to future application of these enzymes in organic synthesis.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department of Chemistry, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative sesquiterpene cyclase
A
346Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054)Mutation(s): 0 
EC: 4.2.3.187
Find proteins for E4MYY0 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054))
Go to UniProtKB:  E4MYY0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
28U
Query on 28U

Download SDF File 
Download CCD File 
A
(3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol
trans-Nerolidol
C15 H26 O
FQTLCLSUCSAZDY-GOFCXVBSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.143 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.440α = 90.00
b = 59.440β = 90.00
c = 182.840γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release