4MC3

Hedycaryol synthase in complex with Nerolidol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1002/cbic.201300708
  • Primary Citation of Related Structures:  
    4MC0, 4MC3, 4MC8

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative sesquiterpene cyclase346Kitasatospora setae KM-6054Mutation(s): 0 
Gene Names: KSE_00200tKSE_76540t
EC: 4.2.3 (PDB Primary Data), 4.2.3.187 (UniProt)
UniProt
Find proteins for E4MYY0 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054))
Explore E4MYY0 
Go to UniProtKB:  E4MYY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4MYY0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
28U
Query on 28U

Download Ideal Coordinates CCD File 
B [auth A](3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol
C15 H26 O
FQTLCLSUCSAZDY-GOFCXVBSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.44α = 90
b = 59.44β = 90
c = 182.84γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
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: 2014-01-29
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-04-03
    Changes: Refinement description