5HC7

Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with S-thiolo-isopentenyldiphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase

Liu, M.X.Chen, C.C.Chen, L.Xiao, X.S.Zheng, Y.Y.Huang, J.W.Liu, W.D.Ko, T.P.Cheng, Y.S.Feng, X.X.Oldfield, E.Guo, R.T.Ma, Y.H.

(2016) Angew.Chem.Int.Ed.Engl. 55: 4721-4724

  • DOI: 10.1002/anie.201600656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the first X-ray structure of the unique "head-to-middle" monoterpene synthase, lavandulyl diphosphate synthase (LPPS). LPPS catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) to form lavandulyl diphosphate, a p ...

    We report the first X-ray structure of the unique "head-to-middle" monoterpene synthase, lavandulyl diphosphate synthase (LPPS). LPPS catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) to form lavandulyl diphosphate, a precursor to the fragrance lavandulol. The structure is similar to that of the bacterial cis-prenyl synthase, undecaprenyl diphosphate synthase (UPPS), and contains an allylic site (S1) in which DMAPP ionizes and a second site (S2) which houses the DMAPP nucleophile. Both S-thiolo-dimethylallyl diphosphate and S-thiolo-isopentenyl diphosphate bind intact to S2, but are cleaved to (thio)diphosphate, in S1. His78 (Asn in UPPS) is essential for catalysis and is proposed to facilitate diphosphate release in S1, while the P1 phosphate in S2 abstracts a proton from the lavandulyl carbocation to form the LPP product. The results are of interest since they provide the first structure and structure-based mechanism of this unusual prenyl synthase.


    Organizational Affiliation

    College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
prenyltransference for protein
A
261Lavandula lanataMutation(s): 0 
EC: 2.5.1.-
Find proteins for A0A140UHQ1 (Lavandula lanata)
Go to UniProtKB:  A0A140UHQ1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DST
Query on DST

Download SDF File 
Download CCD File 
A
DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H14 O6 P2 S
UWSFTDFHOGCIEL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 54.392α = 90.00
b = 141.606β = 90.00
c = 78.918γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2016-04-13
    Type: Database references