5HSS

Linalool dehydratase/isomerase: Ldi with monoterpene substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

X-ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis.

Weidenweber, S.Marmulla, R.Ermler, U.Harder, J.

(2016) FEBS Lett 590: 1375-1383

  • DOI: https://doi.org/10.1002/1873-3468.12165
  • Primary Citation of Related Structures:  
    5HLR, 5HSS

  • PubMed Abstract: 

    Linalool dehydratase/isomerase (Ldi), an enzyme of terpene degradation in Castellaniella defragrans, isomerizes the primary monoterpene alcohol geraniol into the tertiary alcohol (S)-linalool and dehydrates (S)-linalool to the alkene β-myrcene. Here we report on the crystal structures of Ldi with and without terpene substrates, revealing a cofactor-free homopentameric enzyme. The substrates were embedded inside a hydrophobic channel between two monomers of the (α,α)6 barrel fold class and flanked by three clusters of polar residues involved in acid-base catalysis. The detailed view into the active site will guide future biotechnological applications of Ldi, in particular, for industrial butadiene and isoprene production from renewable sources.


  • Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Linalool dehydratase/isomerase
A, B, C, D, E
371Castellaniella defragransMutation(s): 0 
Gene Names: ldi
EC: 4.2.1.127 (PDB Primary Data), 5.4.4.4 (PDB Primary Data)
UniProt
Find proteins for E1XUJ2 (Castellaniella defragrans (strain DSM 12143 / CCUG 39792 / 65Phen))
Explore E1XUJ2 
Go to UniProtKB:  E1XUJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1XUJ2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
64Z
Query on 64Z

Download Ideal Coordinates CCD File 
G [auth A],
M [auth D],
O [auth E]
Geraniol
C10 H18 O
GLZPCOQZEFWAFX-JXMROGBWSA-N
650
Query on 650

Download Ideal Coordinates CCD File 
I [auth B],
J [auth C]
Beta-Myrcene
C10 H18
MZPDTOMKQCMETI-BJMVGYQFSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
K [auth D],
L [auth D],
N [auth E]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.27α = 90
b = 106.29β = 90
c = 221.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFG (Sina Weidenweber)GermanySPP1319

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references