5HLR | pdb_00005hlr

Linalool dehydratase/isomerase: Ldi-apo

• PDB DOI: https://doi.org/10.2210/pdb5HLR/pdb

• Classification: ISOMERASE
• Organism(s): Castellaniella defragrans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-15 Released: 2016-04-27 
• Deposition Author(s): Weidenweber, S., Marmulla, R., Harder, J., Ermler, U.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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

• PubMed: 27062179 
• DOI: https://doi.org/10.1002/1873-3468.12165
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 209.91 kDa 
• Atom Count: 15,222 
• Modeled Residue Count: 1,828 
• Deposited Residue Count: 1,855 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linalool dehydratase/isomerase	A, B, C, D, E	371	Castellaniella defragrans	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG0	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.96	α = 90
b = 106.75	β = 90
c = 223.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Weidenweber, S., Marmulla, R., Harder, J., Ermler, U.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SPP1319 (S. Weidenweber)

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-05-18
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary