5HSS | pdb_00005hss

Linalool dehydratase/isomerase: Ldi with monoterpene substrate

PDB DOI: https://doi.org/10.2210/pdb5HSS/pdb

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

Deposited: 2016-01-26 Released: 2016-04-27
Deposition Author(s): Weidenweber, S., Marmulla, R., Harder, J., Ermler, U.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.223 (Depositor), 0.226 (DCC)
R-Value Work:
0.178 (Depositor), 0.183 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 27062179 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 210.65 kDa
Atom Count: 14,816
Modeled Residue Count: 1,828
Deposited Residue Count: 1,855
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1XUJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
64Z Query on 64Z Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth D] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E]	G [auth A], M [auth D], O [auth E]	Geraniol C₁₀ H₁₈ O GLZPCOQZEFWAFX-JXMROGBWSA-N		Interactions Focus chain G [auth A] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain M [auth D] Focus chain O [auth E]
650 Query on 650 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B]	I [auth B], J [auth C]	Beta-Myrcene C₁₀ H₁₈ MZPDTOMKQCMETI-BJMVGYQFSA-N		Interactions Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth C]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain F [auth A]	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		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.223 (Depositor), 0.226 (DCC)
R-Value Work: 0.178 (Depositor), 0.183 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.27	α = 90
b = 106.29	β = 90
c = 221.33	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-04-27

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SPP1319

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
Version 1.2: 2024-10-23
Changes: Author supporting evidence, Data collection, Database references, Structure summary