5NX6

Crystal structure of 1,8-cineole synthase from Streptomyces clavuligerus in complex with 2-fluoroneryl diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.

Karuppiah, V.Ranaghan, K.E.Leferink, N.G.H.Johannissen, L.O.Shanmugam, M.Ni Cheallaigh, A.Bennett, N.J.Kearsey, L.J.Takano, E.Gardiner, J.M.van der Kamp, M.W.Hay, S.Mulholland, A.J.Leys, D.Scrutton, N.S.

(2017) ACS Catal 7: 6268-6282

  • DOI: 10.1021/acscatal.7b01924
  • Primary Citation of Related Structures:  
    5NX4, 5NX5, 5NX6, 5NX7

  • PubMed Abstract: 
  • Terpenoids form the largest and stereochemically most diverse class of natural products, and there is considerable interest in producing these by biocatalysis with whole cells or purified enzymes, and by metabolic engineering. The monoterpenes are an important class of terpenes and are industrially important as flavors and fragrances ...

    Terpenoids form the largest and stereochemically most diverse class of natural products, and there is considerable interest in producing these by biocatalysis with whole cells or purified enzymes, and by metabolic engineering. The monoterpenes are an important class of terpenes and are industrially important as flavors and fragrances. We report here structures for the recently discovered Streptomyces clavuligerus monoterpene synthases linalool synthase (bLinS) and 1,8-cineole synthase (bCinS), and we show that these are active biocatalysts for monoterpene production using biocatalysis and metabolic engineering platforms. In metabolically engineered monoterpene-producing E. coli strains, use of bLinS leads to 300-fold higher linalool production compared with the corresponding plant monoterpene synthase. With bCinS, 1,8-cineole is produced with 96% purity compared to 67% from plant species. Structures of bLinS and bCinS, and their complexes with fluorinated substrate analogues, show that these bacterial monoterpene synthases are similar to previously characterized sesquiterpene synthases. Molecular dynamics simulations suggest that these monoterpene synthases do not undergo large-scale conformational changes during the reaction cycle, making them attractive targets for structured-based protein engineering to expand the catalytic scope of these enzymes toward alternative monoterpene scaffolds. Comparison of the bLinS and bCinS structures indicates how their active sites steer reactive carbocation intermediates to the desired acyclic linalool (bLinS) or bicyclic 1,8-cineole (bCinS) products. The work reported here provides the analysis of structures for this important class of monoterpene synthase. This should now guide exploitation of the bacterial enzymes as gateway biocatalysts for the production of other monoterpenes and monoterpenoids.


    Organizational Affiliation

    BBSRC/EPSRC Manchester Synthetic Biology Research Centre for Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pentalenene synthaseA, B330Streptomyces clavuligerusMutation(s): 0 
Gene Names: SCLAV_p0982SSCG_00536cnsA
EC: 4.2.3.7 (PDB Primary Data), 4.2.3.108 (UniProt)
UniProt
Find proteins for B5GMG2 (Streptomyces clavuligerus)
Explore B5GMG2 
Go to UniProtKB:  B5GMG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5GMG2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LA6
Query on LA6

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
(2E)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate
C10 H19 F O7 P2
BYJNSLXDWGDGAC-MDZDMXLPSA-N
 Ligand Interaction
NDS
Query on NDS

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
ETHYL DIMETHYL AMMONIO PROPANE SULFONATE
C7 H17 N O3 S
NNCRHRDBFDCWPA-UHFFFAOYSA-N
 Ligand Interaction
9D2
Query on 9D2

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
2-ethyl-2-(hydroxymethyl)propane-1,3-diol
C6 H14 O3
ZJCCRDAZUWHFQH-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.81α = 90.04
b = 60.83β = 92.89
c = 64.1γ = 101.98
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M000354/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references