7OFL | pdb_00007ofl

Crystal structure of the sesquiterpene synthase Copu9 from coniophora puteana in complex with alendronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.231 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Biotechnological potential and initial characterization of two novel sesquiterpene synthases from Basidiomycota Coniophora puteana for heterologous production of delta-cadinol.

Ringel, M.Dimos, N.Himpich, S.Haack, M.Huber, C.Eisenreich, W.Schenk, G.Loll, B.Bruck, T.

(2022) Microb Cell Fact 21: 64-64

  • DOI: https://doi.org/10.1186/s12934-022-01791-8
  • Primary Citation Related Structures: 
    7OFL

  • PubMed Abstract: 

    Terpene synthases are versatile catalysts in all domains of life, catalyzing the formation of an enormous variety of different terpenoid secondary metabolites. Due to their diverse bioactive properties, terpenoids are of great interest as innovative ingredients in pharmaceutical and cosmetic applications. Recent advances in genome sequencing have led to the discovery of numerous terpene synthases, in particular in Basidiomycota like the wood rotting fungus Coniophora puteana, which further enhances the scope for the manufacture of terpenes for industrial purposes. In this study we describe the identification of two novel (+)-δ-cadinol synthases from C. puteana, Copu5 and Copu9. The sesquiterpene (+)-δ-cadinol was previously shown to exhibit cytotoxic activity therefore having an application as possible, new, and sustainably sourced anti-tumor agent. In an Escherichia coli strain, optimized for sesquiterpene production, titers of 225 mg l -1 and 395 mg l -1 , respectively, could be achieved. Remarkably, both enzymes share the same product profile thereby representing the first two terpene synthases from Basidiomycota with identical product profiles. We solved the crystal structure of Copu9 in its closed conformation, for the first time providing molecular details of sesquiterpene synthase from Basidiomycota. Based on the Copu9 structure, we conducted structure-based mutagenesis of amino acid residues lining the active site, thereby altering the product profile. Interestingly, the mutagenesis study also revealed that despite the conserved product profiles of Copu5 and Copu9 different conformational changes may accompany the catalytic cycle of the two enzymes. This observation suggests that the involvement of tertiary structure elements in the reaction mechanism(s) employed by terpene synthases may be more complex than commonly expected. The presented product selectivity and titers of Copu5 and Copu9 may pave the way towards a sustainable, biotechnological production of the potentially new bioactive (+)-δ-cadinol. Furthermore, Copu5 and Copu9 may serve as model systems for further mechanistic studies of terpenoid catalysis.


  • Organizational Affiliation
    • Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.

Macromolecule Content 

  • Total Structure Weight: 87.12 kDa 
  • Atom Count: 6,249 
  • Modeled Residue Count: 669 
  • Deposited Residue Count: 754 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Terpene synthase
A, B
377Coniophora puteana RWD-64-598 SS2Mutation(s): 0 
Gene Names: CONPUDRAFT_118913
EC: 4.2.3
UniProt
Find proteins for A0A5M3MXY8 (Coniophora puteana (strain RWD-64-598))
Explore A0A5M3MXY8 
Go to UniProtKB:  A0A5M3MXY8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5M3MXY8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AHD

Query on AHD



Download:Ideal Coordinates CCD File
C [auth A],
R [auth B]
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE
C4 H9 N O7 P2
OGSPWJRAVKPPFI-UHFFFAOYSA-J
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth B],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
S [auth B]
T [auth B]
D [auth A],
E [auth A],
F [auth A],
S [auth B],
T [auth B],
U [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.455α = 90
b = 76.622β = 90
c = 135.108γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description