7EQL

Crystal structure of (+)-pulegone reductase from Mentha piperita


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis.

Liu, C.Gao, Q.Shang, Z.Liu, J.Zhou, S.Dang, J.Liu, L.Lange, I.Srividya, N.Lange, B.M.Wu, Q.Lin, W.

(2021) Front Plant Sci 12: 780970-780970

  • DOI: https://doi.org/10.3389/fpls.2021.780970
  • Primary Citation of Related Structures:  
    7EQL

  • PubMed Abstract: 

    Monoterpenoids are the main components of plant essential oils and the active components of some traditional Chinese medicinal herbs like Mentha haplocalyx Briq ., Nepeta tenuifolia Briq ., Perilla frutescens (L.) Britt and Pogostemin cablin (Blanco) Benth. Pulegone reductase is the key enzyme in the biosynthesis of menthol and is required for the stereoselective reduction of the Δ 2,8 double bond of pulegone to produce the major intermediate menthone, thus determining the stereochemistry of menthol. However, the structural basis and mechanism underlying the stereoselectivity of pulegone reductase remain poorly understood. In this study, we characterized a novel (-)-pulegone reductase from Nepeta tenuifolia ( Nt PR), which can catalyze (-)-pulegone to (+)-menthone and (-)-isomenthone through our RNA-seq, bioinformatic analysis in combination with in vitro enzyme activity assay, and determined the structure of (+)-pulegone reductase from M. piperita ( Mp PR) by using X-ray crystallography, molecular modeling and docking, site-directed mutagenesis, molecular dynamics simulations, and biochemical analysis. We identified and validated the critical residues in the crystal structure of Mp PR involved in the binding of the substrate pulegone. We also further identified that residues Leu56, Val282, and Val284 determine the stereoselectivity of the substrate pulegone, and mainly contributes to the product stereoselectivity. This work not only provides a starting point for the understanding of stereoselectivity of pulegone reductases, but also offers a basis for the engineering of menthone/menthol biosynthetic enzymes to achieve high-titer, industrial-scale production of enantiomerically pure products.


  • Organizational Affiliation

    School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(+)-pulegone reductase342Mentha x piperitaMutation(s): 0 
EC: 1.3.1.81
UniProt
Find proteins for Q6WAU0 (Mentha piperita)
Explore Q6WAU0 
Go to UniProtKB:  Q6WAU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WAU0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.111α = 90
b = 120.111β = 90
c = 57.626γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2021-09-29 
  • Deposition Author(s): Lin, W.

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2022-04-13
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description