5L4S | pdb_00005l4s

Isopiperitenone reductase from Mentha piperita in complex with NADP and beta-Cyclocitral


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 
    0.183 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted 6KXClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Pinpointing a Mechanistic Switch Between Ketoreduction and "Ene" Reduction in Short-Chain Dehydrogenases/Reductases.

Lygidakis, A.Karuppiah, V.Hoeven, R.Ni Cheallaigh, A.Leys, D.Gardiner, J.M.Toogood, H.S.Scrutton, N.S.

(2016) Angew Chem Int Ed Engl 55: 9596-9600

  • DOI: https://doi.org/10.1002/anie.201603785
  • Primary Citation of Related Structures:  
    5L4S, 5L51, 5L53, 5LCX, 5LDG

  • PubMed Abstract: 

    Three enzymes of the Mentha essential oil biosynthetic pathway are highly homologous, namely the ketoreductases (-)-menthone:(-)-menthol reductase and (-)-menthone:(+)-neomenthol reductase, and the "ene" reductase isopiperitenone reductase. We identified a rare catalytic residue substitution in the last two, and performed comparative crystal structure analyses and residue-swapping mutagenesis to investigate whether this determines the reaction outcome. The result was a complete loss of native activity and a switch between ene reduction and ketoreduction. This suggests the importance of a catalytic glutamate vs. tyrosine residue in determining the outcome of the reduction of α,β-unsaturated alkenes, due to the substrate occupying different binding conformations, and possibly also to the relative acidities of the two residues. This simple switch in mechanism by a single amino acid substitution could potentially generate a large number of de novo ene reductases.


  • Organizational Affiliation

    Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(-)-isopiperitenone reductase318Mentha x piperitaMutation(s): 0 
EC: 1.3.1.82
UniProt
Find proteins for Q6WAU1 (Mentha piperita)
Explore Q6WAU1 
Go to UniProtKB:  Q6WAU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WAU1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
6KX
Query on 6KX

Download Ideal Coordinates CCD File 
B [auth A]beta-cyclocitral
C10 H16 O
MOQGCGNUWBPGTQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.113α = 90
b = 65.612β = 90
c = 94.813γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted 6KXClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J015512/1 and BB/M000354/1

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description