5LDG | pdb_00005ldg

Isopiperitenone reductase from Mentha piperita in complex with Isopiperitenone and NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.146 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.120 (Depositor) 
  • R-Value Observed: 
    0.120 (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

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 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.

Macromolecule Content 

  • Total Structure Weight: 35.47 kDa 
  • Atom Count: 3,164 
  • Modeled Residue Count: 310 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
(-)-isopiperitenone reductase316Mentha 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP



Download:Ideal Coordinates CCD File
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
IT9

Query on IT9



Download:Ideal Coordinates CCD File
C [auth A](-)-Isopiperitenone
C10 H14 O
SEZLYIWMVRUIKT-SECBINFHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.146 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.120 (Depositor) 
  • R-Value Observed: 0.120 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.56α = 90
b = 65.49β = 90
c = 95.109γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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