1QYC | pdb_00001qyc

Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases, and their relationship to isoflavone reductases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.242 (Depositor) 
  • R-Value Work: 
    0.195 (Depositor) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QYC

This is version 1.3 of the entry. See complete history

Literature

Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases.

Min, T.Kasahara, H.Bedgar, D.L.Youn, B.Lawrence, P.K.Gang, D.R.Halls, S.C.Park, H.Hilsenbeck, J.L.Davin, L.B.Lewis, N.G.Kang, C.

(2003) J Biological Chem 278: 50714-50723

  • DOI: https://doi.org/10.1074/jbc.M308493200
  • Primary Citation Related Structures: 
    1QYC, 1QYD

  • PubMed Abstract: 

    Despite the importance of plant lignans and isoflavonoids in human health protection (e.g. for both treatment and prevention of onset of various cancers) as well as in plant biology (e.g. in defense functions and in heartwood development), systematic studies on the enzymes involved in their biosynthesis have only recently begun. In this investigation, three NADPH-dependent aromatic alcohol reductases were comprehensively studied, namely pinoresinol-lariciresinol reductase (PLR), phenylcoumaran benzylic ether reductase (PCBER), and isoflavone reductase (IFR), which are involved in central steps to the various important bioactive lignans and isoflavonoids. Of particular interest was in determining how differing regio- and enantiospecificities are achieved with the different enzymes, despite each apparently going through similar enone intermediates. Initially, the three-dimensional x-ray crystal structures of both PLR_Tp1 and PCBER_Pt1 were solved and refined to 2.5 and 2.2 A resolutions, respectively. Not only do they share high gene sequence similarity, but their structures are similar, having a continuous alpha/beta NADPH-binding domain and a smaller substrate-binding domain. IFR (whose crystal structure is not yet obtained) was also compared (modeled) with PLR and PCBER and was deduced to have the same overall basic structure. The basis for the distinct enantio-specific and regio-specific reactions of PCBER, PLR, and IFR, as well as the reaction mechanism and participating residues involved (as identified by site-directed mutagenesis), are discussed.


  • Organizational Affiliation
    • School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA.

Macromolecule Content 

  • Total Structure Weight: 67.13 kDa 
  • Atom Count: 5,011 
  • Modeled Residue Count: 614 
  • Deposited Residue Count: 616 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
phenylcoumaran benzylic ether reductase PT1
A, B
308Pinus taedaMutation(s): 0 
EC: 1.23.1
UniProt
Find proteins for Q9LL41 (Pinus taeda)
Explore Q9LL41 
Go to UniProtKB:  Q9LL41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LL41
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.242 (Depositor) 
  • R-Value Work:  0.195 (Depositor) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.195α = 90
b = 67.941β = 115.08
c = 75.019γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4data scaling
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references