4REV

Structure of the dirigent protein DRR206


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 angstrom Resolution with Three Isolated Active Sites.

Kim, K.W.Smith, C.A.Daily, M.D.Cort, J.R.Davin, L.B.Lewis, N.G.

(2015) J Biol Chem 290: 1308-1318

  • DOI: https://doi.org/10.1074/jbc.M114.611780
  • Primary Citation of Related Structures:  
    4REV

  • PubMed Abstract: 

    Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (-)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.


  • Organizational Affiliation

    From the Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disease resistance response protein 206
A, B
164Pisum sativumMutation(s): 0 
UniProt
Find proteins for P13240 (Pisum sativum)
Explore P13240 
Go to UniProtKB:  P13240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13240
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.416α = 90
b = 88.416β = 90
c = 196.767γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary