Structure of the pterocarpan synthase dirigent protein GePTS1

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains.

Meng, Q.Moinuddin, S.G.A.Kim, S.J.Bedgar, D.L.Costa, M.A.Thomas, D.G.Young, R.P.Smith, C.A.Cort, J.R.Davin, L.B.Lewis, N.G.

(2020) J Biol Chem 295: 11584-11601

  • DOI: https://doi.org/10.1074/jbc.RA120.012444
  • Primary Citation of Related Structures:  
    6OOC, 6OOD

  • PubMed Abstract: 

    The biochemical activities of dirigent proteins (DPs) give rise to distinct complex classes of plant phenolics. DPs apparently began to emerge during the aquatic-to-land transition, with phylogenetic analyses revealing the presence of numerous DP subfamilies in the plant kingdom. The vast majority (>95%) of DPs in these large multigene families still await discovery of their biochemical functions. Here, we elucidated the 3D structures of two pterocarpan-forming proteins with dirigent-like domains. Both proteins stereospecifically convert distinct diastereomeric chiral isoflavonoid precursors to the chiral pterocarpans, (-)- and (+)-medicarpin, respectively. Their 3D structures enabled comparisons with stereoselective lignan- and aromatic terpenoid-forming DP orthologs. Each protein provides entry into diverse plant natural products classes, and our experiments suggest a common biochemical mechanism in binding and stabilizing distinct plant phenol-derived mono- and bis-quinone methide intermediates during different C-C and C-O bond-forming processes. These observations provide key insights into both their appearance and functional diversification of DPs during land plant evolution/adaptation. The proposed biochemical mechanisms based on our findings provide important clues to how additional physiological roles for DPs and proteins harboring dirigent-like domains can now be rationally and systematically identified.

  • Organizational Affiliation

    Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dirigent protein
A, B, C, D, E
A, B, C, D, E, F
220Glycyrrhiza echinataMutation(s): 0 
Gene Names: PTS1
Find proteins for A0A1V1FH01 (Glycyrrhiza echinata)
Explore A0A1V1FH01 
Go to UniProtKB:  A0A1V1FH01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V1FH01
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.572α = 90
b = 162.572β = 90
c = 99.763γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2020-04-29 
  • Deposition Author(s): Smith, C.A.

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG-0397ER20259

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description