8TH2 | pdb_00008th2

Structure of the isoflavene-forming dirigent protein PsPTS2

• PDB DOI: https://doi.org/10.2210/pdb8TH2/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lathyrus oleraceus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-07-13 Released: 2024-01-31 
• Deposition Author(s): Smith, C.A., Meng, Q., Lewis, N.G., Davin, L.B.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.252 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea.

Meng, Q., Moinuddin, S.G.A., Celoy, R.M., Smith, C.A., Young, R.P., Costa, M.A., Freeman, R.A., Fukaya, M., Kim, D.N., Cort, J.R., Hawes, M.C., van Etten, H.D., Pandey, P., Chittiboyina, A.G., Ferreira, D., Davin, L.B., Lewis, N.G.

(2024) J Biol Chem 300: 105647-105647

• PubMed: 38219818 
• DOI: https://doi.org/10.1016/j.jbc.2024.105647
• Primary Citation Related Structures: 
  8TH2


• PubMed Abstract: 
  

  Pea phytoalexins (-)-maackiain and (+)-pisatin have opposite C6a/C11a configurations, but biosynthetically how this occurs is unknown. Pea dirigent-protein (DP) PsPTS2 generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), and stereoselectivity toward four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers was investigated. Stereoisomer configurations were determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF 20-fold faster than the trans-(3R,4S)-isomer. The 4R-configured substrate's near β-axial OH orientation significantly enhanced its leaving group abilities in generating A-ring mono-quinone methide (QM), whereas 4S-isomer's α-equatorial-OH was a poorer leaving group. Docking simulations indicated that the 4R-configured β-axial OH was closest to Asp ⁵¹ , whereas 4S-isomer's α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S,4R)-DMDIs were substrates, even with the former having C3/C4 stereochemistry as in (+)-pisatin. PsPTS2 used cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and C3/C4 stereoisomers to give 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF). DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and tree legume Bolusanthus speciosus, as DMIF occurs in both species. PsPTS1 utilized cis-(3R,4R)-DMDI to give (-)-maackiain 2200-fold more efficiently than with cis-(3R,4R)-DMI to give (-)-medicarpin. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, reflecting the better 4R configured OH leaving group. PsPTS2 and PsPTS1 provisionally provide the means to enable differing C6a and C11a configurations in (+)-pisatin and (-)-maackiain, via identical DP-engendered mono-QM bound intermediate generation, which PsPTS2 either re-aromatizes to give DMDIF or PsPTS1 intramolecularly cyclizes to afford (-)-maackiain. Substrate docking simulations using PsPTS2 and PsPTS1 indicate cis-(3R,4R)-DMDI binds in the anti-configuration in PsPTS2 to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA.
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA.
National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA; Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi, USA.
Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 145.4 kDa 
• Atom Count: 7,778 
• Modeled Residue Count: 987 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dirigent protein	A, B, C, D, E, F	218	Lathyrus oleraceus	Mutation(s): 3  Gene Names: KIW84_032295
UniProt
Find proteins for A0A9D4XSX2 (Pisum sativum) Explore A0A9D4XSX2  Go to UniProtKB:  A0A9D4XSX2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.252 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.138	α = 90
b = 162.183	β = 90
c = 232.242	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Smith, C.A., Meng, Q., Lewis, N.G., Davin, L.B.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FG-0397ER20259

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references