Structure of 2-hydroxyisoflavanone dehydratase from Pueraria lobate

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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The protein conformational basis of isoflavone biosynthesis.

Wang, X.Pan, H.Sagurthi, S.Paris, V.Zhuo, C.Dixon, R.A.

(2022) Commun Biol 5: 1249-1249

  • DOI: https://doi.org/10.1038/s42003-022-04222-x
  • Primary Citation of Related Structures:  
    8E83, 8EA1, 8EA2

  • PubMed Abstract: 

    Isoflavonoids play important roles in plant defense and also exhibit a range of mammalian health-promoting activities. Their biosynthesis is initiated by two enzymes with unusual catalytic activities; 2-hydroxyisoflavanone synthase (2-HIS), a membrane-bound cytochrome P450 catalyzing a coupled aryl-ring migration and hydroxylation, and 2-hydroxyisoflavanone dehydratase (2-HID), a member of a large carboxylesterase family that paradoxically catalyzes dehydration of 2-hydroxyisoflavanones to isoflavone. Here we report the crystal structures of 2-HIS from Medicago truncatula and 2-HID from Pueraria lobata. The 2-HIS structure reveals a unique cytochrome P450 conformation and heme and substrate binding mode that facilitate the coupled aryl-ring migration and hydroxylation reactions. The 2-HID structure reveals the active site architecture and putative catalytic residues for the dual dehydratase and carboxylesterase activities. Mutagenesis studies revealed key residues involved in substrate binding and specificity. Understanding the structural basis of isoflavone biosynthesis will facilitate the engineering of new bioactive isoflavonoids.

  • Organizational Affiliation

    BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, 76203-5017, USA. Xiaoqiang.Wang@unt.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-hydroxyisoflavanone dehydratase353Pueraria montana var. lobataMutation(s): 0 
Find proteins for E9M5G1 (Pueraria montana var. lobata)
Explore E9M5G1 
Go to UniProtKB:  E9M5G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9M5G1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.309α = 90
b = 102.309β = 90
c = 70.239γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description