Chalcone isomerase and naringenin

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.237 

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This is version 1.3 of the entry. See complete history


Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase.

Jez, J.M.Bowman, M.E.Dixon, R.A.Noel, J.P.

(2000) Nat Struct Biol 7: 786-791

  • DOI: https://doi.org/10.1038/79025
  • Primary Citation of Related Structures:  
    1EYP, 1EYQ

  • PubMed Abstract: 

    Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcone synthesized by chalcone synthase (CHS) into (2S)-naringenin, an essential compound in the biosynthesis of anthocyanin pigments, inducers of Rhizobium nodulation genes, and antimicrobial phytoalexins. The 1.85 A resolution crystal structure of alfalfa CHI in complex with (2S)-naringenin reveals a novel open-faced beta-sandwich fold. Currently, proteins with homologous primary sequences are found only in higher plants. The topology of the active site cleft defines the stereochemistry of the cyclization reaction. The structure and mutational analysis suggest a mechanism in which shape complementarity of the binding cleft locks the substrate into a constrained conformation that allows the reaction to proceed with a second-order rate constant approaching the diffusion controlled limit. This structure raises questions about the evolutionary history of this structurally unique plant enzyme.

  • Organizational Affiliation

    Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
222Medicago sativaMutation(s): 0 
Find proteins for P28012 (Medicago sativa)
Explore P28012 
Go to UniProtKB:  P28012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28012
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.237 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.624α = 90
b = 88.624β = 90
c = 350.369γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations