7YJ9

Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with CoA and Naringenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular and structural characterization of a promiscuous chalcone synthase from the fern species Stenoloma chusanum.

Ni, R.Niu, M.Fu, J.Tan, H.Zhu, T.T.Zhang, J.Lou, H.X.Zhang, P.Li, J.X.Cheng, A.X.

(2022) J Integr Plant Biol 64: 1935-1951

  • DOI: https://doi.org/10.1111/jipb.13335
  • Primary Citation of Related Structures:  
    7YJ5, 7YJ6, 7YJ7, 7YJ8, 7YJ9, 7YJA, 7YJB

  • PubMed Abstract: 

    The key enzymes involved in the flavonoid biosynthesis pathway have been extensively studied in seed plants, but relatively less in ferns. In this study, two 4-Coumarate: coenzyme A ligases (Sc4CL1 and Sc4CL2) and one novel chalcone synthase (ScCHS1) were functionally characterized by mining the Stenoloma chusanum transcriptome database. Recombinant Sc4CLs were able to esterify various hydroxycinnamic acids to corresponding acyl-coenzyme A (CoA). ScCHS1 could catalyze p-coumaroyl-CoA, cinnamoyl-CoA, caffeoyl-CoA, and feruloyl-CoA to form naringenin, pinocembrin, eriodictyol, and homoeriodictyol, respectively. Moreover, enzymatic kinetics studies revealed that the optimal substrates of ScCHS1 were feruloyl-CoA and caffeoyl-CoA, rather than p-coumaroyl-CoA, which was substantially different from the common CHSs. Crystallographic and site-directed mutagenesis experiments indicated that the amino acid residues, Leu87, Leu97, Met165, and Ile200, located in the substrate-binding pocket near the B-ring of products, could exert a significant impact on the unique catalytic activity of ScCHS1. Furthermore, overexpression of ScCHS1 in tt4 mutants could partially rescue the mutant phenotypes. Finally, ScCHS1 and Sc4CL1 were used to synthesize flavanones and flavones with multi-substituted hydroxyl and methoxyl B-ring in Escherichia coli, which can effectively eliminate the need for the cytochrome P450 hydroxylation/O-methyltransferase from simple phenylpropanoid acids. In summary, the identification of these important Stenoloma enzymes provides a springboard for the future production of various flavonoids in E. coli.


  • Organizational Affiliation

    Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, 250100, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
chalcone synthase 1 (ScCHS1)412Odontosoria chusanaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.835α = 90
b = 72.395β = 90
c = 83.105γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770330
National Natural Science Foundation of China (NSFC)China32000228
National Natural Science Foundation of China (NSFC)China31870720

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description