8DLD | pdb_00008dld

Crystal structure of chalcone-isomerase like protein from Physcomitrella patens (PpCHIL-A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Regulatory ligand binding in plant chalcone isomerase-like (CHIL) proteins.

Wolf-Saxon, E.R.Moorman, C.C.Castro, A.Ruiz-Rivera, A.Mallari, J.P.Burke, J.R.

(2023) J Biological Chem 299: 104804-104804

  • DOI: https://doi.org/10.1016/j.jbc.2023.104804
  • Primary Citation Related Structures: 
    8DLC, 8DLD

  • PubMed Abstract: 

    Chalcone isomerase-like (CHIL) protein is a noncatalytic protein that enhances flavonoid content in green plants by serving as a metabolite binder and a rectifier of chalcone synthase (CHS). Rectification of CHS catalysis occurs through direct protein-protein interactions between CHIL and CHS, which alter CHS kinetics and product profiles, favoring naringenin chalcone (NC) production. These discoveries raise questions about how CHIL proteins interact structurally with metabolites and how CHIL-ligand interactions affect interactions with CHS. Using differential scanning fluorimetry on a CHIL protein from Vitis vinifera (VvCHIL), we report that positive thermostability effects are induced by the binding of NC, and negative thermostability effects are induced by the binding of naringenin. NC further causes positive changes to CHIL-CHS binding, whereas naringenin causes negative changes to VvCHIL-CHS binding. These results suggest that CHILs may act as sensors for ligand-mediated pathway feedback by influencing CHS function. The protein X-ray crystal structure of VvCHIL compared with the protein X-ray crystal structure of a CHIL from Physcomitrella patens reveals key amino acid differences at a ligand-binding site of VvCHIL that can be substituted to nullify the destabilizing effect caused by naringenin. Together, these results support a role for CHIL proteins as metabolite sensors that modulate the committed step of the flavonoid pathway.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California, USA.

Macromolecule Content 

  • Total Structure Weight: 23.56 kDa 
  • Atom Count: 1,796 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 216 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chalcone-flavonone isomerase family protein216Physcomitrium patensMutation(s): 0 
Gene Names: PHYPA_030203PHYPADRAFT_167842
UniProt
Find proteins for A9T3E4 (Physcomitrium patens)
Explore A9T3E4 
Go to UniProtKB:  A9T3E4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9T3E4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.55α = 90
b = 49.88β = 110.87
c = 76.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-22
    Changes: Database references