7BUR

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.151 

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Literature

Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean.

Imaizumi, R.Mameda, R.Takeshita, K.Kubo, H.Sakai, N.Nakata, S.Takahashi, S.Kataoka, K.Yamamoto, M.Nakayama, T.Yamashita, S.Waki, T.

(2020) Proteins 

  • DOI: 10.1002/prot.25988
  • Primary Citation of Related Structures:  
    7BUR, 7BUS

  • PubMed Abstract: 
  • Isoflavonoid is one of the groups of flavonoids that play pivotal roles in the survival of land plants. Chalcone synthase (CHS), the first enzyme of the isoflavonoid biosynthetic pathway, catalyzes the formation of a common isoflavonoid precursor. We have previously reported that an isozyme of soybean CHS (termed GmCHS1) is a key component of the isoflavonoid metabolon, a protein complex to enhance efficiency of isoflavonoid production ...

    Isoflavonoid is one of the groups of flavonoids that play pivotal roles in the survival of land plants. Chalcone synthase (CHS), the first enzyme of the isoflavonoid biosynthetic pathway, catalyzes the formation of a common isoflavonoid precursor. We have previously reported that an isozyme of soybean CHS (termed GmCHS1) is a key component of the isoflavonoid metabolon, a protein complex to enhance efficiency of isoflavonoid production. Here, we determined the crystal structure of GmCHS1 as a first step of understanding the metabolon structure, as well as to better understand the catalytic mechanism of GmCHS1.


    Organizational Affiliation

    Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chalcone synthase 1A, B404Glycine maxMutation(s): 0 
Gene Names: CHS1
EC: 2.3.1.74
UniProt
Find proteins for P24826 (Glycine max)
Explore P24826 
Go to UniProtKB:  P24826
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24826
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B L-PEPTIDE LINKINGC3 H7 N O4 SCYS
SME
Query on SME
A, B L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.64α = 90
b = 97.99β = 90
c = 157.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H03938
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101070

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release