7BUS

Chalcone synthase from Glycine max (L.) Merr (soybean)

• PDB DOI: https://doi.org/10.2210/pdb7BUS/pdb

• Classification: TRANSFERASE
• Organism(s): Glycine max
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-04-08 Released: 2020-08-19 
• Deposition Author(s): Imaizumi, R., Mameda, R., Takeshita, K., Waki, T., Kubo, H., Sakai, N., Nakata, S., Takahashi, S., Kataoka, K., Yamamoto, M., Yamashita, S., Nakayama, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.254 
• R-Value Work: 0.189 

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 

• PubMed: 32725893 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 89.3 kDa 
• Atom Count: 6,350 
• Modelled Residue Count: 778 
• Deposited Residue Count: 808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone synthase	A, B	404	Glycine max	Mutation(s): 0  Gene Names: ICHS1, GLYMA_08G109400 EC: 2.3.1.74
UniProt
Find proteins for P24826 (Glycine max) Explore P24826  Go to UniProtKB:  P24826

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
SME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.254 
• R-Value Work: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.76	α = 90
b = 98.94	β = 90
c = 159.29	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Imaizumi, R., Mameda, R., Takeshita, K., Waki, T., Kubo, H., Sakai, N., Nakata, S., Takahashi, S., Kataoka, K., Yamamoto, M., Yamashita, S., Nakayama, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H03938
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101070

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description