8I7P

Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine

• PDB DOI: https://doi.org/10.2210/pdb8I7P/pdb

• Classification: HYDROLASE
• Organism(s): Ricinus communis, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-01 Released: 2023-09-20 
• Deposition Author(s): Goto, M., Sakamoto, N., Higashi, S., Kawata, R., Nagatsu, K., Saito, R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor.

Goto, M., Sakamoto, N., Higashi, S., Kawata, R., Nagatsu, K., Saito, R.

(2023) J Enzyme Inhib Med Chem 38: 2219038-2219038

• PubMed: 37259593 
• DOI: https://doi.org/10.1080/14756366.2023.2219038
• Primary Citation of Related Structures:  
  8I7P


• PubMed Abstract: 
  

  Ricin toxin A chain (RTA), from Ricinus communis , is a deadly protein that inactivates ribosomes by degrading an adenine residue at position 4324 in 28S rRNA. Recently, we have demonstrated that pterin-7-carboxamides with peptide pendants were potent RTA inhibitors. Among these, N -(pterin-7-carbonyl)glycyl-L-tyrosine ( 7PCGY ) is the most potent RTA inhibitor as a small organic molecule. However, despite this fascinating inhibitory activity, the mode of interaction of 7PCGY with RTA remains elusive. This study aimed to elucidate the factors responsible for the high RTA inhibitory activity of 7PCGY based on X-ray crystallographic analysis. Herein, we report the successfully resolved X-ray crystal structure of 7PCGY /RTA complexes, revealing that the interaction between the phenolic hydroxy group in 7PCGY and Asn78 of RTA through a hydrogen bonding and the conformational change of Tyr80 and Asn122 are responsible for the high RTA inhibitory activity of 7PCGY .

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Organizational Affiliation: 

Department of Molecular Bioscience, Toho University, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.52 kDa 
• Atom Count: 2,334 
• Modelled Residue Count: 262 
• Deposited Residue Count: 277 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain	A	274	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-(2-ethyl-4-hydroxyphenyl)-1H-indazole-3-carboxamide	B	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.232 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.803	α = 90
b = 67.803	β = 90
c = 141.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Goto, M., Sakamoto, N., Higashi, S., Kawata, R., Nagatsu, K., Saito, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K05699

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release