9e42

From Proteopedia

RTA-RUNT-192 complex

Structural highlights

9e42 is a 2 chain structure with sequence from Ricinus communis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RICI_RICCO Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).

Publication Abstract from PubMed

Ricin is a category B agent for bioterrorism, and Shiga toxins are the primary virulence factors of Shiga toxin (Stx) producing Escherichia coli. Ricin and Stxs bind the ribosomal P-stalk proteins to depurinate the sarcin/ricin loop on the eukaryotic ribosome and inhibit translation. Both toxins are prime targets for therapeutic intervention because no effective therapy exists for ricin intoxication or Shiga toxin producing Escherichia coli infection. Binding of ricin toxin A subunit (RTA) to the ribosomal P-stalk stimulates depurination of the sarcin/ricin loop by an unknown mechanism. We previously identified compounds that bind the P-stalk pocket of RTA and inhibit catalytic activity. Here we characterize a second-generation lead compound, which binds the P-stalk pocket of RTA with over 30-fold improved affinity relative to the original compound and inhibits the cytotoxicity of ricin holotoxin in Vero cells with no apparent cellular toxicity by itself. This compound also shows protection against Stx2A1. X-ray crystal structure of RTA-inhibitor complexes suggests that the orientation of the carboxylic acid influences the inhibitor contacts at the P-stalk site of RTA and contributes to inhibitor potency. The structural changes triggered at the P-stalk site of RTA were validated by solution NMR-based chemical shift perturbation analysis. A key finding by NMR is that binding-induced conformational changes extend beyond the P-stalk site to residues in the active site cleft of RTA. Collectively, these results provide valuable new insight into the conformational flexibility in the C-terminal domain of RTA and its potential role in mediating the remarkable catalytic activity of ricin.

Binding of small molecules at the P-stalk site of ricin A subunit trigger conformational changes that extend into the active site.,McLaughlin JE, Rudolph MJ, Dutta A, Li XP, Tsymbal AM, Chen Y, Bhattacharya S, Algava B, Goger M, Roberge JY, Tumer NE J Biol Chem. 2025 Mar;301(3):108310. doi: 10.1016/j.jbc.2025.108310. Epub 2025 , Feb 14. PMID:39955060^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ McLaughlin JE, Rudolph MJ, Dutta A, Li XP, Tsymbal AM, Chen Y, Bhattacharya S, Algava B, Goger M, Roberge JY, Tumer NE. Binding of small molecules at the P-stalk site of ricin A subunit trigger conformational changes that extend into the active site. J Biol Chem. 2025 Mar;301(3):108310. PMID:39955060 doi:10.1016/j.jbc.2025.108310