5GU4

rRNA N-glycosylase RTA

Summary for 5GU4

• Entry DOI: 10.2210/pdb5gu4/pdb
• Descriptor: Ricin, GLY-PHE-GLY-LEU-PHE-ASP, GLYCEROL, ... (4 entities in total)
• Functional Keywords: ricin, ribosome-inactivating protein, ribosomal p stalk protein, ribosome, hydrolase
• Biological source: Ricinus communis (Castor bean); More
• Total number of polymer chains: 4
• Total formula weight: 69103.64

Authors

Shi, W.W.,Tang, Y.S.,Sze, S.Y.,Zhu, Z.N.,Wong, K.B.,Shaw, P.C. (deposition date: 2016-08-24, release date: 2016-11-02, Last modification date: 2023-11-08)

Primary citation

Shi, W.W.,Tang, Y.S.,Sze, S.Y.,Zhu, Z.N.,Wong, K.B.,Shaw, P.C.
Crystal Structure of Ribosome-Inactivating Protein Ricin A Chain in Complex with the C-Terminal Peptide of the Ribosomal Stalk Protein P2
Toxins, 8:-, 2016

PubMed Abstract: Ricin is a type 2 ribosome-inactivating protein (RIP), containing a catalytic A chain and a lectin-like B chain. It inhibits protein synthesis by depurinating the N-glycosidic bond at α-sarcin/ricin loop (SRL) of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation center of the ribosome. Here, we present the 1.6 Å crystal structure of Ricin A chain (RTA) complexed to the C-terminal peptide of the ribosomal stalk protein P2, which plays a crucial role in specific recognition of elongation factors and recruitment of eukaryote-specific RIPs to the ribosomes. Our structure reveals that the C-terminal GFGLFD motif of P2 peptide is inserted into a hydrophobic pocket of RTA, while the interaction assays demonstrate the structurally untraced SDDDM motif of P2 peptide contributes to the interaction with RTA. This interaction mode of RTA and P protein is in contrast to that with trichosanthin (TCS), Shiga-toxin (Stx) and the active form of maize RIP (MOD), implying the flexibility of the P2 peptide-RIP interaction, for the latter to gain access to ribosome.

PubMed: 27754366
DOI: 10.3390/toxins8100296

Experimental method

X-RAY DIFFRACTION (1.55 Å)