2JDL

Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin

Summary for 2JDL

• Entry DOI: 10.2210/pdb2jdl/pdb
• Related: 1GIS 1GIU 1J4G 1MRJ 1MRK 1NLI 1QD2 1TCS
• Descriptor: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN, ACIDIC RIBOSOMAL PROTEIN P2 (3 entities in total)
• Functional Keywords: ribosome inactiviating protein, ribosomal protein, protein synthesis inhibitor, toxin, hydrolase, plant defense, antiviral protein
• Biological source: TRICHOSANTHES KIRILOWII (MONGOLIAN SNAKE-GOURD); More
• Total number of polymer chains: 4
• Total formula weight: 56802.25

Authors

Too, P.H.,Mak, A.N.,Zhu, G.,Au, S.W.,Wong, K.B.,Shaw, P.C. (deposition date: 2007-01-11, release date: 2008-02-05, Last modification date: 2023-12-13)

Primary citation

Too, P.H.,Ma, M.K.,Mak, A.N.,Wong, Y.T.,Tung, C.K.,Zhu, G.,Au, S.W.,Wong, K.B.,Shaw, P.C.
The C-Terminal Fragment of the Ribosomal P Protein Complexed to Trichosanthin Reveals the Interaction between the Ribosome-Inactivating Protein and the Ribosome.
Nucleic Acids Res., 37:602-, 2009

PubMed Abstract: Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by enzymatically depurinating a specific adenine residue at the sarcin-ricin loop of the 28S rRNA, which thereby prevents the binding of elongation factors to the GTPase activation centre of the ribosome. Here, we present the 2.2 A crystal structure of trichosanthin (TCS) complexed to the peptide SDDDMGFGLFD, which corresponds to the conserved C-terminal elongation factor binding domain of the ribosomal P protein. The N-terminal region of this peptide interacts with Lys173, Arg174 and Lys177 in TCS, while the C-terminal region is inserted into a hydrophobic pocket. The interaction with the P protein contributes to the ribosome-inactivating activity of TCS. This 11-mer C-terminal P peptide can be docked with selected important plant and bacterial RIPs, indicating that a similar interaction may also occur with other RIPs.

PubMed: 19073700
DOI: 10.1093/NAR/GKN922

Experimental method

X-RAY DIFFRACTION (2.2 Å)