1JBR

Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor

Summary for 1JBR

• Entry DOI: 10.2210/pdb1jbr/pdb
• Related: 1JBS 1JBT 1aqz 430D 480D 483D
• Descriptor: 5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3', 5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3', 31-mer SRD RNA analog, ... (6 entities in total)
• Functional Keywords: protein-rna interaction, specific recognition, restrictocin, ribosomal rna, sarcin/ricin domain, base flipping, hydrolase-rna complex, hydrolase/rna
• Biological source: Aspergillus restrictus; More
• Cellular location: Secreted: P67876
• Total number of polymer chains: 5
• Total formula weight: 54046.38

Authors

Yang, X.,Gerczei, T.,Glover, L.,Correll, C.C. (deposition date: 2001-06-06, release date: 2001-10-26, Last modification date: 2024-10-16)

Primary citation

Yang, X.,Gerczei, T.,Glover, L.T.,Correll, C.C.
Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
Nat.Struct.Biol., 8:968-973, 2001

PubMed Abstract: The cytotoxin sarcin disrupts elongation factor binding and protein synthesis by specifically cleaving one phosphodiester bond in ribosomes. To elucidate the molecular basis of toxin action, we determined three cocrystal structures of the sarcin homolog restrictocin bound to different analogs that mimic the target sarcin/ricin loop (SRL) structure of the rat 28S rRNA. In these structures, restrictocin contacts the bulged-G motif and an unfolded form of the tetraloop of the SRL RNA. In one structure, toxin loops guide selection of the target site by contacting the base critical for recognition (G4319) and the surrounding S-shaped backbone. In another structure, base flipping of the tetraloop enables cleavage by placing the target nucleotide in the active site with the nucleophile nearly inline for attack on the scissile bond. These structures provide the first views of how a site-specific protein endonuclease recognizes and cleaves a folded RNA substrate.

PubMed: 11685244
DOI: 10.1038/nsb1101-968

Experimental method

X-RAY DIFFRACTION (2.15 Å)