PDBsum entry 1jbt

Hydrolase/RNA

PDB id: 1jbt

Contents

Protein chains

149 a.a. *

DNA/RNA

Metals

__K ×6

* Residue conservation analysis

PDB id:

1jbt

Name:

Hydrolase/RNA

Title:

Crystal structure of ribotoxin restrictocin complexed with a 29-mer sarcin/ricin domain RNA analog

Structure:

29-mer sarcin/ricin domain RNA analog. Chain: c, d. Engineered: yes. Restrictocin. Chain: a, b. Synonym: ribonuclease mitogillin. Ec: 3.1.27.-

Source:

Synthetic: yes. Other_details: the RNA sequence contains 14 highly conserved nucleotides among all living species.. Aspergillus restrictus. Organism_taxid: 5064

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.224 R-free: 0.282

Authors:

X.Yang,T.Gerczei,L.Glover,C.C.Correll

Key ref:

X.Yang et al. (2001). Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nat Struct Biol, 8, 968-973. PubMed id: 11685244 DOI: 10.1038/nsb1101-968

Date:

06-Jun-01 Release date: 26-Oct-01

Protein chains

P67876  (RNMG_ASPRE) -  Ribonuclease mitogillin from Aspergillus restrictus

Seq: 176 a.a.

Struc: 149 a.a.

DNA/RNA chains

C-G-C-U-C-C-U-C-A-G-U-A-C-G-A-G-A-G-G-A-A-C-C-G-G-A-G-C-G 29 bases

C-G-C-U-C-C-U-C-A-G-U-A-C-G-A-G-A-G-G-A-A-C-C-G-G-A-G-C-G 29 bases

Enzyme reactions

• Enzyme class: E.C.3.1.27.- - ?????

DOI no: 10.1038/nsb1101-968

Nat Struct Biol 8:968-973 (2001)

PubMed id: 11685244

Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.

X.Yang, T.Gérczei, L.T.Glover, C.C.Correll.

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.

Selected figure(s)

Figure 1.
Figure 1. Structural overview. a, Schematic of the RNA sequence showing the conserved nucleotides (boxed), tetraloop (green) and bulged-G motif (yellow). The sites of 2' modification of the stem (asterisks) and of 4325 and 4326 (plus signs) are shown. The terminal nucleotides are designed to pair and create a blunt end (red); the remainder corresponds to rat 28S nucleotides 4315 -4333 (hereafter, Escherichia coli 23S numbering is in parentheses). The two 29-mer variants (nU4325dA^4326 and mG4325dA^4326) are missing the first and the last nucleotide. When enzyme concentrations exceed that of substrates other than ribosomes, cleavage by the toxin is primarily on the 3' side of purines3. b, A ribbon drawing of the restrictocin -mG4325 (misdocked) complex showing the tetraloop (green) and bulged-G motif (yellow) of the substrate, as well as the bound potassium ions (pink).

Figure 4.
Figure 4. Implications for cleavage and recognition. a, Superposition of the structure of the scissile phosphate groups of the target nucleotide from the uncomplexed substrate SRL RNA^11 (red), the 3' splice site of a splicing endonuclease^19 (yellow) and the ground state forms of the lead-dependent22 (navy) and the hammerhead^20 (blue) ribozymes. b, Superposition of the structures of the two types of S-turn: one in the bound complex (blue) and another in the L11 -RNA complex38 (yellow).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 968-973) copyright 2001.

Figures were selected by an automated process.