1T4L image
Deposition Date 2004-04-29
Release Date 2004-06-01
Last Version Date 2024-05-22
Entry Detail
PDB ID:
1T4L
Title:
Solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with the 5' terminal RNA hairpin of snR47 precursor
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Conformers Calculated:
100
Conformers Submitted:
15
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Ribonuclease III
Gene (Uniprot):RNT1
Chain IDs:B
Chain Length:90
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
Primary Citation
Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III.
Proc.Natl.Acad.Sci.USA 101 8307 8312 (2004)
PMID: 15150409 DOI: 10.1073/pnas.0402627101

Abstact

Specific recognition of double-stranded RNA (dsRNA) by dsRNA-binding domains (dsRBDs) is involved in a large number of biological and regulatory processes. Although structures of dsRBDs in complex with dsRNA have revealed how they can bind to dsRNA in general, these do not explain how a dsRBD can recognize specific RNAs. Rnt1p, a member of the RNase III family of dsRNA endonucleases, is a key component of the Saccharomyces cerevisiae RNA-processing machinery. The Rnt1p dsRBD has been implicated in targeting this endonuclease to its RNA substrates, by recognizing hairpins closed by AGNN tetraloops. We report the solution structure of Rnt1p dsRBD complexed to the 5' terminal hairpin of one of its small nucleolar RNA substrates, the snR47 precursor. The conserved AGNN tetraloop fold is retained in the protein-RNA complex. The dsRBD contacts the RNA at successive minor, major, and tetraloop minor grooves on one face of the helix. Surprisingly, neither the universally conserved G nor the highly conserved A are recognized by specific hydrogen bonds to the bases. Rather, the N-terminal helix fits snugly into the minor groove of the RNA tetraloop and top of the stem, interacting in a non-sequence-specific manner with the sugar-phosphate backbone and the two nonconserved tetraloop bases. Mutational analysis of residues that contact the tetraloop region show that they are functionally important for RNA processing in the context of the entire protein in vivo. These results show how a single dsRBD can convey specificity for particular RNA targets, by structure specific recognition of a conserved tetraloop fold.

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