PDBsum entry: 1t4l

RNA binding protein/RNA

PDB id: 1t4l

Contents

Protein chain

90 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1t4l

Name:

RNA binding protein/RNA

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

Structure:

5' terminal hairpin of snr47 precursor. Chain: a. Fragment: agaa tetraloop RNA hairpin. Engineered: yes. Ribonuclease iii. Chain: b. Fragment: double-stranded RNA binding domain. Synonym: rnase iii. Engineered: yes

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: rnt1, ymr239c, ym9408.01c, ym9959.21. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

NMR struc:

15 models

Authors:

H.Wu,A.Henras,G.Chanfreau,J.Feigon

Key ref:

H.Wu et al. (2004). 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 U S A, 101, 8307-8312. PubMed id: 15150409 DOI: 10.1073/pnas.0402627101

Date:

29-Apr-04 Release date: 01-Jun-04

Protein chain

Q02555  (RNT1_YEAST) -  Ribonuclease 3

Seq: 471 a.a.

Struc: 90 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.26.3 - Ribonuclease Iii.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biochemical function: RNA binding (2 terms)

DOI no: 10.1073/pnas.0402627101

Proc Natl Acad Sci U S A 101:8307-8312 (2004)

PubMed id: 15150409

Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III.

H.Wu, A.Henras, G.Chanfreau, J.Feigon.

ABSTRACT

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.

Selected figure(s)

Figure 2.
Fig. 2. Overview of the Rnt1p dsRBD-snR47h RNA complex. (A) Superposition of the 15 lowest energy structures. The protein is shown in blue, and RNA is shown in green. (B) Solvent-accessible surface of the lowest energy structure. Amino acids contacting successive minor, major, and tetraloop minor grooves on one face of the RNA helix are colored green, cyan, and blue, respectively. The rest of the protein is yellow, and the RNA is white. (C) Stereoview of the lowest energy structure. The RNA is shown in lines with the helical backbone indicated by thin blue cylinder and the protein in ribbons with amino acids at the protein-RNA interface shown as ball and sticks.

Figure 3.
Fig. 3. Interactions between Rnt1p dsRBD and snR47h RNA. Lowest energy structure is shown. (A) Solvent-accessible surface of the RNA showing the major and minor grooves with the AGAA tetraloop nucleotides colored red, blue, and orange, and the protein in yellow ribbon. Protein side chains that interact with the RNA are shown as sticks. (B-D) Details of specific interactions of the protein with the minor groove (B), major groove (C), and tetraloop minor groove (stereoview) (D) are shown. Nucleotides are green, with phosphates and O2' of interacting riboses in red. Protein side chains are sticks, with backbone as yellow ribbon. Direct and water-mediated protein-RNA H-bonds are indicated as orange and blue dashed lines, respectively.

Figures were selected by an automated process.