PDBsum entry: 1t4o

Hydrolase

PDB id: 1t4o

Contents

Protein chains

81 a.a. *

88 a.a. *

Waters ×33

* Residue conservation analysis

PDB id:

1t4o

Name:

Hydrolase

Title:

Crystal structure of rnt1p dsrbd

Structure:

Ribonuclease iii. Chain: a, b. Fragment: dsrbd. Synonym: rnase iii, rnt1p. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: rnt1, ymr239c, ym9408.01c, ym9959.21. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å R-factor: 0.206 R-free: 0.276

Authors:

N.Leulliot,S.Quevillon-Cheruel,M.Graille,H.Van Tilbeurgh, T.C.Leeper,K.S.Godin,T.E.Edwards,S.T.Sigurdsson, N.Rozenkrants,R.J.Nagel,M.Ares Jr.,G.Varani

Key ref:

N.Leulliot et al. (2004). A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III. EMBO J, 23, 2468-2477. PubMed id: 15192703 DOI: 10.1038/sj.emboj.7600260

Date:

30-Apr-04 Release date: 22-Jun-04

Protein chain

Q02555  (RNT1_YEAST) -  Ribonuclease 3

Seq: 471 a.a.

Struc: 81 a.a.

Protein chain

Q02555  (RNT1_YEAST) -  Ribonuclease 3

Seq: 471 a.a.

Struc: 88 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: 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: 10.1038/sj.emboj.7600260

EMBO J 23:2468-2477 (2004)

PubMed id: 15192703

A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.

N.Leulliot, S.Quevillon-Cheruel, M.Graille, H.van Tilbeurgh, T.C.Leeper, K.S.Godin, T.E.Edwards, S.T.Sigurdsson, N.Rozenkrants, R.J.Nagel, M.Ares, G.Varani.

ABSTRACT

Rnt1 endoribonuclease, the yeast homolog of RNAse III, plays an important role in the maturation of a diverse set of RNAs. The enzymatic activity requires a conserved catalytic domain, while RNA binding requires the double-stranded RNA-binding domain (dsRBD) at the C-terminus of the protein. While bacterial RNAse III enzymes cleave double-stranded RNA, Rnt1p specifically cleaves RNAs that possess short irregular stem-loops containing 12-14 base pairs interrupted by internal loops and bulges and capped by conserved AGNN tetraloops. Consistent with this substrate specificity, the isolated Rnt1p dsRBD and the 30-40 amino acids that follow bind to AGNN-containing stem-loops preferentially in vitro. In order to understand how Rnt1p recognizes its cognate processing sites, we have defined its minimal RNA-binding domain and determined its structure by solution NMR spectroscopy and X-ray crystallography. We observe a new carboxy-terminal helix following a canonical dsRBD structure. Removal of this helix reduces binding to Rnt1p substrates. The results suggest that this helix allows the Rnt1p dsRBD to bind to short RNA stem-loops by modulating the conformation of helix alpha1, a key RNA-recognition element of the dsRBD.

Selected figure(s)

Figure 4.
Figure 4 Structure of loop 2. The 2F[o] -F[c] electron density map is contoured at 1 . The flexible loop 2 in the NMR structure (Figure 3A) is stabilized in the X-ray structure by intermolecular interactions (indicated in blue sticks).

Figure 6.
Figure 6 (A) RNA-free Rnt1p medium-dsRBD structure in the same orientations used in the surface representations. (B) A region of positive electrostatic potential on the surface of the Rnt1p dsRBD crystal structure (blue patches) coincides with the RNA-binding surface of the protein. (C) Residues that shift upon RNA binding identify the RNA-binding surface of Rnt1p (red-coded residues). (D) Residues located close to the AGGA tetraloop as identified in the spin-labeling experiments (green-coded residues). The tetraloop interaction site is precisely determined by the spin label experiment and coincides with helix 1, loop 1 and the C-terminus of helix 3.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2468-2477) copyright 2004.

Figures were selected by an automated process.