PDBsum entry: 2wac

Splicing

PDB id: 2wac

Contents

Protein chains

217 a.a. *

Waters ×303

* Residue conservation analysis

PDB id:

2wac

Name:

Splicing

Title:

Extended tudor domain of drosophila melanogaster tudor-sn ( p100)

Structure:

Cg7008-pa. Chain: a, b. Fragment: tsn domain, tudor and sn5, residues 700-916. Synonym: ld20211p, tudor-sn. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.10Å R-factor: 0.229 R-free: 0.269

Authors:

A.Friberg,L.Corsini,M.Sattler

Key ref:

A.Friberg et al. (2009). Structure and Ligand Binding of the Extended Tudor Domain of D. melanogaster Tudor-SN. J Mol Biol, 387, 921-934. PubMed id: 19232356 DOI: 10.1016/j.jmb.2009.02.018

Date:

04-Feb-09 Release date: 03-Mar-09

Protein chains

Q9W0S7  (Q9W0S7_DROME) -  LD20211p

Seq: 926 a.a.

Struc: 217 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1016/j.jmb.2009.02.018

J Mol Biol 387:921-934 (2009)

PubMed id: 19232356

Structure and Ligand Binding of the Extended Tudor Domain of D. melanogaster Tudor-SN.

A.Friberg, L.Corsini, A.Mourão, M.Sattler.

ABSTRACT

The Tudor-SN protein (p100, SND1) has been implicated in a variety of cellular processes, such as transcription, processing of edited double-stranded RNA, and splicing regulation. Molecular details of these functions are not yet understood. Tudor domains have previously been shown to bind methylated ligands, such as methylated lysines and arginines. It has been suggested that the role of Tudor-SN in splicing may involve binding to such methylated ligands or to the methylated 5' cap of spliceosomal snRNAs. Here, we report the crystal structure of the extended Tudor domain of Tudor-SN from Drosophila melanogaster to a resolution of 2.1 A. NMR secondary chemical shifts, relaxation data, and residual dipolar couplings indicate that the solution and crystal structures are similar. Binding of various ligands was investigated by NMR. Binding sites and affinities were characterized by chemical shift perturbations. We show that the aromatic cage of the Tudor domain specifically binds a peptide containing symmetrically dimethylated arginines (sDMA) with micromolar affinity, while the same peptide comprising nonmethylated arginines does not show significant chemical shift perturbations. Tudor-SN preferentially recognizes sDMA over asymmetrically dimethylated arginine (aDMA). In contrast, two 5' cap analogues with different methylation patterns, as well as mono-, di-, and trimethyllysines, show no binding. Our data demonstrate that the Tudor domain of Tudor-SN specifically recognizes sDMA-containing ligands. The aromatic cage of Tudor-SN is very similar to the one in the Tudor domain of the survival of motor neuron protein, which also recognizes sDMA peptides, indicating a conserved binding motif for this methylation mark. Recognition of sDMA in the C-terminal tails of spliceosomal Sm proteins suggests how Tudor-SN may interact with small nuclear ribonucleoprotein particles during the regulation of splicing.

Selected figure(s)

Figure 3.
Fig. 3. Ligands used for NMR titrations. Spheres symbolize methylation modifications.

Figure 4.
Fig. 4. NMR titration experiments with methylated ligands. (a) Titration of methylated and nonmethylated peptides, 1 and 2, to the TSN domain. Left: overlay of ^1H,^15N-HSQC spectra of TSN, 0.2 mM, with different amounts of ligands. Residues in the aromatic cage are labeled. Reference spectrum is in black. Red, green, and blue spectra correspond to a protein:ligand ratio of 1:1, 1:3, and 1:12, respectively, of ligand 1. The magenta spectrum corresponds to a protein:ligand ratio of 1:12 of ligand 2. Middle column: Each of the resonances assigned to the aromatic cage residues are zoomed in. The perturbation at a protein:ligand ratio of 1:12 is indicated by arrows, black for 1 and magenta for 2. If no shift is observed, this is marked by a cross. Right column: The CSP, calculated as View the MathML source- [0?wchp=dGLbVlz-zSkzk] , for each residue in the aromatic cage plotted against ligand concentration. Black and magenta curves are fitted to binding data of 1 and 2, respectively. Both titrations were performed at 900 MHz. (b) Titration of methylated arginines, 3 and 4, to the TSN domain. Left: overlay of ^1H,^15N-HSQC spectra of TSN, 0.1 mM, with different amounts of ligands. Residues in the aromatic cage are labeled. Reference spectrum is in black. Red, green, and blue spectra correspond to a protein:ligand ratio of 1:1, 1:3, and 1:12, respectively, of ligand 3. The magenta spectrum corresponds to a protein:ligand ratio of 1:12 of ligand 4. Middle column: Each of the resonances assigned to the aromatic cage residues are zoomed in. The perturbation at a protein:ligand ratio of 1:12, is indicated by arrows, black for 3 and magenta for 4. Right column: The CSP for each residue in the aromatic cage plotted against ligand concentration. Black and magenta curves are fitted to binding data of 3 and 4, respectively. Titrations of 3 and 4 were performed at 900 and 600 MHz, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 387, 921-934) copyright 2009.

Figures were selected by an automated process.