PDBsum entry 2sxl

RNA-binding domain

PDB id: 2sxl

Contents

Protein chain

88 a.a. *

* Residue conservation analysis

PDB id:

2sxl

Name:

RNA-binding domain

Title:

Sex-lethal rbd1, nmr, minimized average structure

Structure:

Sex-lethal protein. Chain: a. Fragment: RNA-binding domain 1 (rbd1), residues 122 - 209. Engineered: yes. Mutation: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Cell_line: bl21. Organ: fruit. Gene: sex-lethal. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

1 models

Authors:

M.Inoue,Y.Muto,H.Sakamoto,T.Kigawa,K.Takio,Y.Shimura,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Inoue et al. (1997). A characteristic arrangement of aromatic amino acid residues in the solution structure of the amino-terminal RNA-binding domain of Drosophila sex-lethal. J Mol Biol, 272, 82-94. PubMed id: 9299339 DOI: 10.1006/jmbi.1997.1213

Date:

16-Jul-97 Release date: 22-Jul-98

Protein chain

P19339  (SXL_DROME) -  Protein sex-lethal from Drosophila melanogaster

Seq: 354 a.a.

Struc: 88 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.1997.1213

J Mol Biol 272:82-94 (1997)

PubMed id: 9299339

A characteristic arrangement of aromatic amino acid residues in the solution structure of the amino-terminal RNA-binding domain of Drosophila sex-lethal.

M.Inoue, Y.Muto, H.Sakamoto, T.Kigawa, K.Takio, Y.Shimura, S.Yokoyama.

ABSTRACT

The Sex-lethal (Sxl) protein from Drosophila melanogaster has two RNA-binding domains (RBDs). As the amino-terminal RBD (RBD1) of the Sxl protein exhibits low sequence homology to the typical RBDs, particularly at the putative functional residues, it was difficult to unambiguously locate the RNP1 and RNP2 motifs. Therefore, in the present study, we defined the amino and carboxy-terminal borders of the first RNA-binding domain (RBD1) of the Sxl protein by limited tryptic digestion. By replacement of Phe166 by Tyr, we constructed a highly soluble mutant, which exhibits the same RNA-binding properties as those of the wild-type. Using this mutant protein, we performed NMR measurements, and elucidated the secondary and tertiary structures of the Sxl RBD1 in solution. The betaalphabetabetaalphabeta folding pattern is conserved in the solution structure of the Sxl RBD1, as in other reported RBD structures. This allowed us to identify both the RNP1 and RNP2 motifs of the Sxl RBD1 unambiguously. Intriguingly, the RNP2 motif of the Sxl RBD1 has an Ile residue at the second position, which is generally occupied by an aromatic amino acid residue in RBDs and has been suggested to be involved in their RNA binding. Furthermore, the loop region between beta2 and beta3 of the Sxl RBD1 has an exceptional cluster of aromatic amino acid residues, in place of the normal basic amino acid cluster. In contrast, the second RBD of Sxl does not exhibit these characteristic features.

Selected figure(s)

Figure 2.
Figure 2. Schematic representation of the Sxl fragments. The numbering corresponds to the full-length Sxl protein. The putative trypsin-cleavable sites are indicated as vertical lines on LRBD1-2. The major cleavage sites are indicated with triangles.

Figure 12.
Figure 12. Amino acid types (%) in the RNP2 (a) and β2/β3 loop-RNP1 (b) regions of 161 RBDs homologous to either RBD1 or RBD2. Amino acid categorization: aliphatic (A, V, L, I, and M), aromatic (F, Y, and W), basic (K and R), acidic (D and E), neutral (S, T, C, N, Q, and H), and small (G and P). Non-consensus amino acid residues of RBD1 are shown in white letters on black disks. The highest percentage for each residue is indicated in bold letters.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 272, 82-94) copyright 1997.

Figures were selected by an automated process.