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PDBsum entry 2sxl

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RNA-binding domain PDB id
2sxl
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19339  (SXL_DROME) -  Protein sex-lethal
Seq:
Struc:
354 a.a.
88 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     3 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16362043 F.Vitali, A.Henning, F.C.Oberstrass, Y.Hargous, S.D.Auweter, M.Erat, and F.H.Allain (2006).
Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling.
  EMBO J, 25, 150-162.
PDB code: 2evz
12809490 G.C.Pérez-Alvarado, M.Martínez-Yamout, M.M.Allen, R.Grosschedl, H.J.Dyson, and P.E.Wright (2003).
Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.
  Biochemistry, 42, 7348-7357.
PDB code: 1no8
12554879 H.Banerjee, A.Rahn, W.Davis, and R.Singh (2003).
Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding.
  RNA, 9, 88-99.  
11100898 G.Loughran, K.Pinter, P.C.Newell, and J.D.Gross (2000).
Identification of STKA-dependent genes in Dictyostelium discoideum.
  Differentiation, 66, 71-80.  
10734193 M.Inoue, Y.Muto, H.Sakamoto, and S.Yokoyama (2000).
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C.
  Nucleic Acids Res, 28, 1743-1750.
PDB codes: 1d8z 1d9a
10585411 N.J.Richter, G.W.Rogers, J.O.Hensold, and W.C.Merrick (1999).
Further biochemical and kinetic characterization of human eukaryotic initiation factor 4H.
  J Biol Chem, 274, 35415-35424.  
10220389 S.M.Crowder, R.Kanaar, D.C.Rio, and T.Alber (1999).
Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.
  Proc Natl Acad Sci U S A, 96, 4892-4897.
PDB code: 3sxl
10102992 S.W.Chi, Y.Muto, M.Inoue, I.Kim, H.Sakamoto, Y.Shimura, S.Yokoyama, B.S.Choi, and H.Kim (1999).
Chemical shift perturbation studies of the interactions of the second RNA-binding domain of the Drosophila sex-lethal protein with the transformer pre-mRNA polyuridine tract and 3' splice-site sequences.
  Eur J Biochem, 260, 649-660.  
10449418 T.Ito, Y.Muto, M.R.Green, and S.Yokoyama (1999).
Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
  EMBO J, 18, 4523-4534.
PDB codes: 1u2f 2u2f
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.