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. 2001 Jan;21(2):367–379. doi: 10.1128/MCB.21.2.367-379.2001

FIG. 1.

FIG. 1

Modeling of the proposed RRM-1 in the highly conserved, N-terminal region of La protein. Alignment of 13 La sequences (beginning with H. sapiens La and ending with A. thaliana La) available in the protein database was performed by ClustalW. Only the sequences that appeared to be full-length La proteins were included in the alignment, and of these, several have been characterized biochemically as authentic RNA-binding proteins (see text). The sequences aligned here correspond to residues 20 to 92 of hLa (numbered above only for H. sapiens La). Invariant residues are reverse shaded in black columns; conserved residues are in gray columns. The top line reflects the output of the Quadratic logistic secondary structure prediction with homologous sequences (QL w/hom) program (39); H, α helix; E, extended β strand; C, non-α-helix, non-β-strand. Below this is indicated the RRM topology β1-loop 1-α1-loop 2-β-loop 3-β3-loop 4-α2-loop 5-β4 that is used for aligning the RRM core hydrophobic residues according to the work of Birney et al. (14). Below the alignment set is the La consensus (“La cons”) line, in which invariant residues are shown in uppercase; Φ = Y or F; other conserved residues are represented according to the designations of Birney; U = uncharged (L, I, V, A, G, F, W, Y, C, or M); Z = U + S, T. Candidate residues that may be involved in uridylate recognition are underlined (see text). The positions of the putative RNP-2 (in β1) and RNP-1 (in β3) motifs of RRM-1 (La RNPs-2&1) are indicated by horizontal lines. The “La RRM CORE” is shown for comparison to the conserved “RRM CORE” structure according to reference 14. The “CORE con” line shows the RRM core with spacing according to reference 14. The sequences and accession numbers are as follows: H. sapiens (Hs), P05455; B. taurus (Bt), P10881; R. norvegicus (Rn), P38656; M. musculus (Mm), P32067; X. laevis La-B (Xb), P28049; X. laevis La-A (Xa), P28048; A. albopictus (Aa), Q26457; Caenorhabditis elegans (Ce), T30953; D. melanogaster (Dm), P40796; T. brucei (Tb), AAF34598.1; S. pombe (Sp), AAB82145.1; S. cerevisiae (Sc), P33399; A. thaliana (At), AAF09063.