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. Author manuscript; available in PMC: 2015 Dec 29.
Published in final edited form as: Structure. 2003 Jul;11(7):775–789. doi: 10.1016/s0969-2126(03)00127-8

Figure 1. Sequence Alignments of Proteins Containing mbt Repeats.

Figure 1

(A) Multiple sequence alignment of the N-terminal arms of 3mbt repeats from h-l(3)mbt and related family members using CLUSTALW. Secondary structure elements defined by crystal structure of 3mbt repeats are shown above the alignment. α helices, wavy magenta lines; 310 helices, wavy orange lines; β strands, arrows; loops, straight lines. The helices are numbered consecutively from the N terminus. Helical structure αA, featured with a dashed line, only exists in the second and third repeats, while αD exists only in the first repeat. The loop with a dashed line only exists in the second and third repeats. Conserved hydrophobic, aromatic, positively charged, negatively charged, and polar residues are marked with yellow, green, red, blue, and orange. Accession numbers (SWISS-PORT, Genbank, or PIR) are as follows: H. sapiens (brain) l(3)mbt, Q9Y468; H. sapiens (brain) KIAA1798, Q96JM7; H. sapiens (testis), Q9Y4Q9; D. melanogaster, Q9VB52; M. fascicularis, Q95LL9; C. elegans (R06c7.7), Q21769; C. elegans (Y48GIA.6), Q9N3Q7; D. melanogaster SCM, Q9VHA0.

(B) Multiple sequence alignment of the β subunit core of three mbt repeats from h-l(3)mbt and related family members, with defined secondary structure elements as indicated in (A). The β2 region featured with a dashed line only exists in first repeat, while β6 only exists in the first and second repeats. The loop featured with a dashed line only exists in third repeat. Structure-based sequence alignment of the Tudor domain with the mbt β subunit core is shown at the bottom. Mutated residues in SCM and residues of the Tudor domain involved in binding Sm proteins and the GAR domain are boxed. Conserved residues that form the putative drug/peptide binding pocket are highlighted with asterisks, those involved in hydrogen bond formation (Figure 3D) are indicated by closed circles, and those involved in the hydrophobic pentad motif (Figure 3E) are indicated by open circles. The accession number for H. sapiens SMN1-Tudor is Q16637.