User:Wally Novak/Sandbox Whitaker

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function

General Overview

The U5 snRNP consists of several proteins which are highly conserved from yeast to humans. These proteins consist of Prp8, Snu114, Brr2, Prp28, Snu40/52K, and Dib1 ^[3] (Stevens et al., 2001), however, only Prp8, Snu114, and Brr2 remain in complex with the U5 snRNA while the spliceosome is activated (Fabrizio et al., 2009). These proteins are essential for the remodeling of the spliceosome and may play a role in maintaining catalytic activity at the active center of the spliceosome. Assembly of the U5 snRNP is followed by the formation of the U4/U6.U5 tri-snRNP which is the last remaining complex necessary to form the complete spliceosome and is therefore vital for its function.

Structural Highlights

By deletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (iii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site Stem-loop 1: The fungal sequences spanning nt 84 to 110 (S. cerevisiae numbering will be used unless otherwise noted) can be unambiguously aligned with the existing U5 sequences. The central, highly conserved block of 11 nt is flanked, in each case, by two complementary sequences; this region can thus form a stem-loop structure. Internal loop 1: The level of conservation is highest in the 3' half of ILl, where the sequence is invariably CCG in the fungi. In contrast, the fungal and nonfungal sequences that define the 5' halves of ILl are only moderately conserved in comparison to Li and the 3' halves of ILl. Nevertheless, the 5' halves of ILl in all species of U5 include an invariant CG dinucleotide at positions 79 and 80. Sm protein binding site: Putative Sm protein binding sites could be identified in all U5 sequences, thus highlighting the importance of this sequence motif in snRNP assembly (14, 21). The consensus sequence of the fungal U5 Sm sites is R(U)5NGgaa.

Protein Interactions

The U5 snRNA combines with three other structures to form the U5 snRNP which combines with U4 and U6 to form tri-complex which then becomes incorporated into the spliceosome.

3D Structures

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