User:Wally Novak/Sandbox Whitaker
U5 snRNP
This is a default text for your page Wally Novak/Sandbox Whitaker. Click above on edit this page to modify. Be careful with the < and > signs. 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. ContentsFunctionGeneral OverviewThe 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], however, only Prp8, Snu114, and Brr2 remain in complex with the U5 snRNA while the spliceosome is activated [4]. These proteins are necessary for the remodeling of the spliceosome and may play a role in maintaining catalytic activity at the active center of the spliceosome [4]. 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. U5 snRNAThe U5 snRNA interacts directly with the 5’ exon before the first step of splicing and with the 5’ and 3’ exons following the first step of splicing [5]. These U5–exon interactions are essential for tethering and aligning the exons for ligation during the second step of splicing [5]. Brr2♣Structure load='3hib' size='400' frame='true' align='right' caption='Brr2'/♣ Brr2 is an ATPase required for unwinding U4/U6 base-pairing before the first step of splicing and for unwinding U2/U6 base-pairing after the second step of splicing [6]. These conformational changes catalyzed by Brr2 are essential for the progression of the spliceosome cycle. Prp8♣Structure load='3e66' size='400' frame='true' align='right' caption='Prp8'/♣ Prp8 is believed to be the master regulator of the splicing cycle by regulating the spliceosomal DExD/H-box RNA dependent ATPases, specifically Brr2 [7]. Consistent with this regulatory role it has been shown that the C-terminus of Prp8 activates Brr2 helicase function and inhibits Brr20 s U4/U6-dependent ATPase activity in vitro [8]. Structural studies of the Prp8 C-terminus have identified an RNase H-like domain within Prp8 and it has been proposed that this RNase H-domain may form the active site of the spliceosome [4]. Snu114Snu114 is the only GTPase associated with the spliceosome and it has multiple contacts with Prp8 as well as U5 snRNA and Brr2 but its role in spliceosome function is not yet well-defined. [4]. Structural HighlightsFour sequences are highly conserved within the U5 snRNA and it is believed that these sequences play a primary role in the proteins binding capabilities. The four regions are the Stem-loop 1, Internal loop 1, Stem-closing internal loop 1, and Sm protein binding site [9]. Stem-loop 1 spans nucleotides 84 to 110 (S. cerevisiae) and consists of a highly conserved 11 nucleotide block with complementary sequences on either side [9]. These complementary sequences enable local base-pairing to form the stem of the loop [9]. The U5 snRNA stem-loop 1 is necessary for tethering and aligning exons for ligation during the second step of splicing. The U5 snRNA stem 1 and internal loop 1 (IL1) are also highly conserved between yeast and humans, both in size and in structure [9]. The U5 snRNA IL1 was found to be the most important region for the association of Prp8, Snu114 and Brr2 with the U5 snRNA [10]. Genetic analysis also identified the U5 snRNA IL1 as being important for Brr2 function [9]. Overall, the U5 snRNA IL1 appears to be critical for the association of the U5 snRNP proteins Prp8, Snu114 and Brr2 with the U5 snRNA to form the U5 snRNP [9]. Brr2 Structural Highlights♣Structure load='3hib' size='400' frame='true' align='right' caption='Brr2'/♣ Recent structural analysis of Brr2 has revealed that part of the Sec63 like cassettes of the Brr2 helicase domains resemble the DNA helicase Hel308, hinting at an RNA unwinding action of Brr2 similar to that of the DNA unwinding by helicase Hel308 [4]. The activity of Brr2 is regulated by the guanine nucleotide state of Snu114 [4]. Prp8 Structural Highlights♣Structure load='3e66' size='400' frame='true' align='right' caption='Prp8'/♣ Prp8 is a 280 kDa protein component of the U5 snRNP and is also part of the U4/U6.U5 tri-snRNP [4]. Prp8 forms a complex with the assembly factor Aar2 and Snu114 without the U5 snRNA in the cytoplasm, however, Aar2 is replaced with Brr2 in the nucleus [4]. Protein InteractionsThe U5 snRNP is one of the five subunits which come together to form the spliceosome and is, therefore, a key protein for eukaryotic mRNA processing. U5 snRNP is a complex which consists of U5 snRNA, Brr2, Snu114, and Prp8. Prp8 also interacts with other proteins of the spliceosome, the snRNAs and extensively with the pre-mRNA [4]. It has been shown that Prp8 crosslinks directly to the pre-mRNA 5’ splice site, the branch site, and the 3’ splice site as well as U5 and U6 snRNAs localizing it to the heart of the spliceosome [4]. In yeast, Prp8 makes extensive direct contacts with the U5 snRNA including the highly conserved U5 loop 1 and IL1 [4]. Following successful assembly of the U5 snRNP, a tri-snRNP consisting of U4, U5 and U6 is formed which is then incorporated into the active spliceosome. ♣Structure load='5gan' size='400' frame='true' align='right' caption='U4/U6.U5 tri-snRNP'/♣ This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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