Sandbox reserved 981: Difference between revisions

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The Prp8 protein has multiple domains: the RNaseH-like, Jab1/MPN, Aar2, and a large domain consisting of type II endonuclease and the large polymerase-like domains [2]. Most of these domains received their names because of significant sequence similarities they have with domains of other proteins.

The two domains of the large domain are connected through a linker. The type II endonuclease domain (residues 1650 – 1810) is made up of 5 β-sheets surrounded by 3 α-helices <ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref> The large polymerase domain (residues 885-1375) is subdivided into the palm, finger, thumb and endonuclease domains<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The palm domain (residues 1048-1182) is similar in sequence to that of bacterial reverse transcriptase, so it is often referred to as the reverse transcriptase domain. The thumb domain (residues 1257-1375), is characterized by an antiparallel β-sheet and three helix bundles <ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>

The two domains of the large domain are connected through a linker. The type II endonuclease domain (residues 1650 – 1810) is made up of 5 β-sheets surrounded by 3 α-helices <ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The large polymerase domain (residues 885-1375) is subdivided into the palm, finger, thumb and endonuclease domains<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The palm domain (residues 1048-1182) is similar in sequence to that of bacterial reverse transcriptase, so it is often referred to as the reverse transcriptase domain<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The thumb domain (residues 1257-1375), is characterized by an antiparallel β-sheet and three helix bundles<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>.

The RNaseH-like (1840-2090) and Jab1/MPN (2150-2396) domains are connected by disordered linkers, and stabilized by the Aar domain, a U5 snRNP assembly factor[2]. The C-terminal tail of Aar domain reaches out from its main body in order to interact with the junction between RNaseH and Jab1/MPN. In a way, it zips together a β-barrel of Jab1/MPN and β-hairpin from RNaseH domain using a parallel β-sheet. Also, through the Aar domain, RNaseH and Jab1/MPN domains are able to interact with the large polymerase domain [1] Once the Prp8 protein is imported into the nucleus the Aar domain is replaced by a Brr2 domain, an integral U5 snRNP component that is responsible for unwinding the U4/U6 snRNP duplex. This exchange may alter the position of the domains with respect to each other [1].

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 The Prp8 protein has multiple domains: the RNaseH-like, Jab1/MPN, Aar2, and a large domain consisting of type II endonuclease and the large polymerase-like domains [2]. Most of these domains received their names because of significant sequence similarities they have with domains of other proteins.
-The two domains of the large domain are connected through a linker. The type II endonuclease domain (residues 1650 – 1810) is made up of 5 β-sheets surrounded by 3 α-helices <ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref> The large polymerase domain (residues 885-1375) is subdivided into the palm, finger, thumb and endonuclease domains<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The palm domain (residues 1048-1182) is similar in sequence to that of bacterial reverse transcriptase, so it is often referred to as the reverse transcriptase domain. The thumb domain (residues 1257-1375), is characterized by an antiparallel β-sheet and three helix bundles <ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>
+The two domains of the large domain are connected through a linker. The type II endonuclease domain (residues 1650 – 1810) is made up of 5 β-sheets surrounded by 3 α-helices <ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The large polymerase domain (residues 885-1375) is subdivided into the palm, finger, thumb and endonuclease domains<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The palm domain (residues 1048-1182) is similar in sequence to that of bacterial reverse transcriptase, so it is often referred to as the reverse transcriptase domain<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>. The thumb domain (residues 1257-1375), is characterized by an antiparallel β-sheet and three helix bundles<ref>Galej, Wojciech P., Andrew J. Newman, Chris Oubridge, and Kiyoshi Nagai. "Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome." Nature 493.7434 (2013): 638-643. Academic Search Complete. Web. 13 Apr. 2015.</ref>.
 The RNaseH-like (1840-2090) and Jab1/MPN (2150-2396) domains are connected by disordered linkers, and stabilized by the Aar domain, a U5 snRNP assembly factor[2]. The C-terminal tail of Aar domain reaches out from its main body in order to interact with the junction between RNaseH and Jab1/MPN. In a way, it zips together a β-barrel of Jab1/MPN and β-hairpin from RNaseH domain using a parallel β-sheet. Also, through the Aar domain, RNaseH and Jab1/MPN domains are able to interact with the large polymerase domain [1] Once the Prp8 protein is imported into the nucleus the Aar domain is replaced by a Brr2 domain, an integral U5 snRNP component that is responsible for unwinding the U4/U6 snRNP duplex. This exchange may alter the position of the domains with respect to each other [1].