Prp8: Difference between revisions

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The proline rich region is present at the N-terminus of Prp8, approximately running from residues 5 - 78 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. This proline tract is found at the N-terminus of all fungal Prp8 sequences, and two rice sequences but is absent from most other organisms <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The proline rich region usually adopts an extended helical structure with three residues per turn <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The [http://en.wikipedia.org/wiki/Nuclear_localization_sequence nuclear localization signal] is also at the N-terminus of the protein, extending through amino acid residues 81 - 120, and can be located in the first 500 amino acids of the majority of organisms' Prp8 sequences <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The nuclear localization signal contains two clusters of positively charged amino acid residues which are separated by a variable region of 10 - 12 amino acids, and organisms lacking this classical signal motif usually possess an alternative within the N-terminus of their Prp8 <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The bromodomain is the last major region that is present at the N-terminus of Prp8, running from residues 200 - 315 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. It possesses low sequence identity (<14%) with commonplace bromodomains, but appears to contain no insertions or deletions despite its low identity with other sequences <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. The domain consists of four alpha-helices and two loops which generally interact with and recognize lysine residues <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. The recognition is facilitated by several highly conserved amino acids that stabilize the helix bundle <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>.

The reverse transcriptase-like domain is located approximately halfway through Prp8 and extends through residues 950 - 1220 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. This domain is only reverse transcriptase-like because it does contain the conventional core set of alpha-helices and beta-strands that are a general characteristic of RT domains, but lacks key motifs that would normally confer its catalytic activity <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. However, the Prp8 RT-like domain still possesses the potential to bind RNA <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>.

The reverse transcriptase-like domain is located approximately halfway through Prp8 and extends through residues 950 - 1220 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. This domain is only reverse transcriptase-like because it does contain the conventional core set of alpha-helices and beta-strands that are a general characteristic of RT domains, but lacks key motifs that would normally confer its catalytic activity <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. However, the Prp8 RT-like domain still possesses the potential to bind RNA <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. Prp8 also contains an RNase H-like domain towards its C-terminal end (residues 1836 - 2092) <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>

=Function of Prp8=

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 The proline rich region is present at the N-terminus of Prp8, approximately running from residues 5 - 78 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. This proline tract is found at the N-terminus of all fungal Prp8 sequences, and two rice sequences but is absent from most other organisms <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The proline rich region usually adopts an extended helical structure with three residues per turn <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The [http://en.wikipedia.org/wiki/Nuclear_localization_sequence nuclear localization signal] is also at the N-terminus of the protein, extending through amino acid residues  81 - 120, and can be located in the first 500 amino acids of the majority of organisms' Prp8 sequences <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The nuclear localization signal contains two clusters of positively charged amino acid residues which are separated by a variable region of 10 - 12 amino acids, and organisms lacking this classical signal motif usually possess an alternative within the N-terminus of their Prp8 <ref name='Prp8: At the heart of the spliceosome'>DOI:10.1261/rna.2220705</ref>. The bromodomain is the last major region that is present at the N-terminus of Prp8, running from residues 200 - 315 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. It possesses low sequence identity (<14%) with commonplace bromodomains, but appears to contain no insertions or deletions despite its low identity with other sequences <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. The domain consists of four alpha-helices and two loops which generally interact with and recognize lysine residues <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. The recognition is facilitated by several highly conserved amino acids that stabilize the helix bundle <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>.
-The reverse transcriptase-like domain is located approximately halfway through Prp8 and extends through residues 950 - 1220 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. This domain is only reverse transcriptase-like because it does contain the conventional core set of alpha-helices and beta-strands that are a general characteristic of RT domains, but lacks key motifs that would normally confer its catalytic activity <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. However, the Prp8 RT-like domain still possesses the potential to bind RNA <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>.
+The reverse transcriptase-like domain is located approximately halfway through Prp8 and extends through residues 950 - 1220 <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. This domain is only reverse transcriptase-like because it does contain the conventional core set of alpha-helices and beta-strands that are a general characteristic of RT domains, but lacks key motifs that would normally confer its catalytic activity <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. However, the Prp8 RT-like domain still possesses the potential to bind RNA <ref name='Prp8, the pivotal protein of the spliceosomal catalytic center evolved from a retroelement-encoded reverse transcriptase'>DOI:10.1261/rna.2396011</ref>. Prp8 also contains an RNase H-like domain towards its C-terminal end (residues 1836 - 2092) <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>
 =Function of Prp8=