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>. Prp8 also contains an <scene name='Prp8/Rnase_h_domain/1'>RNase H-like domain</scene> towards its C-terminal end (residues 1836 - 2092) <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. The central region of the RNase H-like domain consists of a mixed alpha/beta fold, which resembles the overall shape of a mitten <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. Following this analogy, the central 6 stranded beta sheets (yellow) and alpha helices (red) are the palm with a beta hairpin as the thumb and alpha helices as fingers which is all connected through regions of unstructured protein chain (dark blue). The groove created by the mitten like structure is lined with positive surface potential but also lacks key residues for RNase activity which is perfect for binding RNA, and has a very similar structure to the reverse transcriptase-like domain mentioned above <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. The RNase domain possesses conserved charged residues at D1853/1781, D1854/1782, and Q1907/1835 (yeast/human numbering) which are thought to mediate interactions with the negatively charged backbone of an RNA molecule <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. Finally, the last domain on the C-terminal end of Prp8 is a <scene name='Prp8/Jab1_mpb_domain/1'>metalloprotease/Jab1-like domain</scene> which extends through residues 2112 - 2413. Its overall structure consists of an oval shaped fold containing 12 beta strands (yellow), four alpha helices (red), and four 310 helices (red), which is all interconnected by an unstructured regions (dark blue) <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. They form a mixed beta-barrel made up of seven strands surrounded by the remaining alpha and beta elements <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. This domain also contains unique Prp8 residue substitutions; the commonplace metalloenzyme motif is replaced by Q-X-H-X-Q-X-S-E which allows the domain to coordinate protein-protein contacts instead of a metal ion <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</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 <scene name='Prp8/Rnase_h_domain/1'>RNase H-like domain</scene> towards its C-terminal end (residues 1836 - 2092) <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. The central region of the RNase H-like domain consists of a mixed alpha/beta fold, which resembles the overall shape of a mitten <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. Following this analogy, the central 6 stranded beta sheets (yellow) and alpha helices (red) are the palm with a beta hairpin as the thumb and alpha helices as fingers which is all connected through regions of unstructured protein chain (dark blue). The groove created by the mitten like structure is lined with positive surface potential but also lacks key residues for RNase activity which is perfect for binding RNA, and has a very similar structure to the reverse transcriptase-like domain mentioned above <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. The RNase domain possesses <scene name='Prp8/Rnase_h_domain_catalytic_resid/1'>conserved charged residues</scene> (in pink) at D1853/1781, D1854/1782, and Q1907/1835 (yeast/human numbering) which are thought to mediate interactions with the negatively charged backbone of an RNA molecule <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. Finally, the last domain on the C-terminal end of Prp8 is a <scene name='Prp8/Jab1_mpb_domain/1'>metalloprotease/Jab1-like domain</scene> which extends through residues 2112 - 2413. Its overall structure consists of an oval shaped fold containing 12 beta strands (yellow), four alpha helices (red), and four 310 helices (red), which is all interconnected by an unstructured regions (dark blue) <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. They form a mixed beta-barrel made up of seven strands surrounded by the remaining alpha and beta elements <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. This domain also contains unique Prp8 residue substitutions; the commonplace metalloenzyme motif is replaced by Q-X-H-X-Q-X-S-E which allows the domain to coordinate protein-protein contacts instead of a metal ion <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>.

*Note - Thus far only C-terminal regions of Prp8 have been crystallized which is why only one PDB out of the half a dozen available is represented on this page.

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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>. Prp8 also contains an <scene name='Prp8/Rnase_h_domain/1'>RNase H-like domain</scene> towards its C-terminal end (residues 1836 - 2092) <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. The central region of the RNase H-like domain consists of a mixed alpha/beta fold, which resembles the overall shape of a mitten <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. Following this analogy, the central 6 stranded beta sheets (yellow) and alpha helices (red) are the palm with a beta hairpin as the thumb and alpha helices as fingers which is all connected through regions of unstructured protein chain (dark blue). The groove created by the mitten like structure is lined with positive surface potential but also lacks key residues for RNase activity which is perfect for binding RNA, and has a very similar structure to the reverse transcriptase-like domain mentioned above <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. The RNase domain possesses conserved charged residues at D1853/1781, D1854/1782, and Q1907/1835 (yeast/human numbering) which are thought to mediate interactions with the negatively charged backbone of an RNA molecule <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. Finally, the last domain on the C-terminal end of Prp8 is a <scene name='Prp8/Jab1_mpb_domain/1'>metalloprotease/Jab1-like domain</scene> which extends through residues 2112 - 2413. Its overall structure consists of an oval shaped fold containing 12 beta strands (yellow), four alpha helices (red), and four 310 helices (red), which is all interconnected by an unstructured regions (dark blue) <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. They form a mixed beta-barrel made up of seven strands surrounded by the remaining alpha and beta elements <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. This domain also contains unique Prp8 residue substitutions; the commonplace metalloenzyme motif is replaced by Q-X-H-X-Q-X-S-E which allows the domain to coordinate protein-protein contacts instead of a metal ion <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</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 <scene name='Prp8/Rnase_h_domain/1'>RNase H-like domain</scene> towards its C-terminal end (residues 1836 - 2092) <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. The central region of the RNase H-like domain consists of a mixed alpha/beta fold, which resembles the overall shape of a mitten <ref name='Mechanism for aar2p function as a U5 snRNP assembly factor'>PMID:21764848</ref>. Following this analogy, the central 6 stranded beta sheets (yellow) and alpha helices (red) are the palm with a beta hairpin as the thumb and alpha helices as fingers which is all connected through regions of unstructured protein chain (dark blue). The groove created by the mitten like structure is lined with positive surface potential but also lacks key residues for RNase activity which is perfect for binding RNA, and has a very similar structure to the reverse transcriptase-like domain mentioned above <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. The RNase domain possesses <scene name='Prp8/Rnase_h_domain_catalytic_resid/1'>conserved charged residues</scene> (in pink) at D1853/1781, D1854/1782, and Q1907/1835 (yeast/human numbering) which are thought to mediate interactions with the negatively charged backbone of an RNA molecule <ref name='Structure and function of an RNase H domain at the heart of the spliceosome'>DOI:10.1038/emboj.2008.209</ref>. Finally, the last domain on the C-terminal end of Prp8 is a <scene name='Prp8/Jab1_mpb_domain/1'>metalloprotease/Jab1-like domain</scene> which extends through residues 2112 - 2413. Its overall structure consists of an oval shaped fold containing 12 beta strands (yellow), four alpha helices (red), and four 310 helices (red), which is all interconnected by an unstructured regions (dark blue) <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. They form a mixed beta-barrel made up of seven strands surrounded by the remaining alpha and beta elements <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>. This domain also contains unique Prp8 residue substitutions; the commonplace metalloenzyme motif is replaced by Q-X-H-X-Q-X-S-E which allows the domain to coordinate protein-protein contacts instead of a metal ion <ref name='Structure of a Multipartite Protein-Protein'>DOI:10.1016/j.molcel.2007.01.023</ref>.
 *Note - Thus far only C-terminal regions of Prp8 have been crystallized which is why only one PDB out of the half a dozen available is represented on this page.