Prp24: Difference between revisions

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===Structural Models===

A recent study <ref name="Bae"/> examined the structure of <scene name='Sandbox_Reserved_340/2ghp/16'>the N-terminal domain and first three RRMs</scene>of Prp24 by X-ray crystallography. The resultant structure showed Prp24 as an <scene name='Sandbox_Reserved_340/2ghp/5'>octameric protein</scene>, consisting of eight chains arranged in two nearly symmetrical tetramers<ref name="Bae"/>. This was the first suggested that Prp24 functioned as an multimer, so it is unclear what the significance of this result is <ref name="Bae"/>. Their crystal structure also showed extensive interactions between both <scene name='Sandbox_Reserved_340/2ghp/21'>RRM 1 and 2</scene> and <scene name='Sandbox_Reserved_340/2ghp/22'>RRM 2 and 3</scene>, and NMR analysis of protein fragments containing either RRMs 1 and 2 or RRMs 2 and 3 showed that these interactions existed in solution as well<ref name="Bae"/>. Interestingly, these interactions seemed to block the proposed U6 binding sites of RRM 1 and 2; NMR analysis of the RRM 1 and 2 protein fragment with an RNA oligomer containing the U6 sequences thought to bind the RRMs showed a largely canonical interaction of the RNA with the RRMs, suggesting that Prp24 may undergo conformational changes in the binding of U6<ref name="Bae"/>.

A recent study <ref name="Bae"/> examined the structure of <scene name='Sandbox_Reserved_340/2ghp/16'>the N-terminal domain and first three RRMs</scene>of Prp24 by X-ray crystallography. The resultant structure showed Prp24 as an <scene name='Sandbox_Reserved_340/2ghp/23'>octameric protein</scene>, consisting of eight chains arranged in two nearly symmetrical tetramers<ref name="Bae"/>. This was the first suggested that Prp24 functioned as an multimer, so it is unclear what the significance of this result is <ref name="Bae"/>. Their crystal structure also showed extensive interactions between both <scene name='Sandbox_Reserved_340/2ghp/21'>RRM 1 and 2</scene> and <scene name='Sandbox_Reserved_340/2ghp/22'>RRM 2 and 3</scene>, and NMR analysis of protein fragments containing either RRMs 1 and 2 or RRMs 2 and 3 showed that these interactions existed in solution as well<ref name="Bae"/>. Interestingly, these interactions seemed to block the proposed U6 binding sites of RRM 1 and 2; NMR analysis of the RRM 1 and 2 protein fragment with an RNA oligomer containing the U6 sequences thought to bind the RRMs showed a largely canonical interaction of the RNA with the RRMs, suggesting that Prp24 may undergo conformational changes in the binding of U6<ref name="Bae"/>.

== Functional Interactions ==

~~<Structure load='2ghp' size='300' frame='true' align='right' caption='' scene='Sandbox_Reserved_340/2ghp/3'/>~~

Prp24 is part of the normal U6 snRNP, along with seven Lsm proteins <ref name="Brow review"/>. After interaction with the U4 snRNP to form the U4/U6 di-snRNP, Prp24 departs from the di-snRNP before the addition of U5 to form the tri-snRNP U4/U6.U5 <ref name="Brow review"/>. Through many studies, it has been shown that Prp24 interacts extensively with specific sites on U6, as well with the Lsm protein ring on the 3' terminal end of the U6 snRNA.

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The interactions of Prp24 with U6 and U4/U6 are very important in proper spliceosome assembly, as evidenced by mutations in Prp24 that suppress mutations in U6 or U4. Mutations in RRM 2 and RRM 3 suppress the effects of mutations in the 3' stem of U6, in a region termed the telestem <ref name="Vidaver"/>. A later study showed that RRM 1 binds with high affinity to U6 and is important in interactions with mutations in the 3' region of U6 <ref name="Kwan"/>. Mutations in two RNP consensus domains of Prp24 suppress the effects of mutations in U4 in the stem II region of U4/U6 <ref name="Shannon"/>. Truncation and deletion of internal segments of U6 showed that the central region of U6 is the most important region for interaction with Prp24 and that RRM 1 and RRM 2 are the likely portions of Prp24 that interact with U6 in this region <ref name="Kwan"/>. Deletion of conserved residues in the C-terminal domain of Prp24 caused temperature sensitive growth and reduced levels of U4/U6, suggesting that this region too, containing the fourth RRM, is important for interactions in assembly of the spliceosome <ref name="Rader"/>.

NMR analysis of fragments of U6 sequence and regions of Prp24 have further defined and supported the interactions of the protein with U6 snRNA. Analysis of an RNA oligonucleotide containing sequences identical to nucleotides 41-46 and 83-88 of U6 (the regions proposed to bind to Prp24) with a truncated protein containing RRMs 1 and 2 of Prp24 showed that these RRMs interacted sequence specifically with these nucleotides <ref name="Bae"/>. Another NMR study identified sequence specific interaction of <scene name='Sandbox_Reserved_340/2kh9/3'>RRM 2 with RNA</scene>, and it was determined from this that most likely region of U6 for interaction was the AGAGAU sequence of nucleotides 49-54, within the region of previously predicted interaction <ref name="Martin">PMID:20181740</ref>. From this, it was predicted that RRM 1 would interact with the GAUCAG sequence of nucleotides 55-60 <ref name="Martin"/>.

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@@ Line 38: / Line 38: @@
 ===Structural Models===
-A recent study <ref name="Bae"/> examined the structure of <scene name='Sandbox_Reserved_340/2ghp/16'>the N-terminal domain and first three RRMs</scene>of Prp24 by X-ray crystallography.  The resultant structure showed Prp24 as an <scene name='Sandbox_Reserved_340/2ghp/5'>octameric protein</scene>, consisting of eight chains arranged in two nearly symmetrical tetramers<ref name="Bae"/>.  This was the first suggested that Prp24 functioned as an multimer, so it is unclear what the significance of this result is <ref name="Bae"/>.  Their crystal structure also showed extensive interactions between both <scene name='Sandbox_Reserved_340/2ghp/21'>RRM 1 and 2</scene> and <scene name='Sandbox_Reserved_340/2ghp/22'>RRM 2 and 3</scene>, and NMR analysis of protein fragments containing either RRMs 1 and 2 or RRMs 2 and 3 showed that these interactions existed in solution as well<ref name="Bae"/>.  Interestingly, these interactions seemed to block the proposed U6 binding sites of RRM 1 and 2; NMR analysis of the RRM 1 and 2 protein fragment with an RNA oligomer containing the U6 sequences thought to bind the RRMs showed a largely canonical interaction of the RNA with the RRMs, suggesting that Prp24 may undergo conformational changes in the binding of U6<ref name="Bae"/>.
+A recent study <ref name="Bae"/> examined the structure of <scene name='Sandbox_Reserved_340/2ghp/16'>the N-terminal domain and first three RRMs</scene>of Prp24 by X-ray crystallography.  The resultant structure showed Prp24 as an <scene name='Sandbox_Reserved_340/2ghp/23'>octameric protein</scene>, consisting of eight chains arranged in two nearly symmetrical tetramers<ref name="Bae"/>.  This was the first suggested that Prp24 functioned as an multimer, so it is unclear what the significance of this result is <ref name="Bae"/>.  Their crystal structure also showed extensive interactions between both <scene name='Sandbox_Reserved_340/2ghp/21'>RRM 1 and 2</scene> and <scene name='Sandbox_Reserved_340/2ghp/22'>RRM 2 and 3</scene>, and NMR analysis of protein fragments containing either RRMs 1 and 2 or RRMs 2 and 3 showed that these interactions existed in solution as well<ref name="Bae"/>.  Interestingly, these interactions seemed to block the proposed U6 binding sites of RRM 1 and 2; NMR analysis of the RRM 1 and 2 protein fragment with an RNA oligomer containing the U6 sequences thought to bind the RRMs showed a largely canonical interaction of the RNA with the RRMs, suggesting that Prp24 may undergo conformational changes in the binding of U6<ref name="Bae"/>.
 == Functional Interactions ==
-<Structure load='2ghp' size='300' frame='true' align='right' caption='' scene='Sandbox_Reserved_340/2ghp/3'/>
 Prp24 is part of the normal U6 snRNP, along with seven Lsm proteins <ref name="Brow review"/>.  After interaction with the U4 snRNP to form the U4/U6 di-snRNP, Prp24 departs from the di-snRNP before the addition of U5 to form the tri-snRNP U4/U6.U5 <ref name="Brow review"/>.  Through many studies, it has been shown that Prp24 interacts extensively with specific sites on U6, as well with the Lsm protein ring on the 3' terminal end of the U6 snRNA.
@@ Line 55: / Line 53: @@
 The interactions of Prp24 with U6 and U4/U6 are very important in proper spliceosome assembly, as evidenced by mutations in Prp24 that suppress mutations in U6 or U4.  Mutations in RRM 2 and RRM 3 suppress the effects of mutations in the 3' stem of U6, in a region termed the telestem <ref name="Vidaver"/>.  A later study showed that RRM 1 binds with high affinity to U6 and is important in interactions with mutations in the 3' region of U6 <ref name="Kwan"/>.  Mutations in two RNP consensus domains of Prp24 suppress the effects of mutations in U4 in the stem II region of U4/U6 <ref name="Shannon"/>.  Truncation and deletion of internal segments of U6 showed that the central region of U6 is the most important region for interaction with Prp24 and that RRM 1 and RRM 2 are the likely portions of Prp24 that interact with U6 in this region <ref name="Kwan"/>.  Deletion of conserved residues in the C-terminal domain of Prp24 caused temperature sensitive growth and reduced levels of U4/U6, suggesting that this region too, containing the fourth RRM, is important for interactions in assembly of the spliceosome <ref name="Rader"/>.
+<Structure load='2ghp' size='300' frame='true' align='right' caption='' scene='Sandbox_Reserved_340/2ghp/3'/>
 NMR analysis of fragments of U6 sequence and regions of Prp24 have further defined and supported the interactions of the protein with U6 snRNA.  Analysis of an RNA oligonucleotide containing sequences identical to nucleotides 41-46 and 83-88 of U6 (the regions proposed to bind to Prp24) with a truncated protein containing RRMs 1 and 2 of Prp24 showed that these RRMs interacted sequence specifically with these nucleotides <ref name="Bae"/>.  Another NMR study identified sequence specific interaction of <scene name='Sandbox_Reserved_340/2kh9/3'>RRM 2 with RNA</scene>, and it was determined from this that most likely region of U6 for interaction was the AGAGAU sequence of nucleotides 49-54, within the region of previously predicted interaction <ref name="Martin">PMID:20181740</ref>.  From this, it was predicted that RRM 1 would interact with the GAUCAG sequence of nucleotides 55-60 <ref name="Martin"/>.