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15.5kD/Snu13/L7Ae protein: Difference between revisions

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m 15.5kD/Snu13/L7Ae moved to 15.5kD/Snu13/L7Ae protein: Because it isn't just called '15.5kD' or 'Snu13'. It is 'Snu13 protein' or '15.5 kd protein'.
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A variation of the [[Kink-turn motif|kink-turn motif]], known as the kink-loop motif, can be found in the C/D and H/ACA RNAs <ref name ="gagnon"/>.  Interestingly, the eukaryotic proteins and their archaeal homologue do not interact with the different motifs in the same manner, even though share a conserved sequence similarity <ref name ="oruganti"/>.  For example, while L7Ae exhibits the same binding affinity for both the [[Kink-turn motif|kink-turn]] and kink-loop sRNA motifs, its eukaryotic homologues only bind specifically to the [[Kink-turn motif|kink-turn motif]] and discriminate against the kink-loop motif <ref name ="oruganti"/><ref name ="gagnon"/>.  
A variation of the [[Kink-turn motif|kink-turn motif]], known as the kink-loop motif, can be found in the C/D and H/ACA RNAs <ref name ="gagnon"/>.  Interestingly, the eukaryotic proteins and their archaeal homologue do not interact with the different motifs in the same manner, even though share a conserved sequence similarity <ref name ="oruganti"/>.  For example, while L7Ae exhibits the same binding affinity for both the [[Kink-turn motif|kink-turn]] and kink-loop sRNA motifs, its eukaryotic homologues only bind specifically to the [[Kink-turn motif|kink-turn motif]] and discriminate against the kink-loop motif <ref name ="oruganti"/><ref name ="gagnon"/>.  
   
   
Solved structures of the proteins include: 15.5kD in complex with a U4 snRNA fragment [[1E7K]], 15.5kD in complex with hPrp31 and a U4 snRNA fragment [[2OZB]], Snu13p without RNA [[1ZWZ]], [http://en.wikipedia.org/wiki/Archaeoglobus Archaeoglobus fulgidus] L7Ae-box C/D with RNA [[1RLG]], [http://en.wikipedia.org/wiki/Methanococcus_jannaschii Methanococcus jannaschii] L7Ae-H/ACA with RNA [[1RA4]], and [http://en.wikipedia.org/wiki/Pyrococcus Pyrococcus abyssi] L7Ae without RNA [[1PXW]].
Solved structures of the proteins include:  
*15.5kD in complex with a U4 snRNA fragment, [[1e7k]]
*15.5kD in complex with hPrp31 and a U4 snRNA fragment [[2ozb]]
*Snu13p without RNA - [[1zwz]]
*''[http://en.wikipedia.org/wiki/Archaeoglobus Archaeoglobus fulgidus]'' L7Ae-box C/D with RNA [[1rlg]]
*''[http://en.wikipedia.org/wiki/Methanococcus_jannaschii Methanococcus jannaschii]'' L7Ae-H/ACA with RNA [[1ra4]]
*''[http://en.wikipedia.org/wiki/Pyrococcus Pyrococcus abyssi]'' L7Ae without RNA [[1pxw]].
    
    
=Role in pre-ribosomal RNA processing=
=Role in pre-ribosomal RNA processing=
   
   
[[Ribosomes]] consist of both RNA and protein, and are designated large ribonucleprotein (RNP) particles.  Each ribosome contains two subunits (60S and 40S), four ribosomal RNAs (5S, 5.8S, 18S, and 25/28S rRNA), and approximately 75 associated proteins <ref name ="venema">PMID:10690410</ref>.  The processing of the pre-rRNAs requires a complex set of posttranscriptional modification steps after [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] <ref name ="venema"/>.  One such step involves extensive processing through pseudouridylation and 2’-O-ribose methylation at sites specified by various [http://en.wikipedia.org/wiki/Small_nucleolar_RNA s(no)RNAs] (C/D box s(no)RNAs specify 2’-O-ribose methylation and H/ACA s(no)RNA specify pseudouridylation) and associated proteins to form s(no)RNPs <ref name ="venema"/><ref name ="m-g">PMID:12810916</ref>.  Specifically, the 5’ region of U3 s(no)RNA containing C’/D and B/C box pairs interacts with 5’-ETS and 17S/18S areas of the pre-rRNA<ref name ="m-g"/>.  U3 also binds a set of proteins to form the U3 s(no)RNP complex <ref name ="gagnon"/>.
[[Ribosome|Ribosomes]] consist of both RNA and protein, and are designated large ribonucleprotein (RNP) particles.  Each ribosome contains two subunits (60S and 40S), four ribosomal RNAs (5S, 5.8S, 18S, and 25/28S rRNA), and approximately 75 associated proteins <ref name ="venema">PMID:10690410</ref>.  The processing of the pre-rRNAs requires a complex set of posttranscriptional modification steps after [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] <ref name ="venema"/>.  One such step involves extensive processing through pseudouridylation and 2’-O-ribose methylation at sites specified by various [http://en.wikipedia.org/wiki/Small_nucleolar_RNA s(no)RNAs] (C/D box s(no)RNAs specify 2’-O-ribose methylation and H/ACA s(no)RNA specify pseudouridylation) and associated proteins to form s(no)RNPs <ref name ="venema"/><ref name ="m-g">PMID:12810916</ref>.  Specifically, the 5’ region of U3 s(no)RNA containing C’/D and B/C box pairs interacts with 5’-ETS and 17S/18S areas of the pre-rRNA<ref name ="m-g"/>.  U3 also binds a set of proteins to form the U3 s(no)RNP complex <ref name ="gagnon"/>.
   
   
Snu13p/15.5kD/L7Ae interacts with U3 s(no)RNA through a kink-turn RNA motif <ref name ="venema"/>.  The protein initiates box C/D assembly by binding the kink-turn of the C/D RNAs <ref name ="gagnon"/>.  Once the s(no)RNP is fully assembled the RNA regions bind to complementary regions in target pre-rRNA.  This is followed by catalysis of the methyl transferase reaction by the associated proteins <ref name ="gagnon"/>.
Snu13p/15.5kD/L7Ae interacts with U3 s(no)RNA through a kink-turn RNA motif <ref name ="venema"/>.  The protein initiates box C/D assembly by binding the kink-turn of the C/D RNAs <ref name ="gagnon"/>.  Once the s(no)RNP is fully assembled the RNA regions bind to complementary regions in target pre-rRNA.  This is followed by catalysis of the methyl transferase reaction by the associated proteins <ref name ="gagnon"/>.
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The structure itself may not the most important aspect when comparing the homologues, rather the amino acid composition.  There are five amino acids located at the RNA binding region that are conserved within each of archaea and eukarya, however vary between the two.  One such amino acid lies towards the N-terminal side of the RNA binding region, in L7Ae it is Lys26 (Methanocaldococcus jannashii), and in 15.5kD it is Gln34.  Towards the C-terminal side of the RNA binding region located in loop 9 lie the four remaining residues Leu-Glu-Aal-Ala (L7Ae) and <scene name='Sandbox_503/Valserargpro/2'>Val95-Ser96-Arg97-Pro98 </scene>(15.5kD).  It is the difference between these amino acids that allow L7Ae to bind the kink-loop motif<ref name ="m-g"/>.  
The structure itself may not the most important aspect when comparing the homologues, rather the amino acid composition.  There are five amino acids located at the RNA binding region that are conserved within each of archaea and eukarya, however vary between the two.  One such amino acid lies towards the N-terminal side of the RNA binding region, in L7Ae it is Lys26 (Methanocaldococcus jannashii), and in 15.5kD it is Gln34.  Towards the C-terminal side of the RNA binding region located in loop 9 lie the four remaining residues Leu-Glu-Aal-Ala (L7Ae) and <scene name='Sandbox_503/Valserargpro/2'>Val95-Ser96-Arg97-Pro98 </scene>(15.5kD).  It is the difference between these amino acids that allow L7Ae to bind the kink-loop motif<ref name ="m-g"/>.  
</StructureSection>
</StructureSection>
=Additional Resources=


*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1e7k CRYSTAL STRUCTURE OF THE SPLICEOSOMAL 15.5KD PROTEIN BOUND TO A U4 SNRNA FRAGMENT, in the RCSB Protein Data Bank]
==See Also==
* [[Kink-turn motif]]
* [[RNA motifs]]
* [[Ribosome]]
* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]]
* [[Ribozyme]]
* [[Group I intron]]
* [[Azoarcus group I intron]]
* [[1go1]], [[1go0]], [[1w3e]] and [[1h7m]] – the ''Thermococcus celer'' ribosomal protein L30<ref>PMID: 12627951</ref><ref>PMID: 12824494</ref>
* A-minor motif
* The adenosine wedge motif<ref>PMID: 20038632</ref>
* The G-ribo motif<ref>PMID: 17283211</ref>
* The lonepair triloop motif<ref>PMID: 12473452</ref>
* RNA ribose zipper<ref>PMID: 12096903</ref>
 
=References=
<References/>
 
=Additional External Resources=
 
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1e7k CRYSTAL STRUCTURE OF THE SPLICEOSOMAL 15.5KD PROTEIN BOUND TO A U4 snRNA FRAGMENT, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=2ozb Structure of a human Prp31-15.5K-U4 snRNA complex, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=2ozb Structure of a human Prp31-15.5K-U4 snRNA complex, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1zwz Structural comparison of Yeast snoRNP and splicesomal protein snu13p with its homologs, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1zwz Structural comparison of Yeast snoRNP and splicesomal protein snu13p with its homologs, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1rlg Molecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1rlg Molecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1pxw Crystal structure of L7Ae sRNP core protein from Pyrococcus abyssii, in the RCSB Protein Data Bank]  
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1pxw Crystal structure of L7Ae sRNP core protein from Pyrococcus abyssii, in the RCSB Protein Data Bank]
=References=
<References/>

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Kelly Hrywkiw, Alexander Berchansky, Wayne Decatur
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