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| | <StructureSection load='4w7s' size='340' side='right'caption='[[4w7s]], [[Resolution|resolution]] 2.54Å' scene=''> | | <StructureSection load='4w7s' size='340' side='right'caption='[[4w7s]], [[Resolution|resolution]] 2.54Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4w7s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W7S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4w7s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W7S FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.542Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRP28, YDR243C, YD8419.10C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4w7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7s OCA], [https://pdbe.org/4w7s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w7s RCSB], [https://www.ebi.ac.uk/pdbsum/4w7s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7s ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4w7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w7s OCA], [http://pdbe.org/4w7s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w7s RCSB], [http://www.ebi.ac.uk/pdbsum/4w7s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w7s ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PRP28_YEAST PRP28_YEAST]] ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.<ref>PMID:10024879</ref> <ref>PMID:11172727</ref> <ref>PMID:2010088</ref> | + | [https://www.uniprot.org/uniprot/PRP28_YEAST PRP28_YEAST] ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.<ref>PMID:10024879</ref> <ref>PMID:11172727</ref> <ref>PMID:2010088</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: RNA helicase]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Jacewicz, A]] | + | [[Category: Jacewicz A]] |
| - | [[Category: Schwer, B]] | + | [[Category: Schwer B]] |
| - | [[Category: Shuman, S]] | + | [[Category: Shuman S]] |
| - | [[Category: Smith, P]] | + | [[Category: Smith P]] |
| - | [[Category: Atpase]]
| + | |
| - | [[Category: Dead-box protein]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Splicing factor]]
| + | |
| Structural highlights
4w7s is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.542Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PRP28_YEAST ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.[1] [2] [3]
Publication Abstract from PubMed
Yeast Prp28 is a DEAD-box pre-mRNA splicing factor implicated in displacing U1 snRNP from the 5' splice site. Here we report that the 588-aa Prp28 protein consists of a trypsin-sensitive 126-aa N-terminal segment (of which aa 1-89 are dispensable for Prp28 function in vivo) fused to a trypsin-resistant C-terminal catalytic domain. Purified recombinant Prp28 and Prp28-(127-588) have an intrinsic RNA-dependent ATPase activity, albeit with a low turnover number. The crystal structure of Prp28-(127-588) comprises two RecA-like domains splayed widely apart. AMPPNP*Mg2+ is engaged by the proximal domain, with proper and specific contacts from Phe194 and Gln201 (Q motif) to the adenine nucleobase. The triphosphate moiety of AMPPNP*Mg2+ is not poised for catalysis in the open domain conformation. Guided by the Prp28*AMPPNP structure, and that of the Drosophila Vasa*AMPPNP*Mg2+*RNA complex, we targeted 20 positions in Prp28 for alanine scanning. ATP-site components Asp341 and Glu342 (motif II) and Arg527 and Arg530 (motif VI) and RNA-site constituent Arg476 (motif Va) are essential for Prp28 activity in vivo. Synthetic lethality of double-alanine mutations highlighted functionally redundant contacts in the ATP-binding (Phe194-Gln201, Gln201-Asp502) and RNA-binding (Arg264-Arg320) sites. Overexpression of defective ATP-site mutants, but not defective RNA-site mutants, elicited severe dominant-negative growth defects.
Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28.,Jacewicz A, Schwer B, Smith P, Shuman S Nucleic Acids Res. 2014 Oct 10. pii: gku930. PMID:25303995[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Staley JP, Guthrie C. An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28p. Mol Cell. 1999 Jan;3(1):55-64. PMID:10024879
- ↑ Chen JY, Stands L, Staley JP, Jackups RR Jr, Latus LJ, Chang TH. Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol Cell. 2001 Jan;7(1):227-32. PMID:11172727
- ↑ Strauss EJ, Guthrie C. A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family. Genes Dev. 1991 Apr;5(4):629-41. PMID:2010088
- ↑ Jacewicz A, Schwer B, Smith P, Shuman S. Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Nucleic Acids Res. 2014 Oct 10. pii: gku930. PMID:25303995 doi:http://dx.doi.org/10.1093/nar/gku930
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