1sq9

From Proteopedia

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Revision as of 11:32, 24 December 2020

Structure of Ski8p, a WD repeat protein involved in mRNA degradation and meiotic recombination

Structural highlights

1sq9 is a 1 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	SKI8, REC103, YGL213C (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SKI8_YEAST] Involved in double-strand break (DSB) formation during meiotic recombination through stabilization of SPO11 association with meiotic chromosome and helping SPO11 to recruit other DSB proteins like REC102 and REC104 to meiotic chromosomes. Also component of the SKI complex involved in 3'-mRNA degradation pathway. Represses dsRNA virus propagation by specifically blocking translation of viral mRNAs, perhaps recognizing the absence of CAP or poly(A). Essential for controlling the propagation of M double-stranded RNA (dsRNA) and thus for preventing virus-induced cytopathology.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Ski8p is a 44-kD protein that primarily functions in the regulation of exosome-mediated, 3'--> 5' degradation of damaged mRNA. It does so by forming a complex with two partner proteins, Ski2p and Ski3p, which complete a complex that is capable of recruiting and activating the exosome/Ski7p complex that functions in RNA degradation. Ski8p also functions in meiotic recombination in complex with Spo11 in yeast. It is one of the many hundreds of primarily eukaryotic proteins containing tandem copies of WD repeats (also known as WD40 or beta-transducin repeats), which are short ~40 amino acid motifs, often terminating in a Trp-Asp dipeptide. Genomic analyses have demonstrated that WD repeats are found in 1%-2% of proteins in a typical eukaryote, but are extremely rare in prokaryotes. Almost all structurally characterized WD-repeat proteins are composed of seven such repeats and fold into seven-bladed beta propellers. Ski8p was thought to contain five WD repeats on the basis of primary sequence analysis implying a five-bladed propeller. The 1.9 A crystal structure unexpectedly exhibits a seven-bladed propeller fold with seven structurally authentic WD repeats. Structure-based sequence alignments show additional sequence diversity in the two undetected repeats. This demonstrates that many WD repeats have not yet been identified in sequences and also raises the possibility that the seven-bladed propeller may be the predominant fold for this family of proteins.

The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure.,Madrona AY, Wilson DK Protein Sci. 2004 Jun;13(6):1557-65. PMID:15152089^[13]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ridley SP, Sommer SS, Wickner RB. Superkiller mutations in Saccharomyces cerevisiae suppress exclusion of M2 double-stranded RNA by L-A-HN and confer cold sensitivity in the presence of M and L-A-HN. Mol Cell Biol. 1984 Apr;4(4):761-70. PMID:6371496
↑ Sommer SS, Wickner RB. Gene disruption indicates that the only essential function of the SKI8 chromosomal gene is to protect Saccharomyces cerevisiae from viral cytopathology. Virology. 1987 Mar;157(1):252-6. PMID:3029964
↑ Masison DC, Blanc A, Ribas JC, Carroll K, Sonenberg N, Wickner RB. Decoying the cap- mRNA degradation system by a double-stranded RNA virus and poly(A)- mRNA surveillance by a yeast antiviral system. Mol Cell Biol. 1995 May;15(5):2763-71. PMID:7739557
↑ Gardiner JM, Bullard SA, Chrome C, Malone RE. Molecular and genetic analysis of REC103, an early meiotic recombination gene in yeast. Genetics. 1997 Aug;146(4):1265-74. PMID:9258672
↑ Anderson JS, Parker RP. The 3' to 5' degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3' to 5' exonucleases of the exosome complex. EMBO J. 1998 Mar 2;17(5):1497-506. PMID:9482746 doi:10.1093/emboj/17.5.1497
↑ Brown JT, Bai X, Johnson AW. The yeast antiviral proteins Ski2p, Ski3p, and Ski8p exist as a complex in vivo. RNA. 2000 Mar;6(3):449-57. PMID:10744028
↑ Araki Y, Takahashi S, Kobayashi T, Kajiho H, Hoshino S, Katada T. Ski7p G protein interacts with the exosome and the Ski complex for 3'-to-5' mRNA decay in yeast. EMBO J. 2001 Sep 3;20(17):4684-93. PMID:11532933 doi:10.1093/emboj/20.17.4684
↑ Brown JT, Johnson AW. A cis-acting element known to block 3' mRNA degradation enhances expression of polyA-minus mRNA in wild-type yeast cells and phenocopies a ski mutant. RNA. 2001 Nov;7(11):1566-77. PMID:11720286
↑ Kushner DB, Lindenbach BD, Grdzelishvili VZ, Noueiry AO, Paul SM, Ahlquist P. Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15764-9. Epub 2003 Dec 11. PMID:14671320 doi:10.1073/pnas.2536857100
↑ Kee K, Protacio RU, Arora C, Keeney S. Spatial organization and dynamics of the association of Rec102 and Rec104 with meiotic chromosomes. EMBO J. 2004 Apr 21;23(8):1815-24. Epub 2004 Mar 25. PMID:15044957 doi:10.1038/sj.emboj.7600184
↑ Arora C, Kee K, Maleki S, Keeney S. Antiviral protein Ski8 is a direct partner of Spo11 in meiotic DNA break formation, independent of its cytoplasmic role in RNA metabolism. Mol Cell. 2004 Feb 27;13(4):549-59. PMID:14992724
↑ Nag DK, Pata JD, Sironi M, Flood DR, Hart AM. Both conserved and non-conserved regions of Spo11 are essential for meiotic recombination initiation in yeast. Mol Genet Genomics. 2006 Oct;276(4):313-21. Epub 2006 Jul 1. PMID:16816949 doi:10.1007/s00438-006-0143-7
↑ Madrona AY, Wilson DK. The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure. Protein Sci. 2004 Jun;13(6):1557-65. PMID:15152089 doi:10.1110/ps.04704704

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1sq9"

@@ Line 1: / Line 1: @@
 ==Structure of Ski8p, a WD repeat protein involved in mRNA degradation and meiotic recombination==
-<StructureSection load='1sq9' size='340' side='right' caption='[[1sq9]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1sq9' size='340' side='right'caption='[[1sq9]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1sq9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SQ9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1sq9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SQ9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SKI8, REC103, YGL213C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1sq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sq9 OCA], [http://pdbe.org/1sq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sq9 RCSB], [http://www.ebi.ac.uk/pdbsum/1sq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sq9 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1sq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sq9 OCA], [http://pdbe.org/1sq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sq9 RCSB], [http://www.ebi.ac.uk/pdbsum/1sq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sq9 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sq/1sq9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sq/1sq9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Madrona, A Y]]
 [[Category: Wilson, D K]]

1sq9

From Proteopedia

Revision as of 11:32, 24 December 2020

Structure of Ski8p, a WD repeat protein involved in mRNA degradation and meiotic recombination

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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