1s4u: Difference between revisions

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==Crystal Structure analysis of the beta-propeller protein Ski8p==
==Crystal Structure analysis of the beta-propeller protein Ski8p==
<StructureSection load='1s4u' size='340' side='right' caption='[[1s4u]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='1s4u' size='340' side='right' caption='[[1s4u]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<table><tr><td colspan='2'>[[1s4u]] 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=1S4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S4U FirstGlance]. <br>
<table><tr><td colspan='2'>[[1s4u]] 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=1S4U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S4U FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SKI8, YGL213C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SKI8, 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=1s4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4u OCA], [http://pdbe.org/1s4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s4u RCSB], [http://www.ebi.ac.uk/pdbsum/1s4u PDBsum]</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=1s4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4u OCA], [http://pdbe.org/1s4u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s4u RCSB], [http://www.ebi.ac.uk/pdbsum/1s4u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s4u ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s4/1s4u_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s4/1s4u_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>

Revision as of 09:56, 8 March 2018

Crystal Structure analysis of the beta-propeller protein Ski8pCrystal Structure analysis of the beta-propeller protein Ski8p

Structural highlights

1s4u 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.
Gene:SKI8, 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 WD-repeat protein with an essential role for the Ski complex assembly in an exosome-dependent 3'-to-5' mRNA decay. In addition, Ski8p is involved in meiotic recombination by interacting with Spo11p protein. We have determined the crystal structure of Ski8p from Saccharomyces cerevisiae at 2.2 A resolution. The structure reveals that Ski8p folds into a seven-bladed beta propeller. Mapping sequence conservation and hydrophobicities of amino acids on the molecular surface of Ski8p reveals a prominent site on the top surface of the beta propeller, which is most likely involved in mediating interactions of Ski8p with Ski3p and Spo11p. Mutagenesis combined with yeast two-hybrid and GST pull-down assays identified the top surface of the beta propeller as being required for Ski8p binding to Ski3p and Spo11p. The functional implications for Ski8p function in both mRNA decay and meiotic recombination are discussed.

Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination.,Cheng Z, Liu Y, Wang C, Parker R, Song H Protein Sci. 2004 Oct;13(10):2673-84. Epub 2004 Aug 31. PMID:15340168[13]

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

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
  13. ↑ Cheng Z, Liu Y, Wang C, Parker R, Song H. Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination. Protein Sci. 2004 Oct;13(10):2673-84. Epub 2004 Aug 31. PMID:15340168 doi:10.1110/ps.04856504

1s4u, resolution 2.10Å

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