4a4z: Difference between revisions

Latest revision as of 10:47, 9 May 2024

CRYSTAL STRUCTURE OF THE S. CEREVISIAE DEXH HELICASE SKI2 BOUND TO AMPPNP

Structural highlights

4a4z is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	ANP, EDO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SKI2_YEAST RNA helicase 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 cell growth only in the presence of M1 replicon.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Publication Abstract from PubMed

Ski2 is a cytoplasmic RNA helicase that functions together with the exosome in the turnover and quality control of mRNAs. Ski2 is conserved in eukaryotes and is related to the helicase Mtr4, a cofactor of the nuclear exosome involved in the processing and quality control of a variety of structured RNAs. We have determined the 2.4 A resolution crystal structure of the 113 kDa helicase region of Saccharomyces cerevisiae Ski2. The structure shows that Ski2 has an overall architecture similar to that of Mtr4, with a core DExH region and an extended insertion domain. The insertion is not required for the formation of the Ski2-Ski3-Ski8 complex, but is instead an RNA-binding domain. While this is reminiscent of the Mtr4 insertion, there are specific structural and biochemical differences between the two helicases. The insertion of yeast Mtr4 consists of a beta-barrel domain that is flexibly attached to a helical stalk, contains a KOW signature motif, and binds in vitro-transcribed tRNA(i)(Met), but not single-stranded RNA. The beta-barrel domain of yeast Ski2 does not contain a KOW motif and is tightly packed against the helical stalk, forming a single structural unit maintained by a zinc-binding site. Biochemically, the Ski2 insertion has broad substrate specificity, binding both single-stranded and double-stranded RNAs. We speculate that the Ski2 and Mtr4 insertion domains have evolved with different properties tailored to the type of transcripts that are the substrates of the cytoplasmic and nuclear exosome.

The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome.,Halbach F, Rode M, Conti E RNA. 2012 Jan;18(1):124-34. Epub 2011 Nov 23. PMID:22114319^[14]

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

References

↑ Widner WR, Wickner RB. Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA. Mol Cell Biol. 1993 Jul;13(7):4331-41. PMID:8321235
↑ Toh-E A, Guerry P, Wickner RB. Chromosomal superkiller mutants of Saccharomyces cerevisiae. J Bacteriol. 1978 Dec;136(3):1002-7. PMID:363683
↑ 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
↑ Johnson AW, Kolodner RD. Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control. Mol Cell Biol. 1995 May;15(5):2719-27. PMID:7739552
↑ 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
↑ 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
↑ van Hoof A, Lennertz P, Parker R. Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol Cell Biol. 2000 Jan;20(2):441-52. PMID:10611222
↑ 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
↑ Searfoss AM, Wickner RB. 3' poly(A) is dispensable for translation. Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9133-7. PMID:10922069
↑ 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
↑ Mitchell P, Tollervey D. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation. Mol Cell. 2003 May;11(5):1405-13. PMID:12769863
↑ 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
↑ Halbach F, Rode M, Conti E. The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome. RNA. 2012 Jan;18(1):124-34. Epub 2011 Nov 23. PMID:22114319 doi:10.1261/rna.029553.111

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OCA

[1] Widner WR, Wickner RB. Evidence that the SKI antiviral system of Saccharomyces cerevisiae acts by blocking expression of viral mRNA. Mol Cell Biol. 1993 Jul;13(7):4331-41. PMID:8321235

[2] Toh-E A, Guerry P, Wickner RB. Chromosomal superkiller mutants of Saccharomyces cerevisiae. J Bacteriol. 1978 Dec;136(3):1002-7. PMID:363683

[3] 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

[4] Johnson AW, Kolodner RD. Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control. Mol Cell Biol. 1995 May;15(5):2719-27. PMID:7739552

[5] 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

[6] 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

[7] van Hoof A, Lennertz P, Parker R. Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol Cell Biol. 2000 Jan;20(2):441-52. PMID:10611222

[8] 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

[9] Searfoss AM, Wickner RB. 3' poly(A) is dispensable for translation. Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9133-7. PMID:10922069

[10] 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

[11] 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

[12] Mitchell P, Tollervey D. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation. Mol Cell. 2003 May;11(5):1405-13. PMID:12769863

[13] 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

[14] Halbach F, Rode M, Conti E. The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome. RNA. 2012 Jan;18(1):124-34. Epub 2011 Nov 23. PMID:22114319 doi:10.1261/rna.029553.111

[1]

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[4]

[5]

[6]

[7]

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[14]

@@ Line 3: / Line 3: @@
 <StructureSection load='4a4z' size='340' side='right'caption='[[4a4z]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4a4z]] 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=4A4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A4Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4a4z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A4Z 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=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4a4k|4a4k]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4a4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4z OCA], [https://pdbe.org/4a4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a4z RCSB], [https://www.ebi.ac.uk/pdbsum/4a4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4z ProSAT]</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=4a4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4z OCA], [http://pdbe.org/4a4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4a4z RCSB], [http://www.ebi.ac.uk/pdbsum/4a4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SKI2_YEAST SKI2_YEAST]] RNA helicase 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 cell growth only in the presence of M1 replicon.<ref>PMID:8321235</ref> <ref>PMID:363683</ref> <ref>PMID:6371496</ref> <ref>PMID:7739552</ref> <ref>PMID:7739557</ref> <ref>PMID:9482746</ref> <ref>PMID:10611222</ref> <ref>PMID:10744028</ref> <ref>PMID:10922069</ref> <ref>PMID:11532933</ref> <ref>PMID:11720286</ref> <ref>PMID:12769863</ref> <ref>PMID:14671320</ref>
+[https://www.uniprot.org/uniprot/SKI2_YEAST SKI2_YEAST] RNA helicase 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 cell growth only in the presence of M1 replicon.<ref>PMID:8321235</ref> <ref>PMID:363683</ref> <ref>PMID:6371496</ref> <ref>PMID:7739552</ref> <ref>PMID:7739557</ref> <ref>PMID:9482746</ref> <ref>PMID:10611222</ref> <ref>PMID:10744028</ref> <ref>PMID:10922069</ref> <ref>PMID:11532933</ref> <ref>PMID:11720286</ref> <ref>PMID:12769863</ref> <ref>PMID:14671320</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Helicase|Helicase]]
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: RNA helicase]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Conti, E]]
+[[Category: Conti E]]
-[[Category: Halbach, F]]
+[[Category: Halbach F]]
-[[Category: Rode, M]]
+[[Category: Rode M]]
-[[Category: Atpase]]
-[[Category: Exosome]]
-[[Category: Hydrolase]]
-[[Category: Mrna degradation]]

4a4z: Difference between revisions

Latest revision as of 10:47, 9 May 2024

CRYSTAL STRUCTURE OF THE S. CEREVISIAE DEXH HELICASE SKI2 BOUND TO AMPPNP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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