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| | ==Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate.== | | ==Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate.== |
| - | <StructureSection load='4zkd' size='340' side='right' caption='[[4zkd]], [[Resolution|resolution]] 2.18Å' scene=''> | + | <StructureSection load='4zkd' size='340' side='right'caption='[[4zkd]], [[Resolution|resolution]] 2.18Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4zkd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZKD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4zkd]] 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=4ZKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZKD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.181Å</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=4zkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4zkd RCSB], [http://www.ebi.ac.uk/pdbsum/4zkd PDBsum]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4zkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zkd OCA], [https://pdbe.org/4zkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zkd RCSB], [https://www.ebi.ac.uk/pdbsum/4zkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zkd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SKI7_YEAST SKI7_YEAST]] Represses the expression of non-poly(A) mRNAs like L-A or M viruses and is therefore involved in antiviral system. Mediates interactions via its N-terminus between the exosome and the SKI complex which operate in the 3'-to-5' mRNA-decay pathway. By interacting with NAM7, is also required for nonsense-mediated 3'-to-5' mRNA-decay (NMD). May recognize a stalled 80S ribosome at the 3'-end of a nonstop mRNA which leads to the recruitment of the exosome and SKI complexes to the mRNAs to be degraded.<ref>PMID:10074137</ref> <ref>PMID:11027292</ref> <ref>PMID:11514438</ref> <ref>PMID:11532933</ref> <ref>PMID:11910110</ref> <ref>PMID:12769863</ref> <ref>PMID:12881429</ref> <ref>PMID:14671320</ref> <ref>PMID:15933721</ref> <ref>PMID:6371496</ref> | + | [https://www.uniprot.org/uniprot/SKI7_YEAST SKI7_YEAST] Represses the expression of non-poly(A) mRNAs like L-A or M viruses and is therefore involved in antiviral system. Mediates interactions via its N-terminus between the exosome and the SKI complex which operate in the 3'-to-5' mRNA-decay pathway. By interacting with NAM7, is also required for nonsense-mediated 3'-to-5' mRNA-decay (NMD). May recognize a stalled 80S ribosome at the 3'-end of a nonstop mRNA which leads to the recruitment of the exosome and SKI complexes to the mRNAs to be degraded.<ref>PMID:10074137</ref> <ref>PMID:11027292</ref> <ref>PMID:11514438</ref> <ref>PMID:11532933</ref> <ref>PMID:11910110</ref> <ref>PMID:12769863</ref> <ref>PMID:12881429</ref> <ref>PMID:14671320</ref> <ref>PMID:15933721</ref> <ref>PMID:6371496</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Ski7 is a cofactor of the cytoplasmic exosome in budding yeast, functioning in both mRNA turnover and non-stop decay (NSD), a surveillance pathway that degrades faulty mRNAs lacking a stop codon. The C-terminal region of Ski7 (Ski7C) shares overall sequence similarity with the translational GTPase (trGTPase) Hbs1, but whether Ski7 has retained the properties of a trGTPase is unclear. Here, we report the high-resolution structures of Ski7C bound to either intact guanosine triphosphate (GTP) or guanosine diphosphate-Pi. The individual domains of Ski7C adopt the conformation characteristic of active trGTPases. Furthermore, the nucleotide-binding site of Ski7C shares similar features compared with active trGTPases, notably the presence of a characteristic monovalent cation. However, a suboptimal polar residue at the putative catalytic site and an unusual polar residue that interacts with the gamma-phosphate of GTP distinguish Ski7 from other trGTPases, suggesting it might function rather as a GTP-binding protein than as a GTP-hydrolyzing enzyme. |
| | + | |
| | + | Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases.,Kowalinski E, Schuller A, Green R, Conti E Structure. 2015 May 28. pii: S0969-2126(15)00177-X. doi:, 10.1016/j.str.2015.04.018. PMID:26051716<ref>PMID:26051716</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 4zkd" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Conti, E]] | + | [[Category: Large Structures]] |
| - | [[Category: Kowalinski, E]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Gtp-binding protein]] | + | [[Category: Conti E]] |
| - | [[Category: Gtpase]] | + | [[Category: Kowalinski E]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Ngd]]
| + | |
| - | [[Category: Ski]]
| + | |
| - | [[Category: Translation]]
| + | |
| Structural highlights
Function
SKI7_YEAST Represses the expression of non-poly(A) mRNAs like L-A or M viruses and is therefore involved in antiviral system. Mediates interactions via its N-terminus between the exosome and the SKI complex which operate in the 3'-to-5' mRNA-decay pathway. By interacting with NAM7, is also required for nonsense-mediated 3'-to-5' mRNA-decay (NMD). May recognize a stalled 80S ribosome at the 3'-end of a nonstop mRNA which leads to the recruitment of the exosome and SKI complexes to the mRNAs to be degraded.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10]
Publication Abstract from PubMed
Ski7 is a cofactor of the cytoplasmic exosome in budding yeast, functioning in both mRNA turnover and non-stop decay (NSD), a surveillance pathway that degrades faulty mRNAs lacking a stop codon. The C-terminal region of Ski7 (Ski7C) shares overall sequence similarity with the translational GTPase (trGTPase) Hbs1, but whether Ski7 has retained the properties of a trGTPase is unclear. Here, we report the high-resolution structures of Ski7C bound to either intact guanosine triphosphate (GTP) or guanosine diphosphate-Pi. The individual domains of Ski7C adopt the conformation characteristic of active trGTPases. Furthermore, the nucleotide-binding site of Ski7C shares similar features compared with active trGTPases, notably the presence of a characteristic monovalent cation. However, a suboptimal polar residue at the putative catalytic site and an unusual polar residue that interacts with the gamma-phosphate of GTP distinguish Ski7 from other trGTPases, suggesting it might function rather as a GTP-binding protein than as a GTP-hydrolyzing enzyme.
Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases.,Kowalinski E, Schuller A, Green R, Conti E Structure. 2015 May 28. pii: S0969-2126(15)00177-X. doi:, 10.1016/j.str.2015.04.018. PMID:26051716[11]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Benard L, Carroll K, Valle RC, Masison DC, Wickner RB. The ski7 antiviral protein is an EF1-alpha homolog that blocks expression of non-Poly(A) mRNA in Saccharomyces cerevisiae. J Virol. 1999 Apr;73(4):2893-900. PMID:10074137
- ↑ van Hoof A, Staples RR, Baker RE, Parker R. Function of the ski4p (Csl4p) and Ski7p proteins in 3'-to-5' degradation of mRNA. Mol Cell Biol. 2000 Nov;20(21):8230-43. PMID:11027292
- ↑ He W, Parker R. The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3' termini from partial degradation. Genetics. 2001 Aug;158(4):1445-55. PMID:11514438
- ↑ 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
- ↑ van Hoof A, Frischmeyer PA, Dietz HC, Parker R. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science. 2002 Mar 22;295(5563):2262-4. PMID:11910110 doi:http://dx.doi.org/10.1126/science.1067272
- ↑ 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
- ↑ Takahashi S, Araki Y, Sakuno T, Katada T. Interaction between Ski7p and Upf1p is required for nonsense-mediated 3'-to-5' mRNA decay in yeast. EMBO J. 2003 Aug 1;22(15):3951-9. PMID:12881429 doi:http://dx.doi.org/10.1093/emboj/cdg374
- ↑ 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
- ↑ Inada T, Aiba H. Translation of aberrant mRNAs lacking a termination codon or with a shortened 3'-UTR is repressed after initiation in yeast. EMBO J. 2005 Apr 20;24(8):1584-95. Epub 2005 Mar 31. PMID:15933721 doi:http://dx.doi.org/7600636
- ↑ 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
- ↑ Kowalinski E, Schuller A, Green R, Conti E. Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases. Structure. 2015 May 28. pii: S0969-2126(15)00177-X. doi:, 10.1016/j.str.2015.04.018. PMID:26051716 doi:http://dx.doi.org/10.1016/j.str.2015.04.018
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