This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4zkd

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:11, 26 June 2019

Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate.

Structural highlights

4zkd 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:	SKI7, YOR076C, YOR29-27 (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4zkd"

@@ Line 1: / Line 1: @@
 ==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]] 2.18&Aring;' scene=''>
+<StructureSection load='4zkd' size='340' side='right'caption='[[4zkd]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
 == 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 [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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>
 </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>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SKI7, YOR076C, YOR29-27 ([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=4zkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zkd OCA], [http://pdbe.org/4zkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zkd RCSB], [http://www.ebi.ac.uk/pdbsum/4zkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zkd ProSAT]</span></td></tr>
 </table>
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Atcc 18824]]
+[[Category: Large Structures]]
 [[Category: Conti, E]]
 [[Category: Kowalinski, E]]

4zkd

From Proteopedia

Revision as of 08:11, 26 June 2019

Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox