4a4k

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:47, 9 May 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:4a4k.png|left|200px]]
 
-
<!--
+
==Crystal structure of the S. cerevisiae Ski2 insertion domain==
-
The line below this paragraph, containing "STRUCTURE_4a4k", creates the "Structure Box" on the page.
+
<StructureSection load='4a4k' size='340' side='right'caption='[[4a4k]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[4a4k]] is a 5 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=4A4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A4K FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.25&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_4a4k| PDB=4a4k | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4a4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a4k OCA], [https://pdbe.org/4a4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a4k RCSB], [https://www.ebi.ac.uk/pdbsum/4a4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a4k ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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 ==
 +
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.
-
===Crystal structure of the S. cerevisiae Ski2 insertion domain===
+
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<ref>PMID:22114319</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 4a4k" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_22114319}}, adds the Publication Abstract to the page
+
*[[Helicase 3D structures|Helicase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 22114319 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_22114319}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[4a4k]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A4K OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:022114319</ref><references group="xtra"/>
+
-
[[Category: RNA helicase]]
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Conti, E.]]
+
[[Category: Conti E]]
-
[[Category: Halbach, F.]]
+
[[Category: Halbach F]]
-
[[Category: Rode, M.]]
+
[[Category: Rode M]]
-
[[Category: Dexh helicase]]
+
-
[[Category: Exosome]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Rna degradation]]
+

Current revision

Crystal structure of the S. cerevisiae Ski2 insertion domain

PDB ID 4a4k

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4a4k"
Personal tools