4j7m

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:01, 1 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion==
==Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion==
-
<StructureSection load='4j7m' size='340' side='right' caption='[[4j7m]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+
<StructureSection load='4j7m' size='340' side='right'caption='[[4j7m]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4j7m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J7M FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4j7m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J7M FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=UBD:URIDINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>UBD</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]] 1.7&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene>, <scene name='pdbligand=UBD:URIDINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>UBD</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4j7l|4j7l]], [[4j7n|4j7n]], [[3fqi|3fqi]], [[3fqj|3fqj]]</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=4j7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7m OCA], [https://pdbe.org/4j7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j7m RCSB], [https://www.ebi.ac.uk/pdbsum/4j7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j7m ProSAT]</span></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dom3z, Ng6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=4j7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7m OCA], [http://pdbe.org/4j7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j7m RCSB], [http://www.ebi.ac.uk/pdbsum/4j7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j7m ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DOM3Z_MOUSE DOM3Z_MOUSE]] May possess pyrophosphohydrolase activity towards 5' triphosphorylated RNA (By similarity).
+
[https://www.uniprot.org/uniprot/DXO_MOUSE DXO_MOUSE] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.<ref>PMID:23523372</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Recently, we reported that two homologous yeast proteins, Rai1 and Dxo1, function in a quality control mechanism to clear cells of incompletely 5' end-capped messenger RNAs (mRNAs). Here, we report that their mammalian homolog, Dom3Z (referred to as DXO), possesses pyrophosphohydrolase, decapping, and 5'-to-3' exoribonuclease activities. Surprisingly, we found that DXO preferentially degrades defectively capped pre-mRNAs in cells. Additional studies show that incompletely capped pre-mRNAs are inefficiently spliced at all introns, a fact that contrasts with current understanding, and are also poorly cleaved for polyadenylation. Crystal structures of DXO in complex with substrate mimic and products at a resolution of up to 1.5A provide elegant insights into the catalytic mechanism and molecular basis for their three apparently distinct activities. Our data reveal a pre-mRNA 5' end capping quality control mechanism in mammalian cells, indicating DXO as the central player for this mechanism, and demonstrate an unexpected intimate link between proper 5' end capping and subsequent pre-mRNA processing.
+
-
 
+
-
A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing.,Jiao X, Chang JH, Kilic T, Tong L, Kiledjian M Mol Cell. 2013 Apr 11;50(1):104-15. doi: 10.1016/j.molcel.2013.02.017. Epub 2013 , Mar 21. PMID:23523372<ref>PMID:23523372</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4j7m" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Lk3 transgenic mice]]
+
[[Category: Large Structures]]
-
[[Category: Chang, J H]]
+
[[Category: Mus musculus]]
-
[[Category: Tong, L]]
+
[[Category: Synthetic construct]]
-
[[Category: 5'-3' exoribonuclease]]
+
[[Category: Chang JH]]
-
[[Category: Decapping]]
+
[[Category: Tong L]]
-
[[Category: Hydrolase]]
+
-
[[Category: Hydrolase-rna complex]]
+

Current revision

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion

PDB ID 4j7m

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/4j7m"
Personal tools