2iyk

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:32, 9 May 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2iyk.png|left|200px]]
 
-
<!--
+
==Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1==
-
The line below this paragraph, containing "STRUCTURE_2iyk", creates the "Structure Box" on the page.
+
<StructureSection load='2iyk' size='340' side='right'caption='[[2iyk]], [[Resolution|resolution]] 2.95&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'>[[2iyk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IYK 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]] 2.95&#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_2iyk| PDB=2iyk | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2iyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iyk OCA], [https://pdbe.org/2iyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iyk RCSB], [https://www.ebi.ac.uk/pdbsum/2iyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iyk ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RENT1_HUMAN RENT1_HUMAN] RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability.<ref>PMID:11163187</ref> <ref>PMID:16086026</ref> <ref>PMID:18172165</ref> <ref>PMID:21145460</ref> <ref>PMID:21419344</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/2iyk_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2iyk ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
UPF1 is an essential eukaryotic RNA helicase that plays a key role in various mRNA degradation pathways, notably nonsense-mediated mRNA decay (NMD). In combination with UPF2 and UPF3, it forms part of the surveillance complex that detects mRNAs containing premature stop codons and triggers their degradation in all organisms studied from yeast to human. We describe the 3 A resolution crystal structure of the highly conserved cysteine-histidine-rich domain of human UPF1 and show that it is a unique combination of three zinc-binding motifs arranged into two tandem modules related to the RING-box and U-box domains of ubiquitin ligases. This UPF1 domain interacts with UPF2, and we identified by mutational analysis residues in two distinct conserved surface regions of UPF1 that mediate this interaction. UPF1 residues we identify as important for the interaction with UPF2 are not conserved in UPF1 homologs from certain unicellular parasites that also appear to lack UPF2 in their genomes.
-
===CRYSTAL STRUCTURE OF THE UPF2-INTERACTING DOMAIN OF NONSENSE MEDIATED MRNA DECAY FACTOR UPF1===
+
Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1.,Kadlec J, Guilligay D, Ravelli RB, Cusack S RNA. 2006 Oct;12(10):1817-24. Epub 2006 Aug 24. PMID:16931876<ref>PMID:16931876</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_16931876}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2iyk" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 16931876 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16931876}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2IYK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IYK OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1., Kadlec J, Guilligay D, Ravelli RB, Cusack S, RNA. 2006 Oct;12(10):1817-24. Epub 2006 Aug 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16931876 16931876]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Cusack, S.]]
+
[[Category: Cusack S]]
-
[[Category: Guilligay, D.]]
+
[[Category: Guilligay D]]
-
[[Category: Kadlec, J.]]
+
[[Category: Kadlec J]]
-
[[Category: Ravelli, R B.]]
+
[[Category: Ravelli RB]]
-
[[Category: Alternative splicing]]
+
-
[[Category: Atp-binding]]
+
-
[[Category: Helicase]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Nmd]]
+
-
[[Category: Nonsense mediated mrna decay]]
+
-
[[Category: Nonsense-mediated mrna decay]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Phosphorylation]]
+
-
[[Category: Surveillance complex]]
+
-
[[Category: Upf1]]
+
-
[[Category: Zinc]]
+
-
[[Category: Zinc-finger]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:09:28 2008''
+

Current revision

Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1

PDB ID 2iyk

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/2iyk"
Personal tools