2iyk

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[[Image:2iyk.png|left|200px]]
 
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{{STRUCTURE_2iyk| PDB=2iyk | SCENE= }}
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==Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1==
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<StructureSection load='2iyk' size='340' side='right'caption='[[2iyk]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/2iyk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===CRYSTAL STRUCTURE OF THE UPF2-INTERACTING DOMAIN OF NONSENSE MEDIATED MRNA DECAY FACTOR UPF1===
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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>
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{{ABSTRACT_PUBMED_16931876}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 2iyk" style="background-color:#fffaf0;"></div>
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[[2iyk]] is a 2 chain structure with 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].
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== References ==
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<references/>
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==Reference==
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__TOC__
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<ref group="xtra">PMID:016931876</ref><references group="xtra"/>
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Cusack, S.]]
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[[Category: Large Structures]]
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[[Category: Guilligay, D.]]
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[[Category: Cusack S]]
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[[Category: Kadlec, J.]]
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[[Category: Guilligay D]]
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[[Category: Ravelli, R B.]]
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[[Category: Kadlec J]]
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[[Category: Atp-binding]]
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[[Category: Ravelli RB]]
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[[Category: Helicase]]
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[[Category: Hydrolase]]
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[[Category: Metal-binding]]
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[[Category: Nmd]]
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[[Category: Nonsense mediated mrna decay]]
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[[Category: Nonsense-mediated mrna decay]]
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[[Category: Nucleotide-binding]]
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[[Category: Phosphorylation]]
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[[Category: Surveillance complex]]
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[[Category: Upf1]]
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[[Category: Zinc-finger]]
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Current revision

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

PDB ID 2iyk

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