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2xes

From Proteopedia

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Current revision

Human PatL1 C-terminal domain (loop variant)

Structural highlights

2xes is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Related:	2xeq, 2xer
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PATL1_HUMAN] RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV).^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Pat proteins regulate the transition of mRNAs from a state that is translationally active to one that is repressed, committing targeted mRNAs to degradation. Pat proteins contain a conserved N-terminal sequence, a proline-rich region, a Mid domain and a C-terminal domain (Pat-C). We show that Pat-C is essential for the interaction with mRNA decapping factors (i.e. DCP2, EDC4 and LSm1-7), whereas the P-rich region and Mid domain have distinct functions in modulating these interactions. DCP2 and EDC4 binding is enhanced by the P-rich region and does not require LSm1-7. LSm1-7 binding is assisted by the Mid domain and is reduced by the P-rich region. Structural analysis revealed that Pat-C folds into an alpha-alpha superhelix, exposing conserved and basic residues on one side of the domain. This conserved and basic surface is required for RNA, DCP2, EDC4 and LSm1-7 binding. The multiplicity of interactions mediated by Pat-C suggests that certain of these interactions are mutually exclusive and, therefore, that Pat proteins switch decapping partners allowing transitions between sequential steps in the mRNA decapping pathway.

The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa.,Braun JE, Tritschler F, Haas G, Igreja C, Truffault V, Weichenrieder O, Izaurralde E EMBO J. 2010 Jul 21;29(14):2368-80. Epub 2010 Jun 11. PMID:20543818^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Scheller N, Resa-Infante P, de la Luna S, Galao RP, Albrecht M, Kaestner L, Lipp P, Lengauer T, Meyerhans A, Diez J. Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim Biophys Acta. 2007 Dec;1773(12):1786-92. Epub 2007 Sep 6. PMID:17936923 doi:10.1016/j.bbamcr.2007.08.009
↑ Scheller N, Mina LB, Galao RP, Chari A, Gimenez-Barcons M, Noueiry A, Fischer U, Meyerhans A, Diez J. Translation and replication of hepatitis C virus genomic RNA depends on ancient cellular proteins that control mRNA fates. Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13517-22. doi:, 10.1073/pnas.0906413106. Epub 2009 Jul 23. PMID:19628699 doi:10.1073/pnas.0906413106
↑ Ozgur S, Chekulaeva M, Stoecklin G. Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies. Mol Cell Biol. 2010 Sep;30(17):4308-23. doi: 10.1128/MCB.00429-10. Epub 2010 Jun , 28. PMID:20584987 doi:10.1128/MCB.00429-10
↑ Totaro A, Renzi F, La Fata G, Mattioli C, Raabe M, Urlaub H, Achsel T. The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique. Nucleic Acids Res. 2011 Jan;39(2):635-47. doi: 10.1093/nar/gkq797. Epub 2010 Sep , 17. PMID:20852261 doi:10.1093/nar/gkq797
↑ Braun JE, Tritschler F, Haas G, Igreja C, Truffault V, Weichenrieder O, Izaurralde E. The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. EMBO J. 2010 Jul 21;29(14):2368-80. Epub 2010 Jun 11. PMID:20543818 doi:10.1038/emboj.2010.124
↑ Braun JE, Tritschler F, Haas G, Igreja C, Truffault V, Weichenrieder O, Izaurralde E. The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. EMBO J. 2010 Jul 21;29(14):2368-80. Epub 2010 Jun 11. PMID:20543818 doi:10.1038/emboj.2010.124

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xes"

@@ Line 1: / Line 1: @@
-==HUMAN PATL1 C-TERMINAL DOMAIN (LOOP VARIANT)==
+==Human PatL1 C-terminal domain (loop variant)==
-<StructureSection load='2xes' size='340' side='right' caption='[[2xes]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2xes' size='340' side='right'caption='[[2xes]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xes]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XES FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xes]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XES FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xeq|2xeq]], [[2xer|2xer]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2xeq|2xeq]], [[2xer|2xer]]</div></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=2xes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xes OCA], [http://pdbe.org/2xes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xes RCSB], [http://www.ebi.ac.uk/pdbsum/2xes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xes ProSAT]</span></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=2xes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xes OCA], [https://pdbe.org/2xes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xes RCSB], [https://www.ebi.ac.uk/pdbsum/2xes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xes ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PATL1_HUMAN PATL1_HUMAN]] RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV).<ref>PMID:17936923</ref> <ref>PMID:19628699</ref> <ref>PMID:20584987</ref> <ref>PMID:20852261</ref> <ref>PMID:20543818</ref>
+[[https://www.uniprot.org/uniprot/PATL1_HUMAN PATL1_HUMAN]] RNA-binding protein involved in deadenylation-dependent decapping of mRNAs, leading to the degradation of mRNAs. Acts as a scaffold protein that connects deadenylation and decapping machinery. Required for cytoplasmic mRNA processing body (P-body) assembly. In case of infection, required for translation and replication of hepatitis C virus (HCV).<ref>PMID:17936923</ref> <ref>PMID:19628699</ref> <ref>PMID:20584987</ref> <ref>PMID:20852261</ref> <ref>PMID:20543818</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/xe/2xes_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xe/2xes_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Tritschler, F]]
 [[Category: Weichenrieder, O]]

2xes

From Proteopedia

Current revision

Human PatL1 C-terminal domain (loop variant)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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