3k4e

From Proteopedia

(Difference between revisions)

Current revision

Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site A

Structural highlights

3k4e is a 6 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PUF3_YEAST RNA-binding protein involved in post-transcriptional regulation. Negatively regulates expression of COX17 by binding to the 3'-UTR of COX17 mRNA. Promotes decay of COX17 mRNA by enhancing its rate of deadenylation and subsequent turnover. Predominantly binds to mRNAs encoding mitochondrial proteins and localizes them to the vicinity of mitochondria for translation. Regulates mitochondrial biogenesis, motility and morphology.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

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

A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of Saccharomyces cerevisiae is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity. To do so, we explore the crystal structures of Puf3p complexes with 2 cognate RNAs. The key determinant of Puf3p specificity is an unusual interaction between a distinctive pocket of the protein with an RNA base outside the "core" PUF-binding site. That interaction dramatically affects binding affinity in vitro and is required for regulation in vivo. The Puf3p structures, combined with those of Puf4p in the same organism, illuminate the structural basis of natural PUF-RNA networks. Yeast Puf3p binds its own RNAs because they possess a -2C and is excluded from those of Puf4p which contain an additional nucleotide in the core-binding site.

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.,Zhu D, Stumpf CR, Krahn JM, Wickens M, Hall TM Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20192-7. Epub 2009 Nov 16. PMID:19918084^[8]

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

References

↑ Olivas W, Parker R. The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J. 2000 Dec 1;19(23):6602-11. PMID:11101532 doi:10.1093/emboj/19.23.6602
↑ Jackson JS Jr, Houshmandi SS, Lopez Leban F, Olivas WM. Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast. RNA. 2004 Oct;10(10):1625-36. Epub 2004 Aug 30. PMID:15337848 doi:10.1261/rna.7270204
↑ Ringner M, Krogh M. Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput Biol. 2005 Dec;1(7):e72. Epub 2005 Dec 9. PMID:16355254 doi:10.1371/journal.pcbi.0010072
↑ Houshmandi SS, Olivas WM. Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a loop required for regulation of mRNA decay. RNA. 2005 Nov;11(11):1655-66. PMID:16244132 doi:10.1261/rna.2168505
↑ Garcia-Rodriguez LJ, Gay AC, Pon LA. Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast. J Cell Biol. 2007 Jan 15;176(2):197-207. Epub 2007 Jan 8. PMID:17210948 doi:10.1083/jcb.200606054
↑ Saint-Georges Y, Garcia M, Delaveau T, Jourdren L, Le Crom S, Lemoine S, Tanty V, Devaux F, Jacq C. Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization. PLoS One. 2008 Jun 4;3(6):e2293. doi: 10.1371/journal.pone.0002293. PMID:18523582 doi:10.1371/journal.pone.0002293
↑ Ulbricht RJ, Olivas WM. Puf1p acts in combination with other yeast Puf proteins to control mRNA stability. RNA. 2008 Feb;14(2):246-62. Epub 2007 Dec 19. PMID:18094119 doi:10.1261/rna.847408
↑ Zhu D, Stumpf CR, Krahn JM, Wickens M, Hall TM. A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20192-7. Epub 2009 Nov 16. PMID:19918084 doi:10.1073/pnas.0812079106

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/3k4e"

@@ Line 1: / Line 1: @@
 ==Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site A==
-<StructureSection load='3k4e' size='340' side='right' caption='[[3k4e]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='3k4e' size='340' side='right'caption='[[3k4e]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3k4e]] is a 6 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=3K4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K4E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3k4e]] is a 6 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=3K4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K4E FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k49|3k49]]</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]] 3.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L1325, PUF3, YLL013C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3k4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k4e OCA], [https://pdbe.org/3k4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k4e RCSB], [https://www.ebi.ac.uk/pdbsum/3k4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k4e ProSAT]</span></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=3k4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k4e RCSB], [http://www.ebi.ac.uk/pdbsum/3k4e PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PUF3_YEAST PUF3_YEAST] RNA-binding protein involved in post-transcriptional regulation. Negatively regulates expression of COX17 by binding to the 3'-UTR of COX17 mRNA. Promotes decay of COX17 mRNA by enhancing its rate of deadenylation and subsequent turnover. Predominantly binds to mRNAs encoding mitochondrial proteins and localizes them to the vicinity of mitochondria for translation. Regulates mitochondrial biogenesis, motility and morphology.<ref>PMID:11101532</ref> <ref>PMID:15337848</ref> <ref>PMID:16355254</ref> <ref>PMID:16244132</ref> <ref>PMID:17210948</ref> <ref>PMID:18523582</ref> <ref>PMID:18094119</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/k4/3k4e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/3k4e_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3k4e ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3k4e" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Hall, T M.T]]
+[[Category: Hall TMT]]
-[[Category: Krahn, J M]]
+[[Category: Krahn JM]]
-[[Category: Stumpf, C R]]
+[[Category: Stumpf CR]]
-[[Category: Wickens, M]]
+[[Category: Wickens M]]
-[[Category: Zhu,D]]
+[[Category: Zhu D]]
-[[Category: Membrane]]
-[[Category: Mitochondrial mrna]]
-[[Category: Mitochondrion]]
-[[Category: Mitochondrion outer membrane]]
-[[Category: Phosphoprotein]]
-[[Category: Puf3]]
-[[Category: Pumilio]]
-[[Category: Rna binding]]
-[[Category: Rna binding protein - rna complex]]
-[[Category: Rna-binding]]

3k4e

From Proteopedia

Current revision

Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox