3peu

From Proteopedia

(Difference between revisions)

Current revision

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6

Structural highlights

3peu is a 2 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 2.6Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DBP5_YEAST ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Publication Abstract from PubMed

Superfamily 1 and superfamily 2 RNA helicases are ubiquitous messenger-RNA-protein complex (mRNP) remodelling enzymes that have critical roles in all aspects of RNA metabolism. The superfamily 2 DEAD-box ATPase Dbp5 (human DDX19) functions in mRNA export and is thought to remodel mRNPs at the nuclear pore complex (NPC). Dbp5 is localized to the NPC via an interaction with Nup159 (NUP214 in vertebrates) and is locally activated there by Gle1 together with the small-molecule inositol hexakisphosphate (InsP(6)). Local activation of Dbp5 at the NPC by Gle1 is essential for mRNA export in vivo; however, the mechanistic role of Dbp5 in mRNP export is poorly understood and it is not known how Gle1(InsP6) and Nup159 regulate the activity of Dbp5. Here we report, from yeast, structures of Dbp5 in complex with Gle1(InsP6), Nup159/Gle1(InsP6) and RNA. These structures reveal that InsP(6) functions as a small-molecule tether for the Gle1-Dbp5 interaction. Surprisingly, the Gle1(InsP6)-Dbp5 complex is structurally similar to another DEAD-box ATPase complex essential for translation initiation, eIF4G-eIF4A, and we demonstrate that Gle1(InsP6) and eIF4G both activate their DEAD-box partner by stimulating RNA release. Furthermore, Gle1(InsP6) relieves Dbp5 autoregulation and cooperates with Nup159 in stabilizing an open Dbp5 intermediate that precludes RNA binding. These findings explain how Gle1(InsP6), Nup159 and Dbp5 collaborate in mRNA export and provide a general mechanism for DEAD-box ATPase regulation by Gle1/eIF4G-like activators.

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.,Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K Nature. 2011 Apr 14;472(7342):238-42. Epub 2011 Mar 27. PMID:21441902^[12]

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

References

↑ Tseng SS, Weaver PL, Liu Y, Hitomi M, Tartakoff AM, Chang TH. Dbp5p, a cytosolic RNA helicase, is required for poly(A)+ RNA export. EMBO J. 1998 May 1;17(9):2651-62. PMID:9564047 doi:http://dx.doi.org/10.1093/emboj/17.9.2651
↑ Snay-Hodge CA, Colot HV, Goldstein AL, Cole CN. Dbp5p/Rat8p is a yeast nuclear pore-associated DEAD-box protein essential for RNA export. EMBO J. 1998 May 1;17(9):2663-76. PMID:9564048 doi:http://dx.doi.org/10.1093/emboj/17.9.2663
↑ Schmitt C, von Kobbe C, Bachi A, Pante N, Rodrigues JP, Boscheron C, Rigaut G, Wilm M, Seraphin B, Carmo-Fonseca M, Izaurralde E. Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p. EMBO J. 1999 Aug 2;18(15):4332-47. PMID:10428971 doi:http://dx.doi.org/10.1093/emboj/18.15.4332
↑ Strahm Y, Fahrenkrog B, Zenklusen D, Rychner E, Kantor J, Rosbach M, Stutz F. The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr 255p. EMBO J. 1999 Oct 15;18(20):5761-77. PMID:10610322 doi:10.1093/emboj/18.20.5761
↑ Hodge CA, Colot HV, Stafford P, Cole CN. Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. EMBO J. 1999 Oct 15;18(20):5778-88. PMID:10523319 doi:10.1093/emboj/18.20.5778
↑ Hilleren P, Parker R. Defects in the mRNA export factors Rat7p, Gle1p, Mex67p, and Rat8p cause hyperadenylation during 3'-end formation of nascent transcripts. RNA. 2001 May;7(5):753-64. PMID:11350039
↑ Hammell CM, Gross S, Zenklusen D, Heath CV, Stutz F, Moore C, Cole CN. Coupling of termination, 3' processing, and mRNA export. Mol Cell Biol. 2002 Sep;22(18):6441-57. PMID:12192043
↑ Estruch F, Cole CN. An early function during transcription for the yeast mRNA export factor Dbp5p/Rat8p suggested by its genetic and physical interactions with transcription factor IIH components. Mol Biol Cell. 2003 Apr;14(4):1664-76. PMID:12686617 doi:http://dx.doi.org/10.1091/mbc.E02-09-0602
↑ Takemura R, Inoue Y, Izawa S. Stress response in yeast mRNA export factor: reversible changes in Rat8p localization are caused by ethanol stress but not heat shock. J Cell Sci. 2004 Aug 15;117(Pt 18):4189-97. Epub 2004 Jul 27. PMID:15280434 doi:http://dx.doi.org/10.1242/jcs.01296
↑ Weirich CS, Erzberger JP, Berger JM, Weis K. The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore. Mol Cell. 2004 Dec 3;16(5):749-60. PMID:15574330 doi:10.1016/j.molcel.2004.10.032
↑ Estruch F, Hodge CA, Rodriguez-Navarro S, Cole CN. Physical and genetic interactions link the yeast protein Zds1p with mRNA nuclear export. J Biol Chem. 2005 Mar 11;280(10):9691-7. Epub 2004 Dec 24. PMID:15619606 doi:http://dx.doi.org/M413025200
↑ Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K. A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature. 2011 Apr 14;472(7342):238-42. Epub 2011 Mar 27. PMID:21441902 doi:10.1038/nature09862

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3peu"

@@ Line 3: / Line 3: @@
 <StructureSection load='3peu' size='340' side='right'caption='[[3peu]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3peu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PEU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3peu]] is a 2 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=3PEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PEU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.6&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), BRR3, D1049, GLE1, RSS1, YDL207W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=3peu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3peu OCA], [https://pdbe.org/3peu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3peu RCSB], [https://www.ebi.ac.uk/pdbsum/3peu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3peu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST]] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>  [[https://www.uniprot.org/uniprot/GLE1_YEAST GLE1_YEAST]] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. It is specifically involved in a terminal step of poly(A)+ mRNA transport through the NPC probably by binding the ATP-dependent RNA helicase DBP5 and GFD1 at the cytoplasmic side of the NPC. These interactions are thought to be important for the dissociation of transport proteins such as the heterogeneous nuclear ribonuleoprotein (hnRNP) NAB2 from exported mRNA.<ref>PMID:10523319</ref> <ref>PMID:10610322</ref> <ref>PMID:10684247</ref> <ref>PMID:11336711</ref> <ref>PMID:15208322</ref>
+[https://www.uniprot.org/uniprot/DBP5_YEAST DBP5_YEAST] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. Contributes to the blocking of bulk poly(A)+ mRNA export in ethanol-stressed cells. May also be involved in early transcription.<ref>PMID:9564047</ref> <ref>PMID:9564048</ref> <ref>PMID:10428971</ref> <ref>PMID:10610322</ref> <ref>PMID:10523319</ref> <ref>PMID:11350039</ref> <ref>PMID:12192043</ref> <ref>PMID:12686617</ref> <ref>PMID:15280434</ref> <ref>PMID:15574330</ref> <ref>PMID:15619606</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: RNA helicase]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Berger, J M]]
+[[Category: Berger JM]]
-[[Category: Helmke, K J]]
+[[Category: Helmke KJ]]
-[[Category: Montpetit, B]]
+[[Category: Montpetit B]]
-[[Category: Seeliger, M A]]
+[[Category: Seeliger MA]]
-[[Category: Thomsen, N D]]
+[[Category: Thomsen ND]]
-[[Category: Weis, K]]
+[[Category: Weis K]]
-[[Category: Atpase]]
-[[Category: Dead-box]]
-[[Category: Heat]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Mrna export]]
-[[Category: Nuclear pore]]
-[[Category: Reca]]

3peu

From Proteopedia

Current revision

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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