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==S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp==
==S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp==
<StructureSection load='3rrm' size='340' side='right' caption='[[3rrm]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='3rrm' size='340' side='right' caption='[[3rrm]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rrm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3pez 3pez]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RRM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RRM FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rrm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3pez 3pez]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RRM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RRM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rrn|3rrn]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rrn|3rrn]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), BRR3, D1049, GLE1, RSS1, YDL207W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), NUP158, NUP159, RAT7, YIL115C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DBP5, RAT8, YOR046C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), BRR3, D1049, GLE1, RSS1, YDL207W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), NUP158, NUP159, RAT7, YIL115C ([http://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'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rrm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rrm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rrm RCSB], [http://www.ebi.ac.uk/pdbsum/3rrm PDBsum]</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=3rrm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rrm OCA], [http://pdbe.org/3rrm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rrm RCSB], [http://www.ebi.ac.uk/pdbsum/3rrm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rrm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
Line 19: Line 20:
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 3rrm" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 27: Line 29:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 18824]]
[[Category: RNA helicase]]
[[Category: RNA helicase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Berger, J M]]
[[Category: Berger, J M]]
[[Category: Helmke, K J]]
[[Category: Helmke, K J]]

Revision as of 01:17, 5 August 2016

S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adpS. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp

Structural highlights

3rrm is a 3 chain structure with sequence from Atcc 18824. This structure supersedes the now removed PDB entry 3pez. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Gene:DBP5, RAT8, YOR046C (ATCC 18824), BRR3, D1049, GLE1, RSS1, YDL207W (ATCC 18824), NUP158, NUP159, RAT7, YIL115C (ATCC 18824)
Activity:RNA helicase, with EC number 3.6.4.13
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] [NU159_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. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP159 plays an important role in several nuclear export pathways including poly(A)+ RNA, pre-ribosome, and protein export.[12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [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.[25] [26] [27] [28] [29]

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[30]

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

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ Hurwitz ME, Strambio-de-Castillia C, Blobel G. Two yeast nuclear pore complex proteins involved in mRNA export form a cytoplasmically oriented subcomplex. Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11241-5. PMID:9736720
  13. ↑ Belgareh N, Snay-Hodge C, Pasteau F, Dagher S, Cole CN, Doye V. Functional characterization of a Nup159p-containing nuclear pore subcomplex. Mol Biol Cell. 1998 Dec;9(12):3475-92. PMID:9843582
  14. ↑ Seedorf M, Damelin M, Kahana J, Taura T, Silver PA. Interactions between a nuclear transporter and a subset of nuclear pore complex proteins depend on Ran GTPase. Mol Cell Biol. 1999 Feb;19(2):1547-57. PMID:9891088
  15. ↑ 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
  16. ↑ Bailer SM, Balduf C, Katahira J, Podtelejnikov A, Rollenhagen C, Mann M, Pante N, Hurt E. Nup116p associates with the Nup82p-Nsp1p-Nup159p nucleoporin complex. J Biol Chem. 2000 Aug 4;275(31):23540-8. PMID:10801828 doi:http://dx.doi.org/10.1074/jbc.M001963200
  17. ↑ Strasser K, Bassler J, Hurt E. Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export. J Cell Biol. 2000 Aug 21;150(4):695-706. PMID:10952996
  18. ↑ Allen NP, Huang L, Burlingame A, Rexach M. Proteomic analysis of nucleoporin interacting proteins. J Biol Chem. 2001 Aug 3;276(31):29268-74. Epub 2001 May 31. PMID:11387327 doi:http://dx.doi.org/10.1074/jbc.M102629200
  19. ↑ Gleizes PE, Noaillac-Depeyre J, Leger-Silvestre I, Teulieres F, Dauxois JY, Pommet D, Azum-Gelade MC, Gas N. Ultrastructural localization of rRNA shows defective nuclear export of preribosomes in mutants of the Nup82p complex. J Cell Biol. 2001 Dec 10;155(6):923-36. Epub 2001 Dec 10. PMID:11739405 doi:http://dx.doi.org/10.1083/jcb.200108142
  20. ↑ Bailer SM, Balduf C, Hurt E. The Nsp1p carboxy-terminal domain is organized into functionally distinct coiled-coil regions required for assembly of nucleoporin subcomplexes and nucleocytoplasmic transport. Mol Cell Biol. 2001 Dec;21(23):7944-55. PMID:11689687 doi:http://dx.doi.org/10.1128/MCB.21.23.7944-7955.2001
  21. ↑ Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec;1(12):930-46. PMID:12543930
  22. ↑ Denning DP, Patel SS, Uversky V, Fink AL, Rexach M. Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2450-5. Epub 2003 Feb 25. PMID:12604785 doi:10.1073/pnas.0437902100
  23. ↑ Strawn LA, Shen T, Shulga N, Goldfarb DS, Wente SR. Minimal nuclear pore complexes define FG repeat domains essential for transport. Nat Cell Biol. 2004 Mar;6(3):197-206. Epub 2004 Feb 22. PMID:15039779 doi:10.1038/ncb1097
  24. ↑ 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
  25. ↑ 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
  26. ↑ 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
  27. ↑ Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 2000 Feb 21;148(4):635-51. PMID:10684247
  28. ↑ Jensen TH, Patricio K, McCarthy T, Rosbash M. A block to mRNA nuclear export in S. cerevisiae leads to hyperadenylation of transcripts that accumulate at the site of transcription. Mol Cell. 2001 Apr;7(4):887-98. PMID:11336711
  29. ↑ Suntharalingam M, Alcazar-Roman AR, Wente SR. Nuclear export of the yeast mRNA-binding protein Nab2 is linked to a direct interaction with Gfd1 and to Gle1 function. J Biol Chem. 2004 Aug 20;279(34):35384-91. Epub 2004 Jun 18. PMID:15208322 doi:10.1074/jbc.M402044200
  30. ↑ 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

3rrm, resolution 2.90Å

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