5elx: Difference between revisions

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New page: '''Unreleased structure''' The entry 5elx is ON HOLD Authors: Merchant, M.K., Modis, Y. Description: S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 [[Category: Unreleased Structures...
 
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'''Unreleased structure'''


The entry 5elx is ON HOLD
==S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3==
<StructureSection load='5elx' size='340' side='right'caption='[[5elx]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5elx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_YJM789 Saccharomyces cerevisiae YJM789]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ELX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ELX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=M2A:[(2~{R},3~{R},4~{R},5~{S})-2-(6-AMINOPURIN-9-YL)-4-OXIDANYL-5-[[OXIDANYL(PHOSPHONOOXY)PHOSPHORYL]OXYMETHYL]OXOLAN-3-YL]+2-(METHYLAMINO)BENZOATE'>M2A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></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=5elx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5elx OCA], [https://pdbe.org/5elx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5elx RCSB], [https://www.ebi.ac.uk/pdbsum/5elx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5elx 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>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
mRNA export from the nucleus depends on the ATPase activity of the DEAD-box protein Dbp5/DDX19. Although Dbp5 has measurable ATPase activity alone, several regulatory factors (e.g., RNA, nucleoporin proteins, and the endogenous small molecule InsP6) modulate catalytic activity in vitro and in vivo to facilitate mRNA export. An analysis of the intrinsic and regulator-activated Dbp5 ATPase cycle is necessary to define how these factors control Dbp5 and mRNA export. Here, we report a kinetic and equilibrium analysis of the Saccharomyces cerevisiae Dbp5 ATPase cycle, including the influence of RNA on Dbp5 activity. These data show that ATP binds Dbp5 weakly in rapid equilibrium with a binding affinity (KT~4mM) comparable to the KM for steady-state cycling, while ADP binds an order of magnitude more tightly (KD~0.4mM). The overall intrinsic steady-state cycling rate constant (kcat) is limited by slow, near-irreversible ATP hydrolysis and even slower subsequent phosphate release. RNA increases kcat and rate-limiting Pi release 20-fold, although Pi release continues to limit steady-state cycling in the presence of RNA, in conjunction with RNA binding. Together, this work identifies RNA binding and Pi release as important biochemical transitions within the Dbp5 ATPase cycle and provides a framework for investigating the means by which Dbp5 and mRNA export is modulated by regulatory factors.


Authors: Merchant, M.K., Modis, Y.
Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).,Wong EV, Cao W, Voros J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM J Mol Biol. 2016 Jan 29;428(2 Pt B):492-508. doi: 10.1016/j.jmb.2015.12.018. Epub, 2015 Dec 28. PMID:26730886<ref>PMID:26730886</ref>


Description: S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Merchant, M.K]]
<div class="pdbe-citations 5elx" style="background-color:#fffaf0;"></div>
[[Category: Modis, Y]]
 
==See Also==
*[[Helicase 3D structures|Helicase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae YJM789]]
[[Category: Merchant MK]]
[[Category: Modis Y]]

Latest revision as of 09:33, 5 July 2023

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3

Structural highlights

5elx is a 2 chain structure with sequence from Saccharomyces cerevisiae YJM789. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.81Å
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

mRNA export from the nucleus depends on the ATPase activity of the DEAD-box protein Dbp5/DDX19. Although Dbp5 has measurable ATPase activity alone, several regulatory factors (e.g., RNA, nucleoporin proteins, and the endogenous small molecule InsP6) modulate catalytic activity in vitro and in vivo to facilitate mRNA export. An analysis of the intrinsic and regulator-activated Dbp5 ATPase cycle is necessary to define how these factors control Dbp5 and mRNA export. Here, we report a kinetic and equilibrium analysis of the Saccharomyces cerevisiae Dbp5 ATPase cycle, including the influence of RNA on Dbp5 activity. These data show that ATP binds Dbp5 weakly in rapid equilibrium with a binding affinity (KT~4mM) comparable to the KM for steady-state cycling, while ADP binds an order of magnitude more tightly (KD~0.4mM). The overall intrinsic steady-state cycling rate constant (kcat) is limited by slow, near-irreversible ATP hydrolysis and even slower subsequent phosphate release. RNA increases kcat and rate-limiting Pi release 20-fold, although Pi release continues to limit steady-state cycling in the presence of RNA, in conjunction with RNA binding. Together, this work identifies RNA binding and Pi release as important biochemical transitions within the Dbp5 ATPase cycle and provides a framework for investigating the means by which Dbp5 and mRNA export is modulated by regulatory factors.

Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).,Wong EV, Cao W, Voros J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM J Mol Biol. 2016 Jan 29;428(2 Pt B):492-508. doi: 10.1016/j.jmb.2015.12.018. Epub, 2015 Dec 28. PMID:26730886[12]

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. ↑ Wong EV, Cao W, Voros J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM. Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5). J Mol Biol. 2016 Jan 29;428(2 Pt B):492-508. doi: 10.1016/j.jmb.2015.12.018. Epub, 2015 Dec 28. PMID:26730886 doi:http://dx.doi.org/10.1016/j.jmb.2015.12.018

5elx, resolution 1.81Å

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