2kbe: Difference between revisions

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-[[Image:2kbe.png|left|200px]]
-{{STRUCTURE_2kbe|  PDB=2kbe  |  SCENE=  }}
+==solution structure of amino-terminal domain of Dbp5p==
+<StructureSection load='2kbe' size='340' side='right'caption='[[2kbe]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2kbe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KBE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2kbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kbe OCA], [https://pdbe.org/2kbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kbe RCSB], [https://www.ebi.ac.uk/pdbsum/2kbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kbe 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>
+== 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/kb/2kbe_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/main_output.php?pdb_ID=2kbe ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DEAD-box protein 5 (Dbp5p) plays very important roles in RNA metabolism from transcription, to translation, to RNA decay. It is an RNA helicase and functions as an essential RNA export factor from nucleus. Here, we report the solution NMR structures of the N- and C-terminal domains (NTD and CTD, respectively) of Dbp5p from Saccharomyces cerevisiae (ScDbp5p) and X-ray crystal structure of Dbp5p from Schizosaccharomyces pombe (SpDbp5p) in the absence of nucleotides and RNA. The crystal structure clearly shows that SpDbp5p comprises two RecA-like domains that do not interact with each other. NMR results show that the N-terminal flanking region of ScDpbp5 (M1-E70) is intrinsically unstructured and the region Y71-R121 including the Q motif is highly dynamic on millisecond-microsecond timescales in solution. The C-terminal flanking region of ScDbp5p forms a short beta-strand and a long helix. This helix is unique for ScDbp5p and has not been observed in other DEAD-box proteins. Compared with other DEAD-box proteins, Dbp5p has an extra insert with six residues in the CTD. NMR structure reveals that the insert is located in a solvent-exposed loop capable of interacting with other proteins. ATP and ADP titration experiments show that both ADP and ATP bind to the consensus binding site in the NTD of ScDbp5p but do not interact with the CTD at all. Binding of ATP or ADP to NTD induces significant conformational rearrangement too.
-===solution structure of amino-terminal domain of Dbp5p===
+Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides.,Fan JS, Cheng Z, Zhang J, Noble C, Zhou Z, Song H, Yang D J Mol Biol. 2009 Apr 24;388(1):1-10. Epub 2009 Mar 10. PMID:19281819<ref>PMID:19281819</ref>
-{{ABSTRACT_PUBMED_19281819}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2kbe" style="background-color:#fffaf0;"></div>
-[[2kbe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBE OCA].
 ==See Also==
-*[[Helicase|Helicase]]
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019281819</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Fan, J S.]]
+[[Category: Fan JS]]
-[[Category: Yang, D.]]
+[[Category: Yang D]]
-[[Category: Zhang, J.]]
+[[Category: Zhang J]]
-[[Category: Atp-binding]]
-[[Category: Dbp5p]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Membrane]]
-[[Category: Mrna transport]]
-[[Category: Nuclear pore complex]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Protein transport]]
-[[Category: Rna-binding]]
-[[Category: Translocation]]
-[[Category: Transport]]