2kbe: Difference between revisions
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[[Image: | ==solution structure of amino-terminal domain of Dbp5p== | ||
<StructureSection load='2kbe' size='340' side='right' caption='[[2kbe]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KBE FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2kbf|2kbf]]</td></tr> | |||
<tr><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])</td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kbe RCSB], [http://www.ebi.ac.uk/pdbsum/2kbe PDBsum]</span></td></tr> | |||
<table> | |||
== 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/chain_selection.php?pdb_ID=2ata 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 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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Helicase|Helicase]] | *[[Helicase|Helicase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Fan, J S.]] | [[Category: Fan, J S.]] | ||
Revision as of 06:51, 29 September 2014
solution structure of amino-terminal domain of Dbp5psolution structure of amino-terminal domain of Dbp5p
Structural highlights
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 PubMedDEAD-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 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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