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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8ark]] is a 3 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=8ARK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ARK FirstGlance]. <br>
<table><tr><td colspan='2'>[[8ark]] is a 3 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=8ARK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ARK FirstGlance]. <br>
</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=8ark FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ark OCA], [https://pdbe.org/8ark PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ark RCSB], [https://www.ebi.ac.uk/pdbsum/8ark PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ark ProSAT]</span></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]] 3.22&#8491;</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=8ark FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ark OCA], [https://pdbe.org/8ark PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ark RCSB], [https://www.ebi.ac.uk/pdbsum/8ark PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ark ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/DBP2_YEAST DBP2_YEAST] ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing (PubMed:11585918, PubMed:7883168). Associates directly with chromatin, correlating with transcriptional activity (PubMed:22679025). Required for assembly of mRNA-binding proteins YRA1, NAB2, and MEX67 onto poly(A)+ RNA (PubMed:23721653).<ref>PMID:11585918</ref> <ref>PMID:22679025</ref> <ref>PMID:23721653</ref> <ref>PMID:7883168</ref>  
[https://www.uniprot.org/uniprot/DBP2_YEAST DBP2_YEAST] ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing (PubMed:11585918, PubMed:7883168). Associates directly with chromatin, correlating with transcriptional activity (PubMed:22679025). Required for assembly of mRNA-binding proteins YRA1, NAB2, and MEX67 onto poly(A)+ RNA (PubMed:23721653).<ref>PMID:11585918</ref> <ref>PMID:22679025</ref> <ref>PMID:23721653</ref> <ref>PMID:7883168</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Human DDX5 and its yeast ortholog Dbp2 are ATP-dependent RNA helicases that play a key role in normal cell processes, cancer development and viral infection. The crystal structure of the RecA1-like domain of DDX5 is available, but the global structure of DDX5/Dbp2 subfamily proteins remains to be elucidated. Here, we report the first X-ray crystal structures of the Dbp2 helicase core alone and in complex with adenosine diphosphate nucleotide (ADP) at 3.22 A and 3.05 A resolutions, respectively. The structures of the ADP-bound post-hydrolysis state and apo-state demonstrate the conformational changes that occur when the nucleotides are released. Our results showed that the helicase core of Dbp2 shifted between open and closed conformation in solution, but the unwinding activity was hindered when the helicase core was restricted to a single conformation. A small-angle X-ray scattering (SAXS) experiment showed that the disordered amino- (N-) and carboxy- (C-) tails are flexible in solution. Truncation mutations confirmed that the N- and C-tails were critical for the nucleic acid binding, ATPase, and unwinding activities, with the C-tail being exclusively responsible for the annealing activity. Furthermore, we labeled the terminal tails to observe the conformational changes between the disordered tails and the helicase core upon binding nucleic acid substrates. Specifically, we found that the nonstructural N- and C-tails bind to RNA substrates and tether them to the helicase core domain, thereby conferring full helicase activities to the Dbp2 protein. This distinct structural characteristic provides new insight into the mechanism of DEAD-box RNA helicases.
Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.,Song QX, Liu NN, Liu ZX, Zhang YZ, Rety S, Hou XM, Xi XG J Biol Chem. 2023 Mar 7:104592. doi: 10.1016/j.jbc.2023.104592. PMID:36894019<ref>PMID:36894019</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 8ark" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==

Latest revision as of 08:13, 7 February 2024

Crystal structure of DEAD-box protein Dbp2 in apo form

8ark, resolution 3.22Å

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