1wrb: Difference between revisions

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<StructureSection load='1wrb' size='340' side='right'caption='[[1wrb]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1wrb' size='340' side='right'caption='[[1wrb]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1wrb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dugja Dugja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WRB FirstGlance]. <br>
<table><tr><td colspan='2'>[[1wrb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dugesia_japonica Dugesia japonica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WRB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1wrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wrb OCA], [https://pdbe.org/1wrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wrb RCSB], [https://www.ebi.ac.uk/pdbsum/1wrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wrb ProSAT], [https://www.topsan.org/Proteins/RSGI/1wrb TOPSAN]</span></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=1wrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wrb OCA], [https://pdbe.org/1wrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wrb RCSB], [https://www.ebi.ac.uk/pdbsum/1wrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wrb ProSAT], [https://www.topsan.org/Proteins/RSGI/1wrb TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O97032_DUGJA O97032_DUGJA]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1wrb ConSurf].
</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=1wrb ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Dugesia japonica vasa-like gene B (DjVLGB) protein is a DEAD-box RNA helicase of a planarian, which is well known for its strong regenerative capacity. DjVLGB shares sequence similarity to the Drosophila germ-line-specific DEAD-box RNA helicase Vasa, and even higher similarity to its paralogue, mouse PL10. In this study, we solved the crystal structure of the DjVLGB N-terminal RecA-like domain. The overall fold and the structures of the putative ATPase active site of the DjVLGB N-terminal RecA-like domain are similar to those of the previously reported DEAD-box RNA helicase structures. In contrast, the surface structure of the side opposite to the putative ATPase active site is different from those of the other DEAD-box RNA helicases; the characteristic hydrophobic pockets are formed with aromatic and proline residues. These pocket-forming residues are conserved in the PL10-subfamily proteins, but less conserved in the Vasa orthologues and not conserved in the DEAD-box RNA helicases. Therefore, the structural features that we found are characteristic of the PL10-subfamily proteins and might contribute to their biological roles in germ-line development.
Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein.,Kurimoto K, Muto Y, Obayashi N, Terada T, Shirouzu M, Yabuki T, Aoki M, Seki E, Matsuda T, Kigawa T, Okumura H, Tanaka A, Shibata N, Kashikawa M, Agata K, Yokoyama S J Struct Biol. 2005 Apr;150(1):58-68. PMID:15797730<ref>PMID:15797730</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1wrb" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dugja]]
[[Category: Dugesia japonica]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Agata, K]]
[[Category: Agata K]]
[[Category: Aoki, M]]
[[Category: Aoki M]]
[[Category: Kashikawa, M]]
[[Category: Kashikawa M]]
[[Category: Kigawa, T]]
[[Category: Kigawa T]]
[[Category: Kurimoto, K]]
[[Category: Kurimoto K]]
[[Category: Matsuda, T]]
[[Category: Matsuda T]]
[[Category: Muto, Y]]
[[Category: Muto Y]]
[[Category: Obayashi, N]]
[[Category: Obayashi N]]
[[Category: Okumura, H]]
[[Category: Okumura H]]
[[Category: Structural genomic]]
[[Category: Seki E]]
[[Category: Seki, E]]
[[Category: Shibata N]]
[[Category: Shibata, N]]
[[Category: Shirouzu M]]
[[Category: Shirouzu, M]]
[[Category: Tanaka A]]
[[Category: Tanaka, A]]
[[Category: Terada T]]
[[Category: Terada, T]]
[[Category: Yabuki T]]
[[Category: Yabuki, T]]
[[Category: Yokoyama S]]
[[Category: Yokoyama, S]]
[[Category: Dead box]]
[[Category: Hydrolase]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Rna helicase]]
[[Category: Rsgi]]
[[Category: Vasa]]

Latest revision as of 13:33, 13 March 2024

Crystal structure of the N-terminal RecA-like domain of DjVLGB, a pranarian Vasa-like RNA helicase

1wrb, resolution 2.40Å

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