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[[Image:1vec.jpg|left|200px]]
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{{STRUCTURE_1vec|  PDB=1vec  |  SCENE=  }}
'''Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein'''


==Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein==
<StructureSection load='1vec' size='340' side='right'caption='[[1vec]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vec]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VEC 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]] 2.01&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vec OCA], [https://pdbe.org/1vec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vec RCSB], [https://www.ebi.ac.uk/pdbsum/1vec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vec ProSAT]</span></td></tr>
</table>
== Disease ==
[https://www.uniprot.org/uniprot/DDX6_HUMAN DDX6_HUMAN] Note=A chromosomal aberration involving DDX6 may be a cause of hematopoietic tumors such as B-cell lymphomas. Translocation t(11;14)(q23;q32).
== Function ==
[https://www.uniprot.org/uniprot/DDX6_HUMAN DDX6_HUMAN] In the process of mRNA degradation, may play a role in mRNA decapping.
== 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/ve/1vec_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1vec ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B-cell lymphoma, is a member of the DEAD-box RNA helicase family. Here, the crystal structure of Nc-rck/p54, the N-terminal core domain of rck/p54, revealed that the P-loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P-loop. The results of dynamic light scattering revealed to ATP-induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N-terminal core and C-terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c-myc IRES RNA, whose secondary structure regulates IRES-dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over-expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down-regulation of c-myc expression. These findings altogether suggest that rck/p54 may affect the IRES-dependent translation of c-myc even in the cells.


==Overview==
Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes.,Matsui T, Hogetsu K, Usukura J, Sato T, Kumasaka T, Akao Y, Tanaka N Genes Cells. 2006 Apr;11(4):439-52. PMID:16611246<ref>PMID:16611246</ref>
Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B-cell lymphoma, is a member of the DEAD-box RNA helicase family. Here, the crystal structure of Nc-rck/p54, the N-terminal core domain of rck/p54, revealed that the P-loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P-loop. The results of dynamic light scattering revealed to ATP-induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N-terminal core and C-terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c-myc IRES RNA, whose secondary structure regulates IRES-dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over-expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down-regulation of c-myc expression. These findings altogether suggest that rck/p54 may affect the IRES-dependent translation of c-myc even in the cells.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1VEC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VEC OCA].
</div>
<div class="pdbe-citations 1vec" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes., Matsui T, Hogetsu K, Usukura J, Sato T, Kumasaka T, Akao Y, Tanaka N, Genes Cells. 2006 Apr;11(4):439-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16611246 16611246]
*[[Helicase 3D structures|Helicase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hogetsu, K.]]
[[Category: Hogetsu K]]
[[Category: Kumasaka, T.]]
[[Category: Kumasaka T]]
[[Category: Matsui, T.]]
[[Category: Matsui T]]
[[Category: Sato, T.]]
[[Category: Sato T]]
[[Category: Tanaka, M.]]
[[Category: Tanaka M]]
[[Category: Tanaka, N.]]
[[Category: Tanaka N]]
[[Category: Yukihiro, Y.]]
[[Category: Yukihiro Y]]
[[Category: Dead-box protein]]
[[Category: Rna binding protein]]
[[Category: Rna helicase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:21:11 2008''

Latest revision as of 07:33, 30 October 2024

Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein

1vec, resolution 2.01Å

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