View source for 2dwk


==Crystal structure of the RUN domain of mouse Rap2 interacting protein x==
<StructureSection load='2dwk' size='340' side='right'caption='[[2dwk]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2dwk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wus 1wus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWK FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2cxf|2cxf]], [[2cxl|2cxl]], [[2dwg|2dwg]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rufy3, D5Bwg0860e, Ripx ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=2dwk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dwk OCA], [https://pdbe.org/2dwk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dwk RCSB], [https://www.ebi.ac.uk/pdbsum/2dwk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dwk ProSAT], [https://www.topsan.org/Proteins/RSGI/2dwk TOPSAN]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/RUFY3_MOUSE RUFY3_MOUSE]] Implicated in the formation of a single axon by developing neurons. May inhibit the formation of additional axons by inhibition of PI3K in minor neuronal processes (By similarity). 
== 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/dw/2dwk_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=2dwk ConSurf].
<div style="clear:both"></div>
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== Publication Abstract from PubMed ==
Rap2-interacting protein x (RPIPx) is a homolog of RPIP8, a specific effector of Rap2 GTPase. The N-terminal region of RPIP8, which contains the RUN domain, interacts with Rap2. Using cell-free synthesis and NMR, we determined that the region encompassing residues 83-255 of mouse RPIPx, which is 40-residues larger than the predicted RUN domain (residues 113-245), is the minimum fragment that forms a correctly folded protein. This fragment, the RPIPx RUN domain, interacted specifically with Rap2B in vitro in a nucleotide-dependent manner. The crystal structure of the RPIPx RUN domain was determined at 2.0 A of resolution by the multiwavelength anomalous dispersion (MAD) method. The RPIPx RUN domain comprises eight anti-parallel alpha-helices, which form an extensive hydrophobic core, followed by an extended segment. The residues in the core region are highly conserved, suggesting the conservation of the RUN domain-fold among the RUN domain-containing proteins. The residues forming a positively charged surface are conserved between RPIP8 and its homologs, suggesting that this surface is important for Rap2 binding. In the crystal the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner.

Crystal structure of the RUN domain of the RAP2-interacting protein x.,Kukimoto-Niino M, Takagi T, Akasaka R, Murayama K, Uchikubo-Kamo T, Terada T, Inoue M, Watanabe S, Tanaka A, Hayashizaki Y, Kigawa T, Shirouzu M, Yokoyama S J Biol Chem. 2006 Oct 20;281(42):31843-53. Epub 2006 Aug 23. PMID:16928684<ref>PMID:16928684</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 2dwk" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Lk3 transgenic mice]]
[[Category: Kukimoto-Niino, M]]
[[Category: Murayama, K]]
[[Category: Structural genomic]]
[[Category: Shirouzu, M]]
[[Category: Yokoyama, S]]
[[Category: Bundle]]
[[Category: Effector]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Protein binding]]
[[Category: Rap2]]
[[Category: Rsgi]]
[[Category: Run domain]]