2rkn: Difference between revisions

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-{{Seed}}
-[[Image:2rkn.jpg|left|200px]]
-<!--
+==X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana==
-The line below this paragraph, containing "STRUCTURE_2rkn", creates the "Structure Box" on the page.
+<StructureSection load='2rkn' size='340' side='right'caption='[[2rkn]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2rkn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RKN FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LP3:(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM+4-OXIDE'>LP3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2rkn|  PDB=2rkn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkn OCA], [https://pdbe.org/2rkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rkn RCSB], [https://www.ebi.ac.uk/pdbsum/2rkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rkn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DIRL1_ARATH DIRL1_ARATH] Putative lipid transfer protein required for systemic acquired resistance (SAR) long distance signaling. May interact with a lipid-derived molecule to promote long distance signaling associated with SAR. Together with AZI1, required for glycerol-3-phosphate- (G3P) and azelaic acid- (AA) induced systemic acquired resistance (SAR). Component of plant systemic immunity involved in priming defenses in a AA-dependent manner, by modulating production and/or translocation of a mobile signal(s) during SAR.<ref>PMID:12353036</ref> <ref>PMID:23602565</ref>
+== 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/rk/2rkn_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=2rkn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Screening of transfer DNA (tDNA) tagged lines of Arabidopsis thaliana for mutants defective in systemic acquired resistance led to the characterization of dir1-1 (defective in induced resistance [systemic acquired resistance, SAR]) mutant. It has been suggested that the protein encoded by the dir1 gene, i.e., DIR1, is involved in the long distance signaling associated with SAR. DIR1 displays the cysteine signature of lipid transfer proteins, suggesting that the systemic signal could be lipid molecules. However, previous studies have shown that this signature is not sufficient to define a lipid transfer protein, i.e., a protein capable of binding lipids. In this context, the lipid binding properties and the structure of a DIR1-lipid complex were both determined by fluorescence and X-ray diffraction. DIR1 is able to bind with high affinity two monoacylated phospholipids (dissociation constant in the nanomolar range), mainly lysophosphatidyl cholines, side-by-side in a large internal tunnel. Although DIR1 shares some structural and lipid binding properties with plant LTP2, it displays some specific features that define DIR1 as a new type of plant lipid transfer protein. The signaling function associated with DIR1 may be related to a specific lipid transport that needs to be characterized and to an additional mechanism of recognition by a putative receptor, as the structure displays on the surface the characteristic PxxP structural motif reminiscent of SH3 domain signaling pathways.
-===X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana===
+The structure of "defective in induced resistance" protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein.,Lascombe MB, Bakan B, Buhot N, Marion D, Blein JP, Larue V, Lamb C, Prange T Protein Sci. 2008 Sep;17(9):1522-30. Epub 2008 Jun 13. PMID:18552128<ref>PMID:18552128</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18552128}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2rkn" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18552128 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18552128}}
+__TOC__
+</StructureSection>
-==About this Structure==
-RKN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKN OCA].
-==Reference==
-The structure of "defective in induced resistance" protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein., Lascombe MB, Bakan B, Buhot N, Marion D, Blein JP, Larue V, Lamb C, Prange T, Protein Sci. 2008 Sep;17(9):1522-30. Epub 2008 Jun 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18552128 18552128]
-Crystallization of DIR1, a LTP2-like resistance signalling protein from Arabidopsis thaliana., Lascombe MB, Buhot N, Bakan B, Marion D, Blein JP, Lamb CJ, Prange T, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jul 1;62(Pt, 7):702-4. Epub 2006 Jun 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16820699 16820699]
 [[Category: Arabidopsis thaliana]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bakan, B.]]
+[[Category: Bakan B]]
-[[Category: Buhot, N.]]
+[[Category: Buhot N]]
-[[Category: Lamb, C.]]
+[[Category: Lamb C]]
-[[Category: Lascombe, M B.]]
+[[Category: Lascombe MB]]
-[[Category: Marion, D.]]
+[[Category: Marion D]]
-[[Category: Prange, T.]]
+[[Category: Prange T]]
-[[Category: Defense signaling protein]]
-[[Category: Lipid transport]]
-[[Category: Ltp]]
-[[Category: Signaling protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep  3 13:07:20 2008''