1d5w: Difference between revisions

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-[[Image:1d5w.gif|left|200px]]
-<!--
+==PHOSPHORYLATED FIXJ RECEIVER DOMAIN==
-The line below this paragraph, containing "STRUCTURE_1d5w", creates the "Structure Box" on the page.
+<StructureSection load='1d5w' size='340' side='right'caption='[[1d5w]], [[Resolution|resolution]] 2.30&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'>[[1d5w]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5W 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1d5w|  PDB=1d5w  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5w OCA], [https://pdbe.org/1d5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5w RCSB], [https://www.ebi.ac.uk/pdbsum/1d5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5w ProSAT]</span></td></tr>
+</table>
-'''PHOSPHORYLATED FIXJ RECEIVER DOMAIN'''
+== Function ==
+[https://www.uniprot.org/uniprot/FIXJ_RHIME FIXJ_RHIME] FixJ, when activated by FixL, induces the expression of both nifA, required for activation of classical nif and fix genes, and fixK, required for FixN activation.
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-BACKGROUND: A variety of bacterial adaptative cellular responses to environmental stimuli are mediated by two-component signal transduction pathways. In these phosphorelay cascades, histidine kinases transphosphorylate a conserved aspartate in the receiver domain, a conserved module in the response regulator superfamily. The main effect of this phosphorylation is to alter the conformation of the response regulator in order to modulate its biological function. The response regulator FixJ displays a typical modular arrangement, with a phosphorylatable N-terminal receiver domain and a C-terminal DNA-binding domain. In the symbiotic bacterium Sinorhizobium meliloti, phosphorylation of this response regulator activates transcription of nitrogen-fixation genes. RESULTS: The crystal structures of the phosphorylated and of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) were solved at 2.3 A and 2.4 A resolution, respectively. They reveal the environment of the phosphoaspartate in the active site and the specific conformational changes leading to activation of the response regulator. Phosphorylation of the conserved aspartate induces major structural changes in the beta 4-alpha 4 loop, and in the signaling surface alpha 4-beta 5 that mediates dimerization of the phosphorylated full-length response regulator. A site-directed mutant at this protein-protein interface decreases the affinity of the phosphorylated response regulator for the fixK promoter tenfold. CONCLUSIONS: The cascade of phosphorylation-induced conformational changes in FixJN illustrates the role of conserved residues in stabilizing the phosphoryl group in the active site, triggering the structural transition and achieving the post-phosphorylation signaling events. We propose that these phosphorylation-induced conformational changes underly the activation of response regulators in general.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/1d5w_consurf.spt"</scriptWhenChecked>
-D5W is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5W OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-Conformational changes induced by phosphorylation of the FixJ receiver domain., Birck C, Mourey L, Gouet P, Fabry B, Schumacher J, Rousseau P, Kahn D, Samama JP, Structure. 1999 Dec 15;7(12):1505-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10647181 10647181]
+</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=1d5w ConSurf].
-[[Category: Single protein]]
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Sinorhizobium meliloti]]
-[[Category: Birck, C.]]
+[[Category: Birck C]]
-[[Category: Fabry, B.]]
+[[Category: Fabry B]]
-[[Category: Gouet, P.]]
+[[Category: Gouet P]]
-[[Category: Kahn, D.]]
+[[Category: Kahn D]]
-[[Category: Mourey, L.]]
+[[Category: Mourey L]]
-[[Category: Rousseau, P.]]
+[[Category: Rousseau P]]
-[[Category: Samama, J P.]]
+[[Category: Samama JP]]
-[[Category: Schumacher, J.]]
+[[Category: Schumacher J]]
-[[Category: Doubly wound five-stranded beta/alpha fold]]
-[[Category: Nitrogen fixation regulation]]
-[[Category: Phosphorylated protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:29:09 2008''