This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1d5w

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:46, 13 March 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1d5w.gif|left|200px]]
 
-
{{Structure
+
==PHOSPHORYLATED FIXJ RECEIVER DOMAIN==
-
|PDB= 1d5w |SIZE=350|CAPTION= <scene name='initialview01'>1d5w</scene>, resolution 2.30&Aring;
+
<StructureSection load='1d5w' size='340' side='right'caption='[[1d5w]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+
<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>
-
|ACTIVITY=
+
</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>
-
|GENE=
+
<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>
-
|DOMAIN=
+
<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>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5w OCA], [http://www.ebi.ac.uk/pdbsum/1d5w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d5w RCSB]</span>
+
== 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 ==
-
'''PHOSPHORYLATED FIXJ RECEIVER DOMAIN'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/1d5w_consurf.spt"</scriptWhenChecked>
-
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.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1D5W 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].
+
</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].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
__TOC__
-
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]
+
</StructureSection>
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
[[Category: Sinorhizobium meliloti]]
[[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 Sun Mar 30 19:35:15 2008''
+

Current revision

PHOSPHORYLATED FIXJ RECEIVER DOMAIN

PDB ID 1d5w

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d5w"
Personal tools