1je8: Difference between revisions

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-[[Image:1je8.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1je8", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1je8|  PDB=1je8  |  SCENE=  }}
-'''Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site'''
+==Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site==
+<StructureSection load='1je8' size='340' side='right'caption='[[1je8]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1je8]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JE8 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]] 2.12&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1je8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1je8 OCA], [https://pdbe.org/1je8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1je8 RCSB], [https://www.ebi.ac.uk/pdbsum/1je8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1je8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NARL_ECOLI NARL_ECOLI] This protein activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal transmitted by either the NarX or NarQ proteins.
+== 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/je/1je8_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=1je8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.
-==Overview==
+Dimerization allows DNA target site recognition by the NarL response regulator.,Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE Nat Struct Biol. 2002 Oct;9(10):771-8. PMID:12352954<ref>PMID:12352954</ref>
-Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-JE8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JE8 OCA].
+</div>
+<div class="pdbe-citations 1je8" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Dimerization allows DNA target site recognition by the NarL response regulator., Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE, Nat Struct Biol. 2002 Oct;9(10):771-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12352954 12352954]
+*[[Response regulator 3D structure|Response regulator 3D structure]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bearson, S M.D.]]
+[[Category: Bearson SMD]]
-[[Category: Dickerson, R E.]]
+[[Category: Dickerson RE]]
-[[Category: Gunsalus, R P.]]
+[[Category: Gunsalus RP]]
-[[Category: Jarvis, M R.]]
+[[Category: Jarvis MR]]
-[[Category: Kaczor-Grzeskowiak, M.]]
+[[Category: Kaczor-Grzeskowiak M]]
-[[Category: Kopka, M L.]]
+[[Category: Kopka ML]]
-[[Category: Maris, A E.]]
+[[Category: Maris AE]]
-[[Category: Sawaya, M R.]]
+[[Category: Sawaya MR]]
-[[Category: Schroder, I.]]
+[[Category: Schroder I]]
-[[Category: Dna bending]]
-[[Category: Helix-turn-helix]]
-[[Category: Protein-dna complex]]
-[[Category: Two-component response regulator]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 21:07:02 2008''