1rnl

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[[Image:1rnl.jpg|left|200px]]<br /><applet load="1rnl" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rnl, resolution 2.4&Aring;" />
 
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'''THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL'''<br />
 
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==Overview==
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==THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL==
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The crystal structure analysis of the NarL protein provides a first look, at interactions between receiver and effector domains of a full-length, bacterial response regulator. The N-terminal receiver domain, with 131, amino acids, is folded into a 5-strand beta sheet flanked by 5 alpha, helices, as seen in CheY and in the N-terminal domain of NTRC. The, C-terminal DNA-binding domain, with 62 amino acids, is a compact bundle of, 4 alpha helices, of which the middle 2 form a helix-turn-helix motif, closely related to that of Drosophila paired protein and other H-T-H, DNA-binding proteins. The 2 domains are connected by an alpha helix of 10, amino acids and a 13-residue flexible tether that is not visible and, presumably disordered in the X-ray structure. In this unphosphorylated, form of NarL, the C-terminal domain is turned against the receiver domain, in a manner that would preclude DNA binding. Activation of NarL via, phosphorylation of Asp59 must involve transfer of information to the, interdomain interface and either rotation or displacement of the, DNA-binding C-terminal domain. Docking of a B-DNA duplex against the, isolated C-terminal domain in the manner observed in paired protein and, other H-T-H proteins suggests a stereochemical basis for DNA sequence, preference: T-R-C-C-Y (high affinity) or T-R-C-T-N (low affinity), which, is close to the experimentally observed consensus sequence: T-A-C-Y-N. The, NarL structure is a model for other members of the FixJ or LuxR family of, bacterial transcriptional activators, and possibly to the more distant, OmpR and NtrC families as well.
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<StructureSection load='1rnl' size='340' side='right'caption='[[1rnl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rnl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._W3110 Escherichia coli str. K-12 substr. W3110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RNL FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rnl OCA], [https://pdbe.org/1rnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rnl RCSB], [https://www.ebi.ac.uk/pdbsum/1rnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rnl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/1rnl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1rnl ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1RNL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=PT:'>PT</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=1:Phosphorylation+Site'>1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RNL OCA].
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*[[Response regulator 3D structure|Response regulator 3D structure]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure of the Escherichia coli response regulator NarL., Baikalov I, Schroder I, Kaczor-Grzeskowiak M, Grzeskowiak K, Gunsalus RP, Dickerson RE, Biochemistry. 1996 Aug 27;35(34):11053-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8780507 8780507]
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[[Category: Escherichia coli str. K-12 substr. W3110]]
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Baikalov I]]
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[[Category: Baikalov, I.]]
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[[Category: Dickerson RE]]
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[[Category: Dickerson, R.E.]]
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[[Category: Grzeskowiak K]]
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[[Category: Grzeskowiak, K.]]
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[[Category: Gunsalus RP]]
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[[Category: Gunsalus, R.P.]]
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[[Category: Kaczor-Grzeskowiak M]]
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[[Category: Kaczor-Grzeskowiak, M.]]
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[[Category: Schroder I]]
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[[Category: Schroder, I.]]
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[[Category: GOL]]
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[[Category: PT]]
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[[Category: response regulators]]
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[[Category: signal transduction protein]]
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[[Category: two-component systems]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:01:49 2008''
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Current revision

THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL

PDB ID 1rnl

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