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.


1rnl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:24, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1rnl.jpg|left|200px]]<br /><applet load="1rnl" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1rnl, resolution 2.4&Aring;" />
 
-
'''THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL'''<br />
 
-
==Overview==
+
==THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL==
-
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.
+
<StructureSection load='1rnl' size='340' side='right'caption='[[1rnl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
<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>
 +
</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/rn/1rnl_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1rnl ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
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].
+
*[[Response regulator 3D structure|Response regulator 3D structure]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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]
+
[[Category: Escherichia coli str. K-12 substr. W3110]]
-
[[Category: Escherichia coli]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Baikalov I]]
-
[[Category: Baikalov, I.]]
+
[[Category: Dickerson RE]]
-
[[Category: Dickerson, R E.]]
+
[[Category: Grzeskowiak K]]
-
[[Category: Grzeskowiak, K.]]
+
[[Category: Gunsalus RP]]
-
[[Category: Gunsalus, R P.]]
+
[[Category: Kaczor-Grzeskowiak M]]
-
[[Category: Kaczor-Grzeskowiak, M.]]
+
[[Category: Schroder I]]
-
[[Category: Schroder, I.]]
+
-
[[Category: GOL]]
+
-
[[Category: PT]]
+
-
[[Category: response regulators]]
+
-
[[Category: signal transduction protein]]
+
-
[[Category: two-component systems]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:52:47 2008''
+

Current revision

THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL

PDB ID 1rnl

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/1rnl"
Personal tools