2hza: Difference between revisions

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{{Seed}}
[[Image:2hza.png|left|200px]]


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==Nickel-bound full-length Escherichia coli NikR==
The line below this paragraph, containing "STRUCTURE_2hza", creates the "Structure Box" on the page.
<StructureSection load='2hza' size='340' side='right'caption='[[2hza]], [[Resolution|resolution]] 2.10&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'>[[2hza]] is a 2 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=2HZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HZA 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]] 2.1&#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=3CM:3-CYCLOHEXYLPROPYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>3CM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
{{STRUCTURE_2hza|  PDB=2hza  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hza OCA], [https://pdbe.org/2hza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hza RCSB], [https://www.ebi.ac.uk/pdbsum/2hza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hza ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NIKR_ECOLI NIKR_ECOLI] Transcriptional repressor of the nikABCDE operon. Is active in the presence of excessive concentrations of intracellular nickel.[HAMAP-Rule:MF_00476]
== 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/hz/2hza_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=2hza ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, the isolated repressor at 2.1 A resolution and in a complex with its operator DNA sequence from the nik promoter at 3.1 A resolution. Along with the previously published structure of apo-NikR, these structures allow us to evaluate functional proposals for how metal ions activate NikR, delineate the drastic conformational changes required for operator recognition, and describe the formation of a second metal-binding site in the presence of DNA. They also provide a rare set of structural views of a ligand-responsive transcription factor in the unbound, ligand-induced, and DNA-bound states, establishing a model system for the study of ligand-mediated effects on transcription factor function.


===Nickel-bound full-length Escherichia coli NikR===
NikR-operator complex structure and the mechanism of repressor activation by metal ions.,Schreiter ER, Wang SC, Zamble DB, Drennan CL Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13676-81. Epub 2006 Aug 31. PMID:16945905<ref>PMID:16945905</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_16945905}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2hza" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 16945905 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16945905}}
__TOC__
 
</StructureSection>
==About this Structure==
2HZA 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=2HZA OCA].
 
==Reference==
NikR-operator complex structure and the mechanism of repressor activation by metal ions., Schreiter ER, Wang SC, Zamble DB, Drennan CL, Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13676-81. Epub 2006 Aug 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16945905 16945905]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Drennan, C L.]]
[[Category: Drennan CL]]
[[Category: Schreiter, E R.]]
[[Category: Schreiter ER]]
[[Category: Nickel-binding]]
[[Category: Ribbon-helix-helix]]
[[Category: Transcription factor]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:57:54 2008''

Latest revision as of 01:02, 21 November 2024

Nickel-bound full-length Escherichia coli NikR

2hza, resolution 2.10Å

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