2bj8: Difference between revisions

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[[Image:2bj8.png|left|200px]]


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==NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH and LOW-AFFINITY SITES==
The line below this paragraph, containing "STRUCTURE_2bj8", creates the "Structure Box" on the page.
<StructureSection load='2bj8' size='340' side='right'caption='[[2bj8]], [[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'>[[2bj8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BJ8 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
{{STRUCTURE_2bj8|  PDB=2bj8  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bj8 OCA], [https://pdbe.org/2bj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bj8 RCSB], [https://www.ebi.ac.uk/pdbsum/2bj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bj8 ProSAT], [https://www.topsan.org/Proteins/RSGI/2bj8 TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NIKR_PYRHO NIKR_PYRHO] Transcriptional regulator (Potential).
== 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/bj/2bj8_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=2bj8 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E.coli ortholog. We succeeded in crystallization and structural characterization of PhNikR in the apo form and two nickel bound forms that exhibit different conformations, open and closed. Moreover, we have identified a putative "low-affinity" nickel-binding pocket in the closed form. This binding site has unusual nickel coordination and exhibits high sensitivity to phosphate in the crystal structure. Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins.


===NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH AND LOW-AFFINITY SITES===
Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition.,Chivers PT, Tahirov TH J Mol Biol. 2005 May 6;348(3):597-607. PMID:15826657<ref>PMID:15826657</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_15826657}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2bj8" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15826657 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15826657}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2bj8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BJ8 OCA].
[[Category: Pyrococcus horikoshii OT3]]
 
[[Category: Tahirov TH]]
==Reference==
<ref group="xtra">PMID:15826657</ref><ref group="xtra">PMID:16508086</ref><references group="xtra"/>
[[Category: Pyrococcus horikoshii]]
[[Category: Tahirov, T H.]]
[[Category: Dna-binding]]
[[Category: Metal-binding]]
[[Category: Nickel]]
[[Category: Nikr]]
[[Category: Pyrococcus horikoshii]]
[[Category: Repressor]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Transcription]]
[[Category: Transcription regulation]]

Latest revision as of 12:16, 9 May 2024

NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH and LOW-AFFINITY SITESNIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH and LOW-AFFINITY SITES

Structural highlights

2bj8 is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

NIKR_PYRHO Transcriptional regulator (Potential).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E.coli ortholog. We succeeded in crystallization and structural characterization of PhNikR in the apo form and two nickel bound forms that exhibit different conformations, open and closed. Moreover, we have identified a putative "low-affinity" nickel-binding pocket in the closed form. This binding site has unusual nickel coordination and exhibits high sensitivity to phosphate in the crystal structure. Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins.

Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition.,Chivers PT, Tahirov TH J Mol Biol. 2005 May 6;348(3):597-607. PMID:15826657[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Chivers PT, Tahirov TH. Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition. J Mol Biol. 2005 May 6;348(3):597-607. PMID:15826657 doi:http://dx.doi.org/10.1016/j.jmb.2005.03.017

2bj8, resolution 2.10Å

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