2bj7: Difference between revisions

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-[[Image:2bj7.gif|left|200px]]<br /><applet load="2bj7" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2bj7, resolution 2.10&Aring;" />
-'''NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES'''<br />
-==Overview==
+==NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES==
-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.
+<StructureSection load='2bj7' size='340' side='right'caption='[[2bj7]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2bj7]] 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=2BJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BJ7 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]] 2.1&#8491;</td></tr>
+<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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=2bj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bj7 OCA], [https://pdbe.org/2bj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bj7 RCSB], [https://www.ebi.ac.uk/pdbsum/2bj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bj7 ProSAT], [https://www.topsan.org/Proteins/RSGI/2bj7 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/2bj7_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=2bj7 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.
-==About this Structure==
+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>
-BJ7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with NI, CL, EDO and PG4 as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Pg4 Binding Site For Chain A'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BJ7 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15826657 15826657]
+</div>
-[[Category: Pyrococcus horikoshii]]
+<div class="pdbe-citations 2bj7" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+<references/>
-[[Category: Tahirov, T.H.]]
+__TOC__
-[[Category: CL]]
+</StructureSection>
-[[Category: EDO]]
+[[Category: Large Structures]]
-[[Category: NI]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: PG4]]
+[[Category: Tahirov TH]]
-[[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 genomics]]
-[[Category: transcription]]
-[[Category: transcription regulation]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 18:49:06 2007''