2bj9: Difference between revisions

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-[[Image:2bj9.gif|left|200px]]
- {{Structure
+==NIKR with bound NICKEL and phosphate==
-|PDB= 2bj9 |SIZE=350|CAPTION= <scene name='initialview01'>2bj9</scene>, resolution 3.00&Aring;
+<StructureSection load='2bj9' size='340' side='right'caption='[[2bj9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Pg4+Binding+Site+For+Chain+A'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
+<table><tr><td colspan='2'>[[2bj9]] 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=2BJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BJ9 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bj9 OCA], [https://pdbe.org/2bj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bj9 RCSB], [https://www.ebi.ac.uk/pdbsum/2bj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bj9 ProSAT], [https://www.topsan.org/Proteins/RSGI/2bj9 TOPSAN]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bj9 OCA], [http://www.ebi.ac.uk/pdbsum/2bj9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bj9 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/NIKR_PYRHO NIKR_PYRHO] Transcriptional regulator (Potential).
+== Evolutionary Conservation ==
-'''NIKR WITH BOUND NICKEL AND PHOSPHATE'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bj/2bj9_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=2bj9 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>
-BJ9 is a [[Single protein]] structure of 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=2BJ9 OCA].
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/15826657 15826657]
-[[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
-[[Category: Chivers, P T.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:07:13 2008''
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bj9" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pyrococcus horikoshii OT3]]
+[[Category: Chivers PT]]
+[[Category: Tahirov TH]]