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| | <StructureSection load='2hzv' size='340' side='right'caption='[[2hzv]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='2hzv' size='340' side='right'caption='[[2hzv]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2hzv]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HZV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2hzv]] is a 12 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=2HZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HZV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hza|2hza]], [[1q5v|1q5v]], [[1q5y|1q5y]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nikR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2hzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hzv OCA], [https://pdbe.org/2hzv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hzv RCSB], [https://www.ebi.ac.uk/pdbsum/2hzv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hzv ProSAT]</span></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=2hzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hzv OCA], [https://pdbe.org/2hzv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hzv RCSB], [https://www.ebi.ac.uk/pdbsum/2hzv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hzv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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]
| + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Drennan, C L]] | + | [[Category: Drennan CL]] |
| - | [[Category: Schreiter, E R]] | + | [[Category: Schreiter ER]] |
| - | [[Category: Metal binding protein-dna complex]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Protein-dna complex]]
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| - | [[Category: Ribbon-helix-helix]]
| + | |
| - | [[Category: Transcription factor]]
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| Structural highlights
Function
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
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Schreiter ER, Wang SC, Zamble DB, Drennan CL. NikR-operator complex structure and the mechanism of repressor activation by metal ions. Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13676-81. Epub 2006 Aug 31. PMID:16945905
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