3bkt: Difference between revisions
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==Copper-bound C-terminal Domain of NikR== | ==Copper-bound C-terminal Domain of NikR== | ||
<StructureSection load='3bkt' size='340' side='right' caption='[[3bkt]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='3bkt' size='340' side='right'caption='[[3bkt]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3bkt]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3bkt]] is a 4 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=3BKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BKT FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bkf|3bkf]], [[3bku|3bku]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bkf|3bkf]], [[3bku|3bku]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nikR ([ | <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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkt OCA], [https://pdbe.org/3bkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bkt RCSB], [https://www.ebi.ac.uk/pdbsum/3bkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bkt 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] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bk/3bkt_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bk/3bkt_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
| Line 35: | Line 35: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus coli migula 1895]] | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Large Structures]] | |||
[[Category: Drennan, C L]] | [[Category: Drennan, C L]] | ||
[[Category: Phillips, C M]] | [[Category: Phillips, C M]] | ||
Revision as of 13:45, 12 January 2022
Copper-bound C-terminal Domain of NikRCopper-bound C-terminal Domain of NikR
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 PubMedIn the presence of excess nickel, Escherichia coli NikR regulates cellular nickel uptake by suppressing the transcription of the nik operon, which encodes the nickel uptake transporter, NikABCDE. Previously published in vitro studies have shown that NikR is capable of binding a range of divalent transition metal ions in addition to Ni2+, including Co2+, Cu2+, Zn2+, and Cd2+. To understand how the high-affinity nickel binding site of NikR is able to accommodate these other metal ions, and to improve our understanding of NikR's mechanism of binding to DNA, we have determined structures of the metal-binding domain (MBD) of NikR in the apo form and in complex with Cu2+ and Zn2+ ions and compared them with the previously published structures with Ni2+. We observe that Cu2+ ions bind in a manner very similar to that of Ni2+, with a square planar geometry but with longer bond lengths. Crystals grown in the presence of Zn2+ reveal a protein structure similar to that of apo MBD with a disordered alpha3 helix, but with two electron density peaks near the Ni2+ binding site corresponding to two Zn2+ ions. These structural findings along with biochemical data on NikR support a hypothesis that ordering of the alpha3 helix is important for repressor activation. Structural Basis of the Metal Specificity for Nickel Regulatory Protein NikR(,).,Phillips CM, Schreiter ER, Guo Y, Wang SC, Zamble DB, Drennan CL Biochemistry. 2008 Feb 19;47(7):1938-46. Epub 2008 Jan 15. PMID:18193897[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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