1q5y: Difference between revisions

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<StructureSection load='1q5y' size='340' side='right'caption='[[1q5y]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='1q5y' size='340' side='right'caption='[[1q5y]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1q5y]] is a 4 chain structure with sequence from [http://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=1Q5Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q5Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[1q5y]] is a 4 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=1Q5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q5Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q5v|1q5v]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NIKR ([http://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=1q5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5y OCA], [https://pdbe.org/1q5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q5y RCSB], [https://www.ebi.ac.uk/pdbsum/1q5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q5y ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1q5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5y OCA], [http://pdbe.org/1q5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q5y RCSB], [http://www.ebi.ac.uk/pdbsum/1q5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q5y ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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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</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=1q5y ConSurf].
</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=1q5y ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
NikR is a metal-responsive transcription factor that controls nickel uptake in Escherichia coli by regulating expression of a nickel-specific ATP-binding cassette (ABC) transporter. We have determined the first two structures of NikR: the full-length apo repressor at a resolution of 2.3 A and the nickel-bound C-terminal regulatory domain at a resolution of 1.4 A. NikR is the only known metal-responsive member of the ribbon-helix-helix family of transcription factors, and its structure has a quaternary arrangement consisting of two dimeric DNA-binding domains separated by a tetrameric regulatory domain that binds nickel. The position of the C-terminal regulatory domain enforces a large spacing between the contacts that each NikR DNA-binding domain can make with the nik operator. The regulatory domain of NikR contains four nickel-binding sites at the tetramer interface, each exhibiting a novel square-planar coordination by three histidines and one cysteine side chain.
Crystal structure of the nickel-responsive transcription factor NikR.,Schreiter ER, Sintchak MD, Guo Y, Chivers PT, Sauer RT, Drennan CL Nat Struct Biol. 2003 Oct;10(10):794-9. Epub 2003 Sep 14. PMID:12970756<ref>PMID:12970756</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1q5y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chivers, P T]]
[[Category: Chivers PT]]
[[Category: Drennan, C L]]
[[Category: Drennan CL]]
[[Category: Guo, Y]]
[[Category: Guo Y]]
[[Category: Sauer, R T]]
[[Category: Sauer RT]]
[[Category: Schreiter, E R]]
[[Category: Schreiter ER]]
[[Category: Sintchak, M D]]
[[Category: Sintchak MD]]
[[Category: Beta sandwich]]
[[Category: Metal binding protein]]
[[Category: Nickel binding]]
[[Category: Regulatory domain]]

Latest revision as of 11:13, 14 February 2024

Nickel-Bound C-terminal Regulatory Domain of NikRNickel-Bound C-terminal Regulatory Domain of NikR

Structural highlights

1q5y is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

1q5y, resolution 1.40Å

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