1q5y: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1q5y.jpg|left|200px]]


<!--
==Nickel-Bound C-terminal Regulatory Domain of NikR==
The line below this paragraph, containing "STRUCTURE_1q5y", creates the "Structure Box" on the page.
<StructureSection load='1q5y' size='340' side='right'caption='[[1q5y]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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='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>
{{STRUCTURE_1q5y|  PDB=1q5y  |  SCENE= }}
<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>
 
</table>
'''Nickel-Bound C-terminal Regulatory Domain of NikR'''
== 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 ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q5/1q5y_consurf.spt"</scriptWhenChecked>
1Q5Y is a [[Single protein]] structure of sequence from [http://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].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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:[http://www.ncbi.nlm.nih.gov/pubmed/12970756 12970756]
</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>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[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: Nickel binding]]
[[Category: Regulatory domain]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 05:54:20 2008''

Latest revision as of 08:13, 14 February 2024

Nickel-Bound C-terminal Regulatory Domain of NikR

1q5y, resolution 1.40Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=1q5y&oldid=4053641"