3bkt: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3bkt.png|left|200px]]
-<!--
+==Copper-bound C-terminal Domain of NikR==
-The line below this paragraph, containing "STRUCTURE_3bkt", creates the "Structure Box" on the page.
+<StructureSection load='3bkt' size='340' side='right'caption='[[3bkt]], [[Resolution|resolution]] 1.50&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'>[[3bkt]] 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=3BKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BKT 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]] 1.5&#8491;</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>
-{{STRUCTURE_3bkt|  PDB=3bkt  |  SCENE=  }}
+<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>
+== 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 ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <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>
+    <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=3bkt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In 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.
-===Copper-bound C-terminal Domain of NikR===
+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<ref>PMID:18193897</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18193897}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3bkt" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18193897 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18193897}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BKT is a 4 chains structure of sequences 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=3BKT OCA].
-==Reference==
-<ref group="xtra">PMID:18193897</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Drennan, C L.]]
+[[Category: Large Structures]]
-[[Category: Phillips, C M.]]
+[[Category: Drennan CL]]
-[[Category: Schreiter, E R.]]
+[[Category: Phillips CM]]
-[[Category: Beta sandwich]]
+[[Category: Schreiter ER]]
-[[Category: Dna-binding]]
-[[Category: Metal binding protein]]
-[[Category: Metal-binding]]
-[[Category: Nickel regulatory protein]]
-[[Category: Nikr]]
-[[Category: Repressor]]
-[[Category: Transcription factor]]
-[[Category: Transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:27:52 2009''