3bkf: Difference between revisions

Revision as of 20:52, 4 May 2008

Zinc-bound C-terminal Domain of NikR

OverviewOverview

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.

About this StructureAbout this Structure

3BKF is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sun May 4 20:52:45 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:3bkf.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 3bkf |SIZE=350|CAPTION= <scene name='initialview01'>3bkf</scene>, resolution 1.900&Aring;
+The line below this paragraph, containing "STRUCTURE_3bkf", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+500'>AC1</scene> and <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A+501'>AC2</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE= nikR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+-->
-|DOMAIN=
+{{STRUCTURE_3bkf|  PDB=3bkf  |  SCENE=  }}
-|RELATEDENTRY=[[3bkt|3BKT]], [[3bku|3BKU]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkf OCA], [http://www.ebi.ac.uk/pdbsum/3bkf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bkf RCSB]</span>
-}}
 '''Zinc-bound C-terminal Domain of NikR'''
@@ Line 28: / Line 25: @@
 [[Category: Phillips, C M.]]
 [[Category: Schreiter, E R.]]
-[[Category: beta sandwich]]
+[[Category: Beta sandwich]]
-[[Category: dna-binding]]
+[[Category: Dna-binding]]
-[[Category: metal binding protein]]
+[[Category: Metal binding protein]]
-[[Category: metal-binding]]
+[[Category: Metal-binding]]
-[[Category: nickel regulatory protein]]
+[[Category: Nickel regulatory protein]]
-[[Category: nikr]]
+[[Category: Nikr]]
-[[Category: repressor]]
+[[Category: Repressor]]
-[[Category: transcription factor]]
+[[Category: Transcription factor]]
-[[Category: transcription regulation]]
+[[Category: Transcription regulation]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:52:45 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:27:11 2008''