@article {46411,
	title = {Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli.},
	journal = {Biochemistry},
	volume = {49},
	year = {2010},
	month = {2010 Sep 14},
	pages = {7830-8},
	abstract = {<p>Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for the nik operon: a nanomolar dissociation constant with stoichiometric nickel and a picomolar dissociation constant with excess nickel [Bloom, S. L., and Zamble, D. B. (2004) Biochemistry 43, 10029-10038; Chivers, P. T., and Sauer, R. T. (2002) Chem. Biol. 9, 1141-1148]. While it is known that the stoichiometric nickel ions bind at the NikR tetrameric interface [Schreiter, E. R., et al. (2003) Nat. Struct. Biol. 10, 794-799; Schreiter, E. R., et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681], the binding sites for excess nickel ions have not been fully described. Here we have determined the crystal structure of NikR in the presence of excess nickel to 2.6 A resolution and have obtained nickel anomalous data (1.4845 A) in the presence of excess nickel for both NikR alone and NikR cocrystallized with a 30-nucleotide piece of double-stranded DNA containing the nik operon. These anomalous data show that excess nickel ions do not bind to a single location on NikR but instead reveal a total of 22 possible low-affinity nickel sites on the NikR tetramer. These sites, for which there are six different types, are all on the surface of NikR, and most are found in both the NikR alone and NikR-DNA structures. Using a combination of crystallographic data and molecular dynamics simulations, the nickel sites can be described as preferring octahedral geometry, utilizing one to three protein ligands (typically histidine) and at least two water molecules.</p>
},
	keywords = {Binding Sites, DNA, Escherichia coli, Escherichia coli Proteins, Ligands, Models, Molecular, Nickel, Protein Conformation, Repressor Proteins, Structure-Activity Relationship},
	issn = {1520-4995},
	doi = {10.1021/bi100923j},
	author = {Phillips, Christine M and Schreiter, Eric R and Stultz, Collin M and Drennan, Catherine L}
}
@article {46408,
	title = {Structural basis of the metal specificity for nickel regulatory protein NikR.},
	journal = {Biochemistry},
	volume = {47},
	year = {2008},
	month = {2008 Feb 19},
	pages = {1938-46},
	abstract = {<p>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{\textquoteright}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.</p>
},
	keywords = {Binding Sites, Circular Dichroism, Escherichia coli Proteins, Metals, Models, Molecular, Protein Conformation, Repressor Proteins},
	issn = {0006-2960},
	doi = {10.1021/bi702006h},
	author = {Phillips, Christine M and Schreiter, Eric R and Guo, Yayi and Wang, Sheila C and Zamble, Deborah B and Drennan, Catherine L}
}
