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J. Biol. Chem., Vol. 278, Issue 50, 50322-50329, December 12, 2003

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Crystal Structures of the Liganded and Unliganded Nickel-binding Protein NikA from Escherichia coli^*

Jonathan Heddle, David J. Scott¶||, Satoru Unzai, Sam-Yong Park, and Jeremy R. H. Tame**

From the Protein Design Laboratory, Yokohama City University, Tsurumi, Suehiro 1-7-29, Yokohama 230-0045, Japan and ^¶Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol BS8 1TD, United Kingdom

Bacteria have evolved a number of tightly controlled import and export systems to maintain intracellular levels of the essential but potentially toxic metal nickel. Nickel homeostasis systems include the dedicated nickel uptake system nik found in Escherichia coli, a member of the ABC family of transporters, that involves a periplasmic nickel-binding protein, NikA. This is the initial nickel receptor and mediator of the chemotactic response away from nickel. We have solved the crystal structure of NikA protein in the presence and absence of nickel, showing that it behaves as a "classical" periplasmic binding protein. In contrast to other binding proteins, however, the ligand remains accessible to the solvent and is not completely enclosed. No direct bonds are formed between the metal cation and the protein. The nickel binding site is apolar, quite unlike any previously characterized protein nickel binding site. Despite relatively weak binding, NikA is specific for nickel. Using isothermal titration calorimetry, the dissociation constant for nickel was found to be 10 µM and that for cobalt was approximately 20 times higher.

Received for publication, July 22, 2003 , and in revised form, September 2, 2003.

The atomic coordinates and structure factors (codes 1uiu and 1uiv) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Special Research Fellow of the Japanese Society for the Promotion of Science (JSPS).

^|| Present address: National Centre for Macromolecular Hydrodynamics, Nottingham University, School of Biosciences, Sutton Bonnington, Leicestershire LE12 5RD, United Kingdom.

^** To whom correspondence should be addressed. Tel.: 81-045-508-7228; Fax: 81-045-508-7366; E-mail: jtame{at}tsurumi.yokohamacu.ac.jp.

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