Crystallographic studies of the metal-responsive transcription factor NikR

Metal ion homeostasis is critical to the survival of all cells, because requirements for these essential nutrients must be balanced with their toxicity when present at elevated concentrations. Regulation of nickel concentrations in Escherichia coli is achieved via nickel-induced transcriptional repression of the nickel permease complex, NikABCDE, mediated by the NikR metalloregulatory transcription factor. To understand how this takes place at a molecular level, X-ray crystallography was used to determine three- dimensional structures of the NikR. Structures of apo-NikR and Ni⁺²-NikR show an interesting quaternary arrangement of the functional NikR tetramer, consisting of two dimeric Ribbon-Helix-Helix (RHH) DNA-binding domains separated by a tetrameric regulatory domain that binds metal ions (MBD). NikR is the only known metal- responsive member of the RHH family of transcription factors, and the structural relationships between NikR and other RHH proteins are detailed in this thesis. The high- affinity nickel-binding site of NikR is located at the tetramer interface of the MBD, with square-planar coordination by three histidines and a cysteine sidechain. A structure of NikR in complex with a 30 base-pair oligonucleotide containing the nik operator sequence illustrates the dramatic conformational changes associated with DNA binding, shows the nature of the specific and non-specific contacts between NikR and its operator, and reveals a second functionally relevant metal-binding site created at the interface of the RHH domain and MBD. Binding of nickel ions to the high-affinity site of NikR is proposed to increase affinity for the nik operator through a combination of mechanisms.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemistry.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Schreiter, Eric R. (Eric Robert)

Advisor dc:contributor.advisor

• Catherine L. Drennan.

• Chemistry.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/32495

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/32495