Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn{sup 2+}-binding FCD domains

Journal Article · Wed Apr 01 04:00:00 EDT 2009 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S0907444909004727· OSTI ID:22351172

Zheng, Meiying; Cooper, David R. ^[1]; Grossoehme, Nickolas E. ^[2]; Yu, Minmin ^[3]; Hung, Li-Wei ^[3]; Cieslik, Marcin; Derewenda, Urszula ^[1]; Lesley, Scott A. ^[4]; Wilson, Ian A. ^[4]; Giedroc, David P. ^[2]

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1. Integrated Center for Structure-Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736 (United States)
2. Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102 (United States)
3. Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720 (United States)
4. The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037 (United States)

Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-α-helical regulatory domains classified into two related Pfam families: FadR-C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni{sup 2+} ions but that it is able to bind Zn{sup 2+} with K{sub d} < 70 nM. It is concluded that Zn{sup 2+} is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.

• OSTI ID: 22351172
• Journal Information: Acta Crystallographica. Section D: Biological Crystallography, Journal Name: Acta Crystallographica. Section D: Biological Crystallography Journal Issue: Pt 4 Vol. 65; ISSN ABCRE6; ISSN 0907-4449
• Country of Publication: Denmark
• Language: English

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
ABSORPTION
ABSORPTION SPECTROSCOPY
CRYSTAL STRUCTURE
DNA
ESCHERICHIA COLI
FLUORESCENCE
METALS