3FMS

Crystal structure of TM0439, a GntR transcriptional regulator

Replaces:  3DBW

Summary for 3FMS

• Entry DOI: 10.2210/pdb3fms/pdb
• Descriptor: Transcriptional regulator, GntR family, NICKEL (II) ION, ACETATE ION, ... (4 entities in total)
• Functional Keywords: gntr family, transcriptional regulator, structural genomics, surface entropy reduction, psi-2, protein structure initiative, integrated center for structure and function innovation, isfi, dna-binding, transcription regulation, transcription regulator, transcription
• Biological source: Thermotoga maritima MSB8
• Total number of polymer chains: 1
• Total formula weight: 24690.48

Authors

Zheng, M.,Cooper, D.R.,Yu, M.,Hung, L.-W.,Derewenda, U.,Derewenda, Z.S.,Integrated Center for Structure and Function Innovation (ISFI) (deposition date: 2008-12-22, release date: 2009-02-10, Last modification date: 2024-10-30)

Primary citation

Zheng, M.,Cooper, D.R.,Grossoehme, N.E.,Yu, M.,Hung, L.W.,Cieslik, M.,Derewenda, U.,Lesley, S.A.,Wilson, I.A.,Giedroc, D.P.,Derewenda, Z.S.
Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains.
Acta Crystallogr.,Sect.D, 65:356-365, 2009

PubMed Abstract: 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-alpha-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(2+) ions but that it is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(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.

PubMed: 19307717
DOI: 10.1107/S0907444909004727

Experimental method

X-RAY DIFFRACTION (2.2 Å)