title: Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains.
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.
authors.affiliation: Department of Molecular Physiology and Biological Physics, Integrated Center for Structure-Function Innovation, University of Virginia, Charlottesville, VA 22908-0736, USA.
authors.forename: Meiying
authors.initials: M
authors.lastname: Zheng
authors.forename: David R
authors.initials: DR
authors.lastname: Cooper
authors.forename: Nickolas E
authors.initials: NE
authors.lastname: Grossoehme
authors.forename: Minmin
authors.initials: M
authors.lastname: Yu
authors.forename: Li Wei
authors.initials: LW
authors.lastname: Hung
authors.forename: Marcin
authors.initials: M
authors.lastname: Cieslik
authors.forename: Urszula
authors.initials: U
authors.lastname: Derewenda
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.forename: David P
authors.initials: DP
authors.lastname: Giedroc
authors.forename: Zygmunt S
authors.initials: ZS
authors.lastname: Derewenda
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism; D019281:Dimerization; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D005810:Multigene Family; D009532:Nickel / Q000378:metabolism; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D012097:Repressor Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism; D013329:Structure-Activity Relationship; D020124:Thermotoga maritima / Q000737:chemistry* / Q000235:genetics; D015032:Zinc / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D011993:Recombinant Fusion Proteins; D012097:Repressor Proteins; D009532:Nickel; D015032:Zinc