Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains.
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.
Zheng
Meiying
M
Department of Molecular Physiology and Biological Physics, Integrated Center for Structure-Function Innovation, University of Virginia, Charlottesville, VA 22908-0736, USA.
Cooper
David R
DR
Grossoehme
Nickolas E
NE
Yu
Minmin
M
Hung
Li Wei
LW
Cieslik
Marcin
M
Derewenda
Urszula
U
Lesley
Scott A
SA
Wilson
Ian A
IA
Giedroc
David P
DP
Derewenda
Zygmunt S
ZS
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
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D011993:Recombinant Fusion Proteins; D012097:Repressor Proteins; D009532:Nickel; D015032:Zinc