Crystal Structure of Fad35R from Mycobacterium tuberculosis H37Rv in the Apo-State.
Fad35R from Mycobacterium tuberculosis binds to the promoter site of Fad35 operon and its DNA binding activities are reduced in the presence of tetracycline and palmitoyl-CoA. We resolved the crystal structure of Fad35R using single-wavelength anomalous diffraction method (SAD). Fad35R comprises canonical DNA binding domain (DBD) and ligand binding domain (LBD), but displays several distinct structural features. Two recognition helices of two monomers in the homodimer are separated by ~ 48 Å and two core triangle-shaped ligand binding cavities are well exposed to solvent. Structural comparison with DesT and QacR structures suggests that ligand binding-induced movement of α7, which adopts a straight conformation in the Fad35R, may be crucial to switch the conformational states between repressive and derepressive forms. Two DBDs are packed asymmetrically, creating an alternative dimer interface which coincides with the possible tetramer interface that connects the two canonical dimers. Quaternary state of alternative dimer mimics a closed-state structure in which two recognition helices are distanced at ~ 35 Å and ligand binding pockets are inaccessible. Results of biophysical studies indicate that Fad35R has the propensity to oligomerize in solution in the presence of tetracycline. We present the first structure of a FadR homologue from mycobacterium and the structure reveals DNA and ligand binding features of Fad35R and also provides a view on alternative quaternary states that mimic open and closed forms of the regulator.
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
Appu Kumar
AK
Singh
European Molecular Biology Laboratory, Grenoble Outstation, 38000, France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 38000, France.
Babu
B
Manjasetty
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
G L
GL
Balasubramani
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
Sukirte
S
Koul
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
Abhishek
A
Kaushik
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
Mary Krishna
MK
Ekka
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
Vijay
V
Singh
Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, G.N.Ramachandran Protein Centre, Chandigarh, 160036, India.
S
S
Kumaran
D001059:Apoproteins / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary
D001059:Apoproteins; D001426:Bacterial Proteins; D008024:Ligands; D004247:DNA