![]() A project was undertaken aimed at obtaining structural information on the HutC subfamily ligand-binding domain using X-ray crystallography. However, its specific regulatory function, its ligand, or the operator sites have not yet been established. Based on its sequence similarity to the HutC proteins, PhnF is predicted to regulate the expression of the phn genes and respond to alkylphosphonates. PhnF from Escherichia coli, which is the focus of this article, belongs to the phn operon that is involved in transport and biodegradation of phosphonates, (Pn)-compounds having carbon–phosphorous (C–P) bonds ( Metcalf and Wanner 1993). 1994), the trehalose operon repressor TreR from Bacillus subtilis that is inhibited by trehalose-6-phosphate ( Schock and Dahl 1996), and a number of proteins (KorSA, KorA, and TraR) that are repressors of the genes involved in conjugative plasmid transfer in Streptomyces species ( Kendall and Cohen 1988 Hagege et al. Other characterized members of the HutC family include FarR from Escherichia coli, which regulates the expression of citric acid cycle genes and responds to long-chain fatty acids ( Quail et al. It had been named after the HutC regulator from Pseudomonas putida, which represses the expression of histidine utilization genes and is, in turn, inactivated by the binding of uroconate ( Allison and Phillips 1990). ![]() The HutC subfamily represents more then 30% of all GntR members. 2001), no structural information is available for the other three subfamilies of GntR-like regulators. While the structure of FadR alone and in complex with its effector and operator DNA has been recently determined ( van Aalten et al. According to this analysis, the GntR family has been divided into four major subfamilies, FadR, HutC, MocR, and YtrA, where each subfamily is categorized by a specific type of the C-terminal domain. Recent sequence analysis of the GntR proteins revealed the presence of several distinct groups with different types of the C-terminal signaling domains ( Rigali et al. This output domain is coupled with the C-terminal signaling domain responding to a range of stimuli in the form of different small molecules. The proteins in the GntR family share a characteristic version of the N-terminal winged helix-turn-helix (wHTH) DNA-binding domain. This is true for the GntR family of transcriptional regulators, which gathers close to 2000 members in both bacterial and archael genomes ( Haydon and Guest 1991 Rigali et al. With extensive sequence similarity in the DNA-binding domain, these large families often contain proteins with different types of the effector domains fused to similar DNA-binding domains ( Rosinski and Atchley 1999 Perez-Rueda and Collado-Vides 2000). 1994), GntR ( Haydon and Guest 1991), and AraC ( Gallegos et al. Some of the largest such families ( Perez-Rueda et al. Based on sequence similarity, predominantly in the DNA binding domain one-component systems identified in sequenced genomes are assembled into protein families usually named after the best-characterized member. Signal transduction in prokaryotes is dominated by such systems, where small molecule-binding domains constitute the majority of the input domains and helix-turn-helix (HTH) DNA-binding domains are the most common output domains ( Ulrich et al. The structural comparison of the C-PhnF and UbiC proteins allows us to propose that a similar site in the PhnF structure is adapted for effector binding.Ī protein containing a sensor input domain and a functional output domain is described as a one-component system ( Ulrich et al. C-PhnF shares strong structural similarity with the chorismate lyase fold, which features a buried active site locked behind two helix-turn-helix loops. C-PhnF monomers form a dimer by establishing interdomain eight-strand β-sheets that include core antiparallel and N-terminal two-strand parallel β-sheets from each monomer. The structure represents a mixture of α-helices and β-strands, with a six-stranded antiparallel β-sheet at the core. The C-PhnF structure provides for the first time the scaffold of this domain for the HutC subfamily, which covers about 31% of GntR-like regulators. Members of this family share similar N-terminal DNA-binding domains, but are divided into four subfamilies according to their heterogenic C-terminal domains, which are involved in effector binding and oligomerization. The PhnF protein belongs to the HutC subfamily of the large GntR transcriptional regulator family. The crystal structure of Escherichia coli PhnF C-terminal domain (C-PhnF) was solved at 1.7 Å resolution by the single wavelength anomalous dispersion (SAD) method. ![]()
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