A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein fromBacillus subtilis

Abstract

In Bacillus subtilis the concentration of L-arginine is controlled by the transcriptional regulator AhrC, which interacts with 18 bp DNA operator sites called ARG boxes in the promoters of arginine biosynthetic and catabolic operons. AhrC is a 100 kDa homohexamer, with each subunit having two domains. The C-terminal domains form the core, mediating intersubunit interactions and binding of the co-repressor L-arginine, whilst the N-terminal domains contain a winged helix-turn-helix DNA-binding motif and are arranged around the periphery. The N-terminal domain of AhrC has been expressed, purified and characterized and it has been shown that the fragment still binds DNA operators as a recombinant monomer. The DNA-binding domain has also been crystallized and the crystal structure refined to 1.0 A resolution is presented.

Structure and Function of the Arginine Repressor-Operator Complex from Bacillus subtilis

“…Side-chain interactions across the interface are almost exclusively hydrophobic, apart from hydrogen bonds between His49 and Asn56; the latter is disordered in the monomeric NAhrC structure. 28 Beneath the β-wing dimer interface, the phosphate backbone of the minor groove (T10 and A11) is contacted by the side chains of Lys52 and the conserved Tyr62, respectively (Fig. 2b).…”

“…NMR was used to determine the structure of the Nterminal domain of E. coli ArgR (NArgR), 27 and estab- lished the presence of a similar winged helix-turnhelix DNA-binding motif to that in the Bacillus homologues, and a high resolution crystal structure of the same domain from AhrC has been reported (NAhrC). 28 No structure is available for a DNA complex in any of these systems, leaving open critical questions concerning the details of sequence-specific recognition and the mechanism of co-repressor activation. Here, we report the first atomic details of an arginine repressor interacting with its DNA operator sequence; a dimer of the N-terminal domains of AhrC in complex with an 18 bp DNA ARG box operator.…”

Crystal Structure of the Arginine Repressor Protein in Complex with the DNA Operator from Mycobacterium tuberculosis

“…7,8 Also, the structures of the (isolated) C-terminal domains of apo ArgR from Escherichia coli (Ec) and Mtb and of the N-terminal domains of EcArgR and BsAhrC have been determined. [9][10][11][12] In the case of arginine-bound proteins, structures of only the C-terminal domains of EcArgR, BstArgR, BsAhrC, and MtbArgR are known. 7,9,12,13 Recently, the structure of the isolated N-terminal domains of BsAhrC in complex with an 18-bp segment of DNA has been published.…”

The Structure of the Arginine Repressor from Mycobacterium tuberculosis Bound with its DNA Operator and Co-repressor, L-Arginine

“…The Nterminal domain is the DNA-binding domain (DBD) and the C-terminal (core) domain is responsible for oligomerization and for arginine binding. [4][5][6][7][8][9][10][11][12][13] The ArgR/AhrC protomers form trimers and hexamers that are in equilibrium and their oligomerization state is controlled by the presence of the arginine corepressor. 4,12 Some features of ArgRs are more prominent in MtbArgR than in the other ArgR/ AhrC proteins (Fig.…”