Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding

Abstract

The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 A resolution. The structure establishes a 10-stranded beta fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

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“…While the structure of AtcR has not yet been determined, threading of the AtcR sequence onto the AgrA:DNA complex structure suggests that AtcR and AgrA have similar structures (Miller et al 2014a;Sidote et al 2008). Ramachandran plotting provided strong support for the predicted AtcR structure as 89.36% of the residues were calculated to have favorable bond angles (Miller et al 2014a).…”

“…The predicted AtcR structural model suggests that the interaction of AtcR with DNA is also likely to be similar to that of AgrA with strong potential for residues within the loops of AtcR to insert into the major grooves of potential LytTR-DNA motifs. AgrA residues H169, N201, and R233 have been demonstrated to be in direct contact with DNA (Sidote et al 2008). Sequence alignment revealed that AtcR residues H157, R191, and R221 are positionally analogous to the AgrA-DNA contact residues.…”

“…Most RRs interact with DNA through a recognition alpha helix located within a DNA binding domain. Studies of the S. aureus AgrA (accessory gene regulator A), a LytTR RR, have provided insight into the LytTR-DNA interaction (Koenig et al 2004;Nicod et al 2014;Rode et al 2007;Sidote et al 2008;Traber and Novick 2006). AgrA is a cytoplasmic protein that possesses an N-terminal REC domain of 124 amino acids and a C-terminal LytTR domain of 98 residues.…”

“…AgrA is a cytoplasmic protein that possesses an N-terminal REC domain of 124 amino acids and a C-terminal LytTR domain of 98 residues. As in other LytTR RRs, the DNA binding domain consists largely of beta-strands (10 stranded beta fold) interspersed by variable loops (Sidote et al 2008). The DNA recognition sequence for the AgrA dimer consists of a 9 base pair imperfect direct repeats separated by an 11-nucleotide spacer that varies in sequence.…”

“…Among most bacterial LytTR regulated genes, this spacer ranges from 11 to 13 nucleotides (Galperin 2008). Positively charged amino acids located within loop domains of AgrA monomers insert into two consecutive successive major grooves of the DNA recognition sequence (Sidote et al 2008) allowing specific side chains to insert within the intervening minor groove. Salt bridges between AgrA and the DNA phosphate backbone further stabilize the interaction.…”