Phosphorylation-dependent conformational changes and domain rearrangements in Staphylococcus aureus VraR activation

Abstract

Staphylococcus aureus VraR, a vancomycin-resistance-associated response regulator, activates a cell-wall–stress stimulon in response to antibiotics that inhibit cell wall formation. X-ray crystal structures of VraR in both unphosphorylated and beryllofluoride-activated states have been determined, revealing a mechanism of phosphorylation-induced dimerization that features a deep hydrophobic pocket at the center of the receiver domain interface. Unphosphorylated VraR exists in a closed conformation that inhibits dimer formation. Phosphorylation at the active site promotes conformational changes that are propagated throughout the receiver domain, promoting the opening of a hydrophobic pocket that is essential for homodimer formation and enhanced DNA-binding activity. This prominent feature in the VraR dimer can potentially be exploited for the development of novel therapeutics to counteract antibiotic resistance in this important pathogen.

Interaction of the RcsB Response Regulator with Auxiliary Transcription Regulators in Escherichia coli

“…For other response regulators of this family, such as the homodimeric NarL, VraR, and DesR, it was shown that the DNA-binding domain is buried or inhibited by the non-phosphorylated form of the receiver domain (48,52,53). The phosphorylation of the receiver domain induces an interdomain structural change that releases the DNA-binding domain, allowing its dimerization and/or DNA binding.…”

Sensor–response regulator interactions in a cross-regulated signal transduction network

“…This implies that NarP makes different interdomain contacts than NarL, a plausible supposition considering their substantial differences in primary sequence (less than 50% identity). Indeed, available structures for NarL-type response regulators, those containing a GerE effector domain, reveal nonconserved interdomain packing interactions (Leonard et al, 2013).…”

Structure of the response regulator ChrA in the haem-sensing two-component system ofCorynebacterium diphtheriae

“…On the other hand, another dimerization interface (1 and 5) has been proposed from the recent structural analysis of beryllofluoride-activated VraR (Leonard et al, 2013). In addition, the crystal packing of spr1814 suggested another interface consisting of the 4 helix, the 5-6 loop and a portion of the linker helix 6 (Park et al, 2013).…”

“…Indeed, the unique structural characteristics of ChrA are clearly manifested in structural comparisons with the overall structures of other structurally characterized full-length RRs of NarL/FixJ family members (Fig. 3): in Escherichia coli NarL is involved in nitrate/nitrite signal transduction (39% sequence identity; PDB entry 1rnl; Baikalov et al, 1996), in Staphylococcus aureus VraR is involved in vancomycin resistance-associated responses (34% sequence identity; PDB entry 4gvp; Leonard et al, 2013), in Streptococcus pneumoniae spr1814 is involved in the gene regulation of antibiotic transporters (26% sequence identity; PDB entry 4hye; Park et al, 2013) and in Pseudomonas fluorescens StyR is involved in styrene catabolism (34% sequence identity; PDB entry 1yio; Milani et al, 2005). Each of the regulatory and DNA-binding domains in the RRs of this family shows topologically similar structures (see below), but the relative orientations of the two domains and the conformations of the linker regions differ substantially among them.…”

“…Several full-length crystal structures of NarL/ FixJ family members have been determined and showed conserved folds in each domain, but with various relative orientations of the two domains (Baikalov et al, 1996;Leonard et al, 2013;Milani et al, 2005;Park et al, 2013). The C-terminal DNA-binding domain contains a single helix-turnhelix (HTH) motif in the middle of a four-helix bundle (Baikalov et al, 1996).…”