Catalyzes the specific phosphorylation of arginine residues in a large number of proteins. Is part of the bacterial stress response system, where it is involved in regulating the global heat shock repressor CtsR; phosphorylates arginine residues in the winged helix-turn-helix domain of CtsR, thereby preventing its binding to DNA and consequently inducing the expression of repressed genes. The transcriptional repressor HrcA, the chaperone GroEL, the unfoldase ClpC, together with several ribosomal subunits, represent other physiological targets of McsB under stress conditions. Protein arginine phosphorylation has a physiologically important role and is involved in the regulation of many critical cellular processes, such as protein homeostasis, motility, competence, and stringent and stress responses, by regulating gene expression and protein activity. Functions as an adapter whose kinase activity is required for ClpCP-mediated degradation of CtsR during heat stress. Is required for the delocalization of competence proteins from the cell poles, probably via a role in the degradation of anchor proteins. ATP + L-arginyl-[protein] = ADP + H(+) + N(omega)-phospho-L-arginyl-[protein] Appears to be allosterically activated by the binding of pArg-containing polypeptides to the pArg-binding pocket localized in the C-terminal domain of McsB (By similarity). The McsB kinase is inhibited in nonstressed cells by direct interaction with ClpC; upon heat exposure, the interaction of McsB with ClpC is dramatically decreased, leading to McsB release and activation during heat stress. Its kinase activity is counteracted by the protein-arginine-phosphatase YwlE in vivo. Requires McsA for full kinase activity. Interacts with CtsR in its autophosphorylated form. Interacts with McsA in nonstressed as well as in heat-stressed cells, whereas strongly interacts with ClpC only in nonstressed cells. Localizes to the cell poles in competent cells, but not in non-competent cells. Is repressed by the transcriptional regulator CtsR. Forms part of an operon with ctsR, mcsA and clpC. Autophosphorylated on Arg residues. Phosphorylation on Arg-40 and Arg-86 are up-regulated upon stress conditions. Cells lacking this gene show a defect in the delocalization of competence proteins that is not related to altered expression of the com genes on the levels of either transcription or translation. Inactivation of mcsB also decreases transformability (PubMed:19226326). CtsR is no more degraded (PubMed:30962626). Belongs to the ATP:guanido phosphotransferase family.