Phosphorylates mevalonate 3-phosphate to form mevalonate 3,5-bisphosphate. Functions in an alternative mevalonate pathway, only present in extreme acidophiles of the Thermoplasmatales order, which passes through mevalonate 3-phosphate rather than mevalonate 5-phosphate. (R)-3-phosphomevalonate + ATP = (R)-3,5-bisphosphomevalonate + ADP + H(+) kcat is 9.0 sec(-1). Does not demonstrate significant pH dependence in the pH range of 6.5-9.0. Optimum temperature is 60 degrees Celsius. Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via mevalonate pathway. It is proposed that Thermoplasmatales adapted the classical archaeal mevalonate pathway by replacing mevalonate 5-phosphate decarboxylase (MMD) with two specialized enzymes (mevalonate-3-phosphate 5-kinase and mevalonate 3,5-bisphosphate decarboxylase) in order to produce isoprenoids in extremely acidic environments. It was found that at low pH, the dual function enzyme MMD is unable to carry out the first phosphorylation step, yet retains its ability to perform decarboxylation.