Involved in the biosynthesis of the phosphonic acid antibiotic FR900098, a potential anti-malarial drug, which acts as a potent inhibitor of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), the first enzyme in the nonmevalonate pathway for isoprenoid biosynthesis. Catalyzes the condensation between acetyl-CoA and phosphonopyruvate to yield (R)-2-(phosphonomethyl)malate. 3-phosphonopyruvate + acetyl-CoA + H2O = (R)-2-(phosphonomethyl)malate + CoA + H(+) Antibiotic biosynthesis. Belongs to the alpha-IPM synthase/homocitrate synthase family.