Catalysis of the reaction: 2 Fe(3+) + 4 H2O + L-histidyl- + N(6)-(pyridoxal phosphate)-L-lysyl- = (2S)-2-amino-5-hydroxy-4-oxopentanoyl- + 3-oxopropanoate + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 2 Fe(2+) + 2 H+ + L-lysyl-.
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP